dna ladders  (Thermo Fisher)


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  • 99
    Name:
    100 bp DNA Ladder
    Description:
    Invitrogen 100 bp DNA Ladder is designed for sizing and approximate quantification of double-stranded DNA in the range of 100 bp to 2,000 bp. 100 bp DNA Ladder consists of 13 individual chromatography-purified DNA fragments and has reference bands at 2000, 1500, and 600 bp for easy orientation. 100 bp DNA Ladder is ideal for separation on 1–2% agarose gels. Highlights of 100 bp DNA Ladder: • Sharp, clear bands—chromatography purified fragments for consistent and reliable results • Convenient—provided with 10X BlueJuice Gel Loading Buffer for tracking of sample DNA migration • Precise—an exact amount of DNA in each band Product use The double-stranded DNA ladder can be visualized on 1–2% agarose gels after ethidium bromide or SYBR Safe staining. The ladder is designed with a uniform intensity of DNA bands for a clear view of each band. An exact amount of DNA in each band allows approximate quantification of DNA samples. This ladder can be radiolabeled with T4 polynucleotide kinase or T4 DNA polymerase.
    Catalog Number:
    15628019
    Price:
    None
    Applications:
    100
    Size:
    50 µg
    Category:
    Standards, Ladders & Controls, DNA⁄RNA Ladders, DNA Ladders
    Score:
    85
    Buy from Supplier


    Structured Review

    Thermo Fisher dna ladders
    Generation and testing of a conditional (“floxed”) tbx20 allele. a . Experimental design. b . Genotyping of adult fish for intron 2 loxP site. c . Results of nested PCR screening for loxP integration into intron 1. d . Sequence of intron 1 loxP integration in recovered tpl145 floxed tbx20 allele. e . Genotyping of “F1” adults. Primer binding sites are shown as black arrows, loxP sites as red or blue triangles, exon as an open box. f, g . Induction of tbx20 loss of function by injection of Cre mRNA. f . One quarter of embryos obtained by in-crossing tbx20 tpl145 heterozygotes and injected with Cre mRNA display a consistent, severe heart development defect. g . Genotyping of embryos with severe heart defects (lanes 1–3) and phenotypically normal siblings (lanes 4–8). L, <t>GeneRuler</t> <t>DNA</t> Ladder (ThermoFisher Scientific). Genotyping lanes 1 and 5 correspond to images in f . h, i . Induction of tbx20 deletion by 4-hydroxytamoxifen. tbx20 tpl145 heterozygote was crossed to Tg( ubi :CreERT2) line. GFP-positive embryos were collected at 2dpf and incubated with 5μM 4-HT for 24 hours. j . Adults raised from Cre-injected tbx20 tpl145/+ embryos were incrossed, resulting in approximately 1/4 of embryos (36/128, 28%) with severe heart defects. k . Confirmation of Cre-mediated excision of the second intron of tbx20 by sequence analysis. l, m . Analysis of excision efficiency by qPCR. l . Excision efficiency was assessed by qPCR in embryos treated with 4-HT at various concentrations at different time points and in two different ubb :CreERT2 driver lines. The y-axis indicates un-excised tpl 145 normalized to the untreated control. m . Images of tbx20 phenotypes shown after treatment with 4-HT. Individuals 1, 2, and 3 from l correspond to images labeled 1, 2, and 3.
    Invitrogen 100 bp DNA Ladder is designed for sizing and approximate quantification of double-stranded DNA in the range of 100 bp to 2,000 bp. 100 bp DNA Ladder consists of 13 individual chromatography-purified DNA fragments and has reference bands at 2000, 1500, and 600 bp for easy orientation. 100 bp DNA Ladder is ideal for separation on 1–2% agarose gels. Highlights of 100 bp DNA Ladder: • Sharp, clear bands—chromatography purified fragments for consistent and reliable results • Convenient—provided with 10X BlueJuice Gel Loading Buffer for tracking of sample DNA migration • Precise—an exact amount of DNA in each band Product use The double-stranded DNA ladder can be visualized on 1–2% agarose gels after ethidium bromide or SYBR Safe staining. The ladder is designed with a uniform intensity of DNA bands for a clear view of each band. An exact amount of DNA in each band allows approximate quantification of DNA samples. This ladder can be radiolabeled with T4 polynucleotide kinase or T4 DNA polymerase.
    https://www.bioz.com/result/dna ladders/product/Thermo Fisher
    Average 99 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
    dna ladders - by Bioz Stars, 2019-10
    99/100 stars

    Images

    1) Product Images from "Conditional mutagenesis by oligonucleotide-mediated integration of loxP sites in zebrafish"

    Article Title: Conditional mutagenesis by oligonucleotide-mediated integration of loxP sites in zebrafish

    Journal: PLoS Genetics

    doi: 10.1371/journal.pgen.1007754

    Generation and testing of a conditional (“floxed”) tbx20 allele. a . Experimental design. b . Genotyping of adult fish for intron 2 loxP site. c . Results of nested PCR screening for loxP integration into intron 1. d . Sequence of intron 1 loxP integration in recovered tpl145 floxed tbx20 allele. e . Genotyping of “F1” adults. Primer binding sites are shown as black arrows, loxP sites as red or blue triangles, exon as an open box. f, g . Induction of tbx20 loss of function by injection of Cre mRNA. f . One quarter of embryos obtained by in-crossing tbx20 tpl145 heterozygotes and injected with Cre mRNA display a consistent, severe heart development defect. g . Genotyping of embryos with severe heart defects (lanes 1–3) and phenotypically normal siblings (lanes 4–8). L, GeneRuler DNA Ladder (ThermoFisher Scientific). Genotyping lanes 1 and 5 correspond to images in f . h, i . Induction of tbx20 deletion by 4-hydroxytamoxifen. tbx20 tpl145 heterozygote was crossed to Tg( ubi :CreERT2) line. GFP-positive embryos were collected at 2dpf and incubated with 5μM 4-HT for 24 hours. j . Adults raised from Cre-injected tbx20 tpl145/+ embryos were incrossed, resulting in approximately 1/4 of embryos (36/128, 28%) with severe heart defects. k . Confirmation of Cre-mediated excision of the second intron of tbx20 by sequence analysis. l, m . Analysis of excision efficiency by qPCR. l . Excision efficiency was assessed by qPCR in embryos treated with 4-HT at various concentrations at different time points and in two different ubb :CreERT2 driver lines. The y-axis indicates un-excised tpl 145 normalized to the untreated control. m . Images of tbx20 phenotypes shown after treatment with 4-HT. Individuals 1, 2, and 3 from l correspond to images labeled 1, 2, and 3.
    Figure Legend Snippet: Generation and testing of a conditional (“floxed”) tbx20 allele. a . Experimental design. b . Genotyping of adult fish for intron 2 loxP site. c . Results of nested PCR screening for loxP integration into intron 1. d . Sequence of intron 1 loxP integration in recovered tpl145 floxed tbx20 allele. e . Genotyping of “F1” adults. Primer binding sites are shown as black arrows, loxP sites as red or blue triangles, exon as an open box. f, g . Induction of tbx20 loss of function by injection of Cre mRNA. f . One quarter of embryos obtained by in-crossing tbx20 tpl145 heterozygotes and injected with Cre mRNA display a consistent, severe heart development defect. g . Genotyping of embryos with severe heart defects (lanes 1–3) and phenotypically normal siblings (lanes 4–8). L, GeneRuler DNA Ladder (ThermoFisher Scientific). Genotyping lanes 1 and 5 correspond to images in f . h, i . Induction of tbx20 deletion by 4-hydroxytamoxifen. tbx20 tpl145 heterozygote was crossed to Tg( ubi :CreERT2) line. GFP-positive embryos were collected at 2dpf and incubated with 5μM 4-HT for 24 hours. j . Adults raised from Cre-injected tbx20 tpl145/+ embryos were incrossed, resulting in approximately 1/4 of embryos (36/128, 28%) with severe heart defects. k . Confirmation of Cre-mediated excision of the second intron of tbx20 by sequence analysis. l, m . Analysis of excision efficiency by qPCR. l . Excision efficiency was assessed by qPCR in embryos treated with 4-HT at various concentrations at different time points and in two different ubb :CreERT2 driver lines. The y-axis indicates un-excised tpl 145 normalized to the untreated control. m . Images of tbx20 phenotypes shown after treatment with 4-HT. Individuals 1, 2, and 3 from l correspond to images labeled 1, 2, and 3.

    Techniques Used: Fluorescence In Situ Hybridization, Nested PCR, Sequencing, Binding Assay, Injection, Incubation, Real-time Polymerase Chain Reaction, Labeling

    2) Product Images from "Conditional mutagenesis by oligonucleotide-mediated integration of loxP sites in zebrafish"

    Article Title: Conditional mutagenesis by oligonucleotide-mediated integration of loxP sites in zebrafish

    Journal: PLoS Genetics

    doi: 10.1371/journal.pgen.1007754

    Generation and testing of a conditional (“floxed”) tbx20 allele. a . Experimental design. b . Genotyping of adult fish for intron 2 loxP site. c . Results of nested PCR screening for loxP integration into intron 1. d . Sequence of intron 1 loxP integration in recovered tpl145 floxed tbx20 allele. e . Genotyping of “F1” adults. Primer binding sites are shown as black arrows, loxP sites as red or blue triangles, exon as an open box. f, g . Induction of tbx20 loss of function by injection of Cre mRNA. f . One quarter of embryos obtained by in-crossing tbx20 tpl145 heterozygotes and injected with Cre mRNA display a consistent, severe heart development defect. g . Genotyping of embryos with severe heart defects (lanes 1–3) and phenotypically normal siblings (lanes 4–8). L, GeneRuler DNA Ladder (ThermoFisher Scientific). Genotyping lanes 1 and 5 correspond to images in f . h, i . Induction of tbx20 deletion by 4-hydroxytamoxifen. tbx20 tpl145 heterozygote was crossed to Tg( ubi :CreERT2) line. GFP-positive embryos were collected at 2dpf and incubated with 5μM 4-HT for 24 hours. j . Adults raised from Cre-injected tbx20 tpl145/+ embryos were incrossed, resulting in approximately 1/4 of embryos (36/128, 28%) with severe heart defects. k . Confirmation of Cre-mediated excision of the second intron of tbx20 by sequence analysis. l, m . Analysis of excision efficiency by qPCR. l . Excision efficiency was assessed by qPCR in embryos treated with 4-HT at various concentrations at different time points and in two different ubb :CreERT2 driver lines. The y-axis indicates un-excised tpl 145 normalized to the untreated control. m . Images of tbx20 phenotypes shown after treatment with 4-HT. Individuals 1, 2, and 3 from l correspond to images labeled 1, 2, and 3.
    Figure Legend Snippet: Generation and testing of a conditional (“floxed”) tbx20 allele. a . Experimental design. b . Genotyping of adult fish for intron 2 loxP site. c . Results of nested PCR screening for loxP integration into intron 1. d . Sequence of intron 1 loxP integration in recovered tpl145 floxed tbx20 allele. e . Genotyping of “F1” adults. Primer binding sites are shown as black arrows, loxP sites as red or blue triangles, exon as an open box. f, g . Induction of tbx20 loss of function by injection of Cre mRNA. f . One quarter of embryos obtained by in-crossing tbx20 tpl145 heterozygotes and injected with Cre mRNA display a consistent, severe heart development defect. g . Genotyping of embryos with severe heart defects (lanes 1–3) and phenotypically normal siblings (lanes 4–8). L, GeneRuler DNA Ladder (ThermoFisher Scientific). Genotyping lanes 1 and 5 correspond to images in f . h, i . Induction of tbx20 deletion by 4-hydroxytamoxifen. tbx20 tpl145 heterozygote was crossed to Tg( ubi :CreERT2) line. GFP-positive embryos were collected at 2dpf and incubated with 5μM 4-HT for 24 hours. j . Adults raised from Cre-injected tbx20 tpl145/+ embryos were incrossed, resulting in approximately 1/4 of embryos (36/128, 28%) with severe heart defects. k . Confirmation of Cre-mediated excision of the second intron of tbx20 by sequence analysis. l, m . Analysis of excision efficiency by qPCR. l . Excision efficiency was assessed by qPCR in embryos treated with 4-HT at various concentrations at different time points and in two different ubb :CreERT2 driver lines. The y-axis indicates un-excised tpl 145 normalized to the untreated control. m . Images of tbx20 phenotypes shown after treatment with 4-HT. Individuals 1, 2, and 3 from l correspond to images labeled 1, 2, and 3.

    Techniques Used: Fluorescence In Situ Hybridization, Nested PCR, Sequencing, Binding Assay, Injection, Incubation, Real-time Polymerase Chain Reaction, Labeling

    Related Articles

    Amplification:

    Article Title: Is There a Correlation between Helicobacter Pylori and Enterohepatic Helicobacter Species and Gallstone Cholecystitis?
    Article Snippet: Paragraph title: Helicobacter species-specific PCR amplification and PCR conditions ... For this reason, PCR products were applied to the gel in parallel with DNA ladders (GeneRuler™ 100 bp Plus DNA Ladder Fermentas, Germany) to determine reaction product sizes.

    Article Title: Detection of Free-Living Amoebae Using Amoebal Enrichment in a Wastewater Treatment Plant of Gauteng Province, South Africa
    Article Snippet: To detect Acanthamoeba sp., the reaction tubes were initially activated at 95°C for 15 minutes followed by 40 cycles of amplification using denaturation at 94°C for 45 s. Annealing was done at 57°C for 45 s and extension at 72°C for 1 minute followed by a final extension cycle at 72°C for 3 minutes. .. 5 µ L of 100 bp DNA marker (Fermentas O'GeneRuler DNA ladder, Canada) was loaded into the first well of the gel and into the remaining wells 10 µ L each sample (including positive and negative controls) mixed with 3 µ L of loading dye (Fermentas Orange × 6 Loading Dye, Canada).

    Article Title: Study of Lactic Acid Bacteria Community From Raw Milk of Iranian One Humped Camel and Evaluation of Their Probiotic Properties
    Article Snippet: The reaction mixture was then incubated at 65°C and 37°C for Taq I and Hhal, respectively for 1.5 hour. .. The Amplified Ribosomal DNA Restriction Analysis (ARDRA)profiles were examined using 1.5% (w/v) agarose gels in 0.5X Tris/Borate/Ethylenediaminetetraacetic acid (TBE) buffer at 75 V for 90 minutes with a DNA ladder (GeneRuler™ 100 bp) (Fermentas, USA). .. Representative isolates of different ARDRA profiles were amplified by PCR.

    Article Title: Polymorphism of the melatonin receptor 1A (MNTR1A) gene and association with seasonality of reproductive activity in a local Greek sheep breed
    Article Snippet: Restriction fragment length polymorphism (RFLP) analysis was performed on the amplified products, using the Rsa I restriction endonuclease. .. Restriction patterns were visualized in a 2.5 % agarose gel, stained with ethidium bromide and the fragments were sized according to a 100 bp DNA ladder (GeneRuler 100 bp, Fermentas, Vilnius, Lithuania).

    Article Title: β-Arrestin Regulates Estradiol Membrane-Initiated Signaling in Hypothalamic Neurons
    Article Snippet: In addition, PCR products were electrophoresed on a 2% agarose gel containing ethidium bromide (1.12 g agarose, Sigma #A9539; 50.4 mL dd H20; 5.6 mL 10x TAE buffer, Sigma #T8280; 1 uL EtBr) and visualized using the FluorChem E imager (ProteinSimple; Santa Clara, CA). .. A DNA ladder (GeneRuler 100 bp DNA ladder, Thermo Scientific) was run alongside samples for verification of amplicon size. .. All PCR products yielded single peaks in the melting curve analysis and single bands in agarose gel electrophoresis ( .).

    Mass Spectrometry:

    Article Title: Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification
    Article Snippet: The length of LAMP products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA). .. The length of LAMP products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA).

    Positive Control:

    Article Title: Detection of Free-Living Amoebae Using Amoebal Enrichment in a Wastewater Treatment Plant of Gauteng Province, South Africa
    Article Snippet: A positive control was used in each experiment which comprised all the reagents mentioned above other than template DNA which was replaced with 10 µ L of genomic DNA extracted from the reference strains of Acanthamoeba spp. .. 5 µ L of 100 bp DNA marker (Fermentas O'GeneRuler DNA ladder, Canada) was loaded into the first well of the gel and into the remaining wells 10 µ L each sample (including positive and negative controls) mixed with 3 µ L of loading dye (Fermentas Orange × 6 Loading Dye, Canada).

    Synthesized:

    Article Title: Is There a Correlation between Helicobacter Pylori and Enterohepatic Helicobacter Species and Gallstone Cholecystitis?
    Article Snippet: All oligonucleotide primers were synthesized by CinaGene (CinaGene Co, Tehran, Iran). .. For this reason, PCR products were applied to the gel in parallel with DNA ladders (GeneRuler™ 100 bp Plus DNA Ladder Fermentas, Germany) to determine reaction product sizes.

    Autoradiography:

    Article Title: The NIP7 protein is required for accurate pre-rRNA processing in human cells
    Article Snippet: Northern blot was performed using [32 P]-labeled oligonucleotide probes (P1–P7) complementary to specific regions of the 47S precursor RNA and submitted to autoradiography. .. For metabolic labeling of RNA, HEK293 cells cultured on 100-mm plates at ∼70–80% confluence were pre-incubated for 30 min in phosphate-free DMEM (GIBCO) supplemented with 10% FCS.

    Quantitative RT-PCR:

    Article Title: Serine 26 in the PomB Subunit of the Flagellar Motor Is Essential for Hypermotility of Vibrio cholerae
    Article Snippet: Steps 2 and 3 were repeated 39 times. .. The correct size (134 bp) of the qRT-PCR products was confirmed by gel-electrophoresis using a 100 bp DNA ladder (GeneRuler, Thermo Scientific). .. Primer efficiencies (with 100 ng, 10 ng, 1 ng, 0.1 ng cDNA as template) and relative gene expression of pomB from the V . cholerae reference strain and V . cholerae ΔpomAB pAB were quantified using the CFX Manager software (Bio-Rad, version 2.1.1022.0523).

    Real-time Polymerase Chain Reaction:

    Article Title: β-Arrestin Regulates Estradiol Membrane-Initiated Signaling in Hypothalamic Neurons
    Article Snippet: Paragraph title: Real-Time PCR ... A DNA ladder (GeneRuler 100 bp DNA ladder, Thermo Scientific) was run alongside samples for verification of amplicon size.

    Random Hexamer Labeling:

    Article Title: Serine 26 in the PomB Subunit of the Flagellar Motor Is Essential for Hypermotility of Vibrio cholerae
    Article Snippet: The SuperScript III First-Strand Synthesis System for RT-PCR (Invitrogen) was used for the synthesis of cDNA according to the manufacturer’s protocol using random hexamer primers. .. The correct size (134 bp) of the qRT-PCR products was confirmed by gel-electrophoresis using a 100 bp DNA ladder (GeneRuler, Thermo Scientific).

    Expressing:

    Article Title: Serine 26 in the PomB Subunit of the Flagellar Motor Is Essential for Hypermotility of Vibrio cholerae
    Article Snippet: The SensiFAST SYBR & Fluorescein Kit (Bioline) was used to determine the expression level of pomB in qRT-PCR reactions using primer pairs “pomB fwd” (5´-CGCAGTTTCGGTGGCGCAAG-3´) and “pomB rev” (5´-TGCCCGTTGCGCTTCGGTAT-3´). .. The correct size (134 bp) of the qRT-PCR products was confirmed by gel-electrophoresis using a 100 bp DNA ladder (GeneRuler, Thermo Scientific).

    Article Title: Stimulation of BK Virus DNA Replication by NFI Family Transcription Factors
    Article Snippet: All samples were fractionated by SDS-PAGE and analyzed by Coomassie blue staining, followed by Western blotting. .. HEK293 cells (approximately 6 × 106 cells) were transfected with expression vectors by using LipofectAMINE and Plus reagent (Invitrogen) in 100-mm-diameter plates as previously described ( ). .. At 48 h, the cells were lysed with 750 μl of a solution containing 1% Triton lysis buffer (50 mM Tris-Cl [pH 8.0], 150 mM NaCl, 1% Triton X-100, 30 μM ethidium bromide, 1 mM PMSF, complete protease inhibitor cocktail [Roche], 1× PhosSTOP phosphatase inhibitors [Roche]) by rotation for 1 h at 4°C, and lysates were cleared by centrifugation at 20,000 × g in a Sorvall SA-600 rotor for 30 min at 4°C.

    Knock-In:

    Article Title: Mutant Huntingtin Impairs Post-Golgi Trafficking to Lysosomes by Delocalizing Optineurin/Rab8 Complex from the Golgi Apparatus
    Article Snippet: Golgi fractions from knockin cells were prepared at 4°C as described in , with few modifications ( ). .. Briefly, twenty-two 100-mm plates (NUNC A/S) per condition were pelleted and washed twice in cold PBS (10 min at 500 × g ) and lysis buffer (10 mM Tris-HCl, 0.25 M sucrose, 1 mM phenylmethylsulfonyl fluoride [PMSF], 10 μg/ml aprotinin, and 1 μg/ml leupeptin, pH 7.4).

    Western Blot:

    Article Title: Stimulation of BK Virus DNA Replication by NFI Family Transcription Factors
    Article Snippet: HEK293 cells (approximately 6 × 106 cells) were transfected with expression vectors by using LipofectAMINE and Plus reagent (Invitrogen) in 100-mm-diameter plates as previously described ( ). .. HEK293 cells (approximately 6 × 106 cells) were transfected with expression vectors by using LipofectAMINE and Plus reagent (Invitrogen) in 100-mm-diameter plates as previously described ( ).

    Article Title: A Novel Mutant of rLj-RGD3 (rLj-112) Suppressed the Proliferation and Metastasis of B16 Cells through the EGFR Signaling Pathway
    Article Snippet: Paragraph title: 4.5. Western Blotting ... B16 cells seeded in the 100-mm-diameter plates (Thermo Scientific, USA) were treated with PBS or rLj-112 at different concentrations (0.5, 1.5, and 2.5 μM) for 24 h at 37 °C.

    Transfection:

    Article Title: Stimulation of BK Virus DNA Replication by NFI Family Transcription Factors
    Article Snippet: All samples were fractionated by SDS-PAGE and analyzed by Coomassie blue staining, followed by Western blotting. .. HEK293 cells (approximately 6 × 106 cells) were transfected with expression vectors by using LipofectAMINE and Plus reagent (Invitrogen) in 100-mm-diameter plates as previously described ( ). .. At 48 h, the cells were lysed with 750 μl of a solution containing 1% Triton lysis buffer (50 mM Tris-Cl [pH 8.0], 150 mM NaCl, 1% Triton X-100, 30 μM ethidium bromide, 1 mM PMSF, complete protease inhibitor cocktail [Roche], 1× PhosSTOP phosphatase inhibitors [Roche]) by rotation for 1 h at 4°C, and lysates were cleared by centrifugation at 20,000 × g in a Sorvall SA-600 rotor for 30 min at 4°C.

    Article Title: Techniques for augmentation of exogenous DNA uptake by ovine spermatozoa
    Article Snippet: 16) by ANOVA, expressed as the mean±SEM and when ANOVA revealed significant effects, values were compared by the least significant difference pair wise multiple comparison post hoc test. .. Experimental design Method 1: Use of lipofectamine in sperm transfection 100, 300 and 600 ng of plasmid with 0.4, 1.2 and 2.4 µL of lipofectamineTM 2000 (invitrogen), respectively, were incubated in 10 µL TCM in RT for 20 min in 1.5 ml tubes. .. A concentration of 1 × 106 washed ejaculated spermatozoa in 10 µL TCM from each ram was added to these tubes and incubated at 37°C, 5% CO2 and 95% humidity for 60 min. To assess the effect of incubation time, spermatozoa were incubated with DNA/liposome complex (100 ng/0.4 µL) for 60 and 120 min. After incubating, sperms were examined for DNA uptake rate, intensity and patterns.

    Concentration Assay:

    Article Title: Detection of Free-Living Amoebae Using Amoebal Enrichment in a Wastewater Treatment Plant of Gauteng Province, South Africa
    Article Snippet: The primers at a concentration of 10 µ M each were transferred into a reaction tube containing 10 µ L template DNA, 2 mM MgCl2 , 2.5 U of taq DNA polymerase (Life Technologies, SA), 100 µ M each deoxynucleoside triphosphate and 8 µ L ultrapure water (Fermentas, Canada), and 0.2 µ L hotStar Taq Polymerase. .. 5 µ L of 100 bp DNA marker (Fermentas O'GeneRuler DNA ladder, Canada) was loaded into the first well of the gel and into the remaining wells 10 µ L each sample (including positive and negative controls) mixed with 3 µ L of loading dye (Fermentas Orange × 6 Loading Dye, Canada).

    Article Title: Mutant Huntingtin Impairs Post-Golgi Trafficking to Lysosomes by Delocalizing Optineurin/Rab8 Complex from the Golgi Apparatus
    Article Snippet: Briefly, twenty-two 100-mm plates (NUNC A/S) per condition were pelleted and washed twice in cold PBS (10 min at 500 × g ) and lysis buffer (10 mM Tris-HCl, 0.25 M sucrose, 1 mM phenylmethylsulfonyl fluoride [PMSF], 10 μg/ml aprotinin, and 1 μg/ml leupeptin, pH 7.4). .. The cell pellet was then resuspended in 4 volumes of lysis buffer and homogenized using the Ball-Balch homogenizer device.

    SYBR Green Assay:

    Article Title: Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification
    Article Snippet: The length of LAMP products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA). .. The length of LAMP products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA).

    Northern Blot:

    Article Title: The NIP7 protein is required for accurate pre-rRNA processing in human cells
    Article Snippet: Northern blot was performed using [32 P]-labeled oligonucleotide probes (P1–P7) complementary to specific regions of the 47S precursor RNA and submitted to autoradiography. .. For metabolic labeling of RNA, HEK293 cells cultured on 100-mm plates at ∼70–80% confluence were pre-incubated for 30 min in phosphate-free DMEM (GIBCO) supplemented with 10% FCS.

    Cell Culture:

    Article Title: The NIP7 protein is required for accurate pre-rRNA processing in human cells
    Article Snippet: [32 P]-labeled-oligonucleotides MM21, MM30, MM36, MM44, MM54, MM64 and MM74 ( ) were used as molecular markers corresponding to 21, 30, 36, 44, 54, 64 and 74 nt, respectively. .. For metabolic labeling of RNA, HEK293 cells cultured on 100-mm plates at ∼70–80% confluence were pre-incubated for 30 min in phosphate-free DMEM (GIBCO) supplemented with 10% FCS. .. Subsequently, [32 P]-orthophosphate (15 μCi/ml) was added to the cultures that were incubated for 45 min and the medium was replaced by cold MEM (GIBCO) supplemented with 10% FCS.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Serine 26 in the PomB Subunit of the Flagellar Motor Is Essential for Hypermotility of Vibrio cholerae
    Article Snippet: The SuperScript III First-Strand Synthesis System for RT-PCR (Invitrogen) was used for the synthesis of cDNA according to the manufacturer’s protocol using random hexamer primers. .. The correct size (134 bp) of the qRT-PCR products was confirmed by gel-electrophoresis using a 100 bp DNA ladder (GeneRuler, Thermo Scientific).

    Article Title: β-Arrestin Regulates Estradiol Membrane-Initiated Signaling in Hypothalamic Neurons
    Article Snippet: The RT reaction was performed at 50°C for 50 minutes, followed by a 5 minute termination at 85°C. cDNA was used immediately for RT-PCR or stored at −20°C for ≤ 1 month. .. A DNA ladder (GeneRuler 100 bp DNA ladder, Thermo Scientific) was run alongside samples for verification of amplicon size.

    Molecular Weight:

    Article Title: The design of a new truncated and engineered alpha1-antitrypsin based on theoretical studies: an antiprotease therapeutics for pulmonary diseases
    Article Snippet: The cells were removed and the supernatant was precipitated by using 100% Aceton solution. .. After drying, the pellet was resuspended in loading buffer (10% w/v SDS, 10 nM β-mercaptoethanol, 20% v/v Glycerol, 0.2 M Tris–HCl, pH 6.8, 0.05% Bromophenol blue w/v), heated for 10 min, in boiling water and electrophoresed at 12% SDS-PAGE/100 V along with molecular weight marker (Fermentas). .. Gel was stained with silver nitrate according to Celis and coworkers [ ].

    Nucleic Acid Electrophoresis:

    Article Title: Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification
    Article Snippet: Results of LAMP were observed by naked-eye, under UV light or after gel electrophoresis in 2 % agarose gels stained with ethidium bromide (0.5 µg/ml). .. The length of LAMP products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA).

    Article Title: Serine 26 in the PomB Subunit of the Flagellar Motor Is Essential for Hypermotility of Vibrio cholerae
    Article Snippet: Steps 2 and 3 were repeated 39 times. .. The correct size (134 bp) of the qRT-PCR products was confirmed by gel-electrophoresis using a 100 bp DNA ladder (GeneRuler, Thermo Scientific). .. Primer efficiencies (with 100 ng, 10 ng, 1 ng, 0.1 ng cDNA as template) and relative gene expression of pomB from the V . cholerae reference strain and V . cholerae ΔpomAB pAB were quantified using the CFX Manager software (Bio-Rad, version 2.1.1022.0523).

    Isolation:

    Article Title: Mutant Huntingtin Impairs Post-Golgi Trafficking to Lysosomes by Delocalizing Optineurin/Rab8 Complex from the Golgi Apparatus
    Article Snippet: Paragraph title: Isolation of Golgi Membranes ... Briefly, twenty-two 100-mm plates (NUNC A/S) per condition were pelleted and washed twice in cold PBS (10 min at 500 × g ) and lysis buffer (10 mM Tris-HCl, 0.25 M sucrose, 1 mM phenylmethylsulfonyl fluoride [PMSF], 10 μg/ml aprotinin, and 1 μg/ml leupeptin, pH 7.4).

    Labeling:

    Article Title: The NIP7 protein is required for accurate pre-rRNA processing in human cells
    Article Snippet: [32 P]-labeled-oligonucleotides MM21, MM30, MM36, MM44, MM54, MM64 and MM74 ( ) were used as molecular markers corresponding to 21, 30, 36, 44, 54, 64 and 74 nt, respectively. .. For metabolic labeling of RNA, HEK293 cells cultured on 100-mm plates at ∼70–80% confluence were pre-incubated for 30 min in phosphate-free DMEM (GIBCO) supplemented with 10% FCS. .. Subsequently, [32 P]-orthophosphate (15 μCi/ml) was added to the cultures that were incubated for 45 min and the medium was replaced by cold MEM (GIBCO) supplemented with 10% FCS.

    Polymerase Chain Reaction:

    Article Title: Serine 26 in the PomB Subunit of the Flagellar Motor Is Essential for Hypermotility of Vibrio cholerae
    Article Snippet: Paragraph title: Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) ... The correct size (134 bp) of the qRT-PCR products was confirmed by gel-electrophoresis using a 100 bp DNA ladder (GeneRuler, Thermo Scientific).

    Article Title: Is There a Correlation between Helicobacter Pylori and Enterohepatic Helicobacter Species and Gallstone Cholecystitis?
    Article Snippet: Aliquots of 10 μL of PCR amplified products were separated electrophoretically. .. For this reason, PCR products were applied to the gel in parallel with DNA ladders (GeneRuler™ 100 bp Plus DNA Ladder Fermentas, Germany) to determine reaction product sizes. .. Constant voltages of 80 V for 30 min were used for products separation.

    Article Title: Detection of Free-Living Amoebae Using Amoebal Enrichment in a Wastewater Treatment Plant of Gauteng Province, South Africa
    Article Snippet: Paragraph title: 2.4.2. PCR Assays ... 5 µ L of 100 bp DNA marker (Fermentas O'GeneRuler DNA ladder, Canada) was loaded into the first well of the gel and into the remaining wells 10 µ L each sample (including positive and negative controls) mixed with 3 µ L of loading dye (Fermentas Orange × 6 Loading Dye, Canada).

    Article Title: Study of Lactic Acid Bacteria Community From Raw Milk of Iranian One Humped Camel and Evaluation of Their Probiotic Properties
    Article Snippet: The 16S rRNA- ITS gene PCR product from each LAB isolate was cut with restriction endonuclease enzyme: Taql and Hhal (Fermentas, USA), following the manufacturer’s instructions. .. The Amplified Ribosomal DNA Restriction Analysis (ARDRA)profiles were examined using 1.5% (w/v) agarose gels in 0.5X Tris/Borate/Ethylenediaminetetraacetic acid (TBE) buffer at 75 V for 90 minutes with a DNA ladder (GeneRuler™ 100 bp) (Fermentas, USA).

    Article Title: Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification
    Article Snippet: The PCR products were separated in 2 % agarose gel stained with ethidium bromide (0.5 µg/ml). .. The length of PCR products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA). .. In order to determine the optimal conditions of LAMP, MS reference strain (ATCC 25204) was used as the target template.

    Article Title: Polymorphism of the melatonin receptor 1A (MNTR1A) gene and association with seasonality of reproductive activity in a local Greek sheep breed
    Article Snippet: Eight microliters of each PCR product was digested for 3 h at 37 °C, with 8 units of Rsa I (Thermo Scientific, Dreieich, Germany), in a reaction of 20 μl total volume, containing 2 μl of 10× buffer Tango and 9.2 μl nuclease-free water. .. Restriction patterns were visualized in a 2.5 % agarose gel, stained with ethidium bromide and the fragments were sized according to a 100 bp DNA ladder (GeneRuler 100 bp, Fermentas, Vilnius, Lithuania).

    Article Title: Morphologic, Genetic, and Biochemical Characterization of Helicobacter Magdeburgensis, a Novel Species Isolated from the Intestine of Laboratory Mice
    Article Snippet: Five microliters aliquots of each PCR reaction or 20 µL restriction digests were electrophoretically analyzed in 0.8–2.0 g/mL agarose gels containing 0.5 µg/mL ethidium bromide in 1× Tris acetate running buffer. .. The 1-kb or 100-bp DNA ladder (Fermentas GeneRuler) was used as the size marker (M) in all gels.

    Article Title: β-Arrestin Regulates Estradiol Membrane-Initiated Signaling in Hypothalamic Neurons
    Article Snippet: In addition, PCR products were electrophoresed on a 2% agarose gel containing ethidium bromide (1.12 g agarose, Sigma #A9539; 50.4 mL dd H20; 5.6 mL 10x TAE buffer, Sigma #T8280; 1 uL EtBr) and visualized using the FluorChem E imager (ProteinSimple; Santa Clara, CA). .. A DNA ladder (GeneRuler 100 bp DNA ladder, Thermo Scientific) was run alongside samples for verification of amplicon size.

    Microscopy:

    Article Title: Techniques for augmentation of exogenous DNA uptake by ovine spermatozoa
    Article Snippet: To assess the rate, intensity and pattern of DNA uptake, spermatozoa were observed by the same microscope by green filter (510-580 nm) and ×100 magnifying (at least 3 view and 100 spermatozoa). .. Experimental design Method 1: Use of lipofectamine in sperm transfection 100, 300 and 600 ng of plasmid with 0.4, 1.2 and 2.4 µL of lipofectamineTM 2000 (invitrogen), respectively, were incubated in 10 µL TCM in RT for 20 min in 1.5 ml tubes.

    Lysis:

    Article Title: Mutant Huntingtin Impairs Post-Golgi Trafficking to Lysosomes by Delocalizing Optineurin/Rab8 Complex from the Golgi Apparatus
    Article Snippet: Golgi fractions from knockin cells were prepared at 4°C as described in , with few modifications ( ). .. Briefly, twenty-two 100-mm plates (NUNC A/S) per condition were pelleted and washed twice in cold PBS (10 min at 500 × g ) and lysis buffer (10 mM Tris-HCl, 0.25 M sucrose, 1 mM phenylmethylsulfonyl fluoride [PMSF], 10 μg/ml aprotinin, and 1 μg/ml leupeptin, pH 7.4). .. The cell pellet was then resuspended in 4 volumes of lysis buffer and homogenized using the Ball-Balch homogenizer device.

    Article Title: Stimulation of BK Virus DNA Replication by NFI Family Transcription Factors
    Article Snippet: HEK293 cells (approximately 6 × 106 cells) were transfected with expression vectors by using LipofectAMINE and Plus reagent (Invitrogen) in 100-mm-diameter plates as previously described ( ). .. At 48 h, the cells were lysed with 750 μl of a solution containing 1% Triton lysis buffer (50 mM Tris-Cl [pH 8.0], 150 mM NaCl, 1% Triton X-100, 30 μM ethidium bromide, 1 mM PMSF, complete protease inhibitor cocktail [Roche], 1× PhosSTOP phosphatase inhibitors [Roche]) by rotation for 1 h at 4°C, and lysates were cleared by centrifugation at 20,000 × g in a Sorvall SA-600 rotor for 30 min at 4°C.

    Silver Staining:

    Article Title: The design of a new truncated and engineered alpha1-antitrypsin based on theoretical studies: an antiprotease therapeutics for pulmonary diseases
    Article Snippet: Paragraph title: SDS-PAGE and silver staining ... After drying, the pellet was resuspended in loading buffer (10% w/v SDS, 10 nM β-mercaptoethanol, 20% v/v Glycerol, 0.2 M Tris–HCl, pH 6.8, 0.05% Bromophenol blue w/v), heated for 10 min, in boiling water and electrophoresed at 12% SDS-PAGE/100 V along with molecular weight marker (Fermentas).

    SDS Page:

    Article Title: Stimulation of BK Virus DNA Replication by NFI Family Transcription Factors
    Article Snippet: HEK293 cells (approximately 6 × 106 cells) were transfected with expression vectors by using LipofectAMINE and Plus reagent (Invitrogen) in 100-mm-diameter plates as previously described ( ). .. HEK293 cells (approximately 6 × 106 cells) were transfected with expression vectors by using LipofectAMINE and Plus reagent (Invitrogen) in 100-mm-diameter plates as previously described ( ).

    Article Title: The design of a new truncated and engineered alpha1-antitrypsin based on theoretical studies: an antiprotease therapeutics for pulmonary diseases
    Article Snippet: Paragraph title: SDS-PAGE and silver staining ... After drying, the pellet was resuspended in loading buffer (10% w/v SDS, 10 nM β-mercaptoethanol, 20% v/v Glycerol, 0.2 M Tris–HCl, pH 6.8, 0.05% Bromophenol blue w/v), heated for 10 min, in boiling water and electrophoresed at 12% SDS-PAGE/100 V along with molecular weight marker (Fermentas).

    Article Title: A Novel Mutant of rLj-RGD3 (rLj-112) Suppressed the Proliferation and Metastasis of B16 Cells through the EGFR Signaling Pathway
    Article Snippet: B16 cells seeded in the 100-mm-diameter plates (Thermo Scientific, USA) were treated with PBS or rLj-112 at different concentrations (0.5, 1.5, and 2.5 μM) for 24 h at 37 °C. .. The cells were lysed with lysis buffer for 15 min at 4 °C and the supernatant was harvested after centrifugation.

    Plasmid Preparation:

    Article Title: Techniques for augmentation of exogenous DNA uptake by ovine spermatozoa
    Article Snippet: 16) by ANOVA, expressed as the mean±SEM and when ANOVA revealed significant effects, values were compared by the least significant difference pair wise multiple comparison post hoc test. .. Experimental design Method 1: Use of lipofectamine in sperm transfection 100, 300 and 600 ng of plasmid with 0.4, 1.2 and 2.4 µL of lipofectamineTM 2000 (invitrogen), respectively, were incubated in 10 µL TCM in RT for 20 min in 1.5 ml tubes. .. A concentration of 1 × 106 washed ejaculated spermatozoa in 10 µL TCM from each ram was added to these tubes and incubated at 37°C, 5% CO2 and 95% humidity for 60 min. To assess the effect of incubation time, spermatozoa were incubated with DNA/liposome complex (100 ng/0.4 µL) for 60 and 120 min. After incubating, sperms were examined for DNA uptake rate, intensity and patterns.

    Software:

    Article Title: Techniques for augmentation of exogenous DNA uptake by ovine spermatozoa
    Article Snippet: Statistical analysis Data were analyzed using statistical software SPSS® (ver. .. Experimental design Method 1: Use of lipofectamine in sperm transfection 100, 300 and 600 ng of plasmid with 0.4, 1.2 and 2.4 µL of lipofectamineTM 2000 (invitrogen), respectively, were incubated in 10 µL TCM in RT for 20 min in 1.5 ml tubes.

    Electrophoresis:

    Article Title: Is There a Correlation between Helicobacter Pylori and Enterohepatic Helicobacter Species and Gallstone Cholecystitis?
    Article Snippet: For this reason, PCR products were applied to the gel in parallel with DNA ladders (GeneRuler™ 100 bp Plus DNA Ladder Fermentas, Germany) to determine reaction product sizes. .. For this reason, PCR products were applied to the gel in parallel with DNA ladders (GeneRuler™ 100 bp Plus DNA Ladder Fermentas, Germany) to determine reaction product sizes.

    Article Title: The NIP7 protein is required for accurate pre-rRNA processing in human cells
    Article Snippet: For metabolic labeling of RNA, HEK293 cells cultured on 100-mm plates at ∼70–80% confluence were pre-incubated for 30 min in phosphate-free DMEM (GIBCO) supplemented with 10% FCS. .. Subsequently, [32 P]-orthophosphate (15 μCi/ml) was added to the cultures that were incubated for 45 min and the medium was replaced by cold MEM (GIBCO) supplemented with 10% FCS.

    Article Title: Base-Pair Resolution Genome-Wide Mapping Of Active RNA polymerases using Precision Nuclear Run-On (PRO-seq)
    Article Snippet: Paragraph title: Electrophoresis ... Gel loading dye, Orange G 6× (NEB, cat. no. B7022S) 100 bp DNA ladder (Life Technologies, cat. no. 15628-019) 10 bp DNA ladder (Life Technologies, cat. no. 10821-015).

    Article Title: Morphologic, Genetic, and Biochemical Characterization of Helicobacter Magdeburgensis, a Novel Species Isolated from the Intestine of Laboratory Mice
    Article Snippet: The electrophoresis was for 2 hours at 100V. .. The 1-kb or 100-bp DNA ladder (Fermentas GeneRuler) was used as the size marker (M) in all gels.

    Negative Control:

    Article Title: Is There a Correlation between Helicobacter Pylori and Enterohepatic Helicobacter Species and Gallstone Cholecystitis?
    Article Snippet: For this reason, PCR products were applied to the gel in parallel with DNA ladders (GeneRuler™ 100 bp Plus DNA Ladder Fermentas, Germany) to determine reaction product sizes. .. After electrophoresis, the gel was stained with ethidium bromide and images were obtained by UVIdoc gel documentation systems (UK).

    Article Title: Detection of Free-Living Amoebae Using Amoebal Enrichment in a Wastewater Treatment Plant of Gauteng Province, South Africa
    Article Snippet: A negative control was also used in each experiment which comprised all the reagents mentioned above other than template DNA which was replaced with 10 µ L of PCR water. .. 5 µ L of 100 bp DNA marker (Fermentas O'GeneRuler DNA ladder, Canada) was loaded into the first well of the gel and into the remaining wells 10 µ L each sample (including positive and negative controls) mixed with 3 µ L of loading dye (Fermentas Orange × 6 Loading Dye, Canada).

    Agarose Gel Electrophoresis:

    Article Title: Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification
    Article Snippet: The PCR products were separated in 2 % agarose gel stained with ethidium bromide (0.5 µg/ml). .. The length of PCR products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA).

    Article Title: Polymorphism of the melatonin receptor 1A (MNTR1A) gene and association with seasonality of reproductive activity in a local Greek sheep breed
    Article Snippet: Eight microliters of each PCR product was digested for 3 h at 37 °C, with 8 units of Rsa I (Thermo Scientific, Dreieich, Germany), in a reaction of 20 μl total volume, containing 2 μl of 10× buffer Tango and 9.2 μl nuclease-free water. .. Restriction patterns were visualized in a 2.5 % agarose gel, stained with ethidium bromide and the fragments were sized according to a 100 bp DNA ladder (GeneRuler 100 bp, Fermentas, Vilnius, Lithuania). .. Statistical analysis was carried out using the SPSS package (ver.

    Article Title: Morphologic, Genetic, and Biochemical Characterization of Helicobacter Magdeburgensis, a Novel Species Isolated from the Intestine of Laboratory Mice
    Article Snippet: Paragraph title: Agarose Gel Electrophoresis ... The 1-kb or 100-bp DNA ladder (Fermentas GeneRuler) was used as the size marker (M) in all gels.

    Article Title: β-Arrestin Regulates Estradiol Membrane-Initiated Signaling in Hypothalamic Neurons
    Article Snippet: In addition, PCR products were electrophoresed on a 2% agarose gel containing ethidium bromide (1.12 g agarose, Sigma #A9539; 50.4 mL dd H20; 5.6 mL 10x TAE buffer, Sigma #T8280; 1 uL EtBr) and visualized using the FluorChem E imager (ProteinSimple; Santa Clara, CA). .. A DNA ladder (GeneRuler 100 bp DNA ladder, Thermo Scientific) was run alongside samples for verification of amplicon size.

    Incubation:

    Article Title: Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification
    Article Snippet: The length of LAMP products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA). .. The length of LAMP products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA).

    Article Title: Study of Lactic Acid Bacteria Community From Raw Milk of Iranian One Humped Camel and Evaluation of Their Probiotic Properties
    Article Snippet: The reaction mixture was then incubated at 65°C and 37°C for Taq I and Hhal, respectively for 1.5 hour. .. The Amplified Ribosomal DNA Restriction Analysis (ARDRA)profiles were examined using 1.5% (w/v) agarose gels in 0.5X Tris/Borate/Ethylenediaminetetraacetic acid (TBE) buffer at 75 V for 90 minutes with a DNA ladder (GeneRuler™ 100 bp) (Fermentas, USA).

    Article Title: Stimulation of BK Virus DNA Replication by NFI Family Transcription Factors
    Article Snippet: HEK293 cells (approximately 6 × 106 cells) were transfected with expression vectors by using LipofectAMINE and Plus reagent (Invitrogen) in 100-mm-diameter plates as previously described ( ). .. At 48 h, the cells were lysed with 750 μl of a solution containing 1% Triton lysis buffer (50 mM Tris-Cl [pH 8.0], 150 mM NaCl, 1% Triton X-100, 30 μM ethidium bromide, 1 mM PMSF, complete protease inhibitor cocktail [Roche], 1× PhosSTOP phosphatase inhibitors [Roche]) by rotation for 1 h at 4°C, and lysates were cleared by centrifugation at 20,000 × g in a Sorvall SA-600 rotor for 30 min at 4°C.

    Article Title: Techniques for augmentation of exogenous DNA uptake by ovine spermatozoa
    Article Snippet: 16) by ANOVA, expressed as the mean±SEM and when ANOVA revealed significant effects, values were compared by the least significant difference pair wise multiple comparison post hoc test. .. Experimental design Method 1: Use of lipofectamine in sperm transfection 100, 300 and 600 ng of plasmid with 0.4, 1.2 and 2.4 µL of lipofectamineTM 2000 (invitrogen), respectively, were incubated in 10 µL TCM in RT for 20 min in 1.5 ml tubes. .. A concentration of 1 × 106 washed ejaculated spermatozoa in 10 µL TCM from each ram was added to these tubes and incubated at 37°C, 5% CO2 and 95% humidity for 60 min. To assess the effect of incubation time, spermatozoa were incubated with DNA/liposome complex (100 ng/0.4 µL) for 60 and 120 min. After incubating, sperms were examined for DNA uptake rate, intensity and patterns.

    Article Title: A Novel Mutant of rLj-RGD3 (rLj-112) Suppressed the Proliferation and Metastasis of B16 Cells through the EGFR Signaling Pathway
    Article Snippet: B16 cells seeded in the 100-mm-diameter plates (Thermo Scientific, USA) were treated with PBS or rLj-112 at different concentrations (0.5, 1.5, and 2.5 μM) for 24 h at 37 °C. .. B16 cells seeded in the 100-mm-diameter plates (Thermo Scientific, USA) were treated with PBS or rLj-112 at different concentrations (0.5, 1.5, and 2.5 μM) for 24 h at 37 °C.

    Activation Assay:

    Article Title: β-Arrestin Regulates Estradiol Membrane-Initiated Signaling in Hypothalamic Neurons
    Article Snippet: Reactions were run on an Mx3000p thermal cycler (Agilent; Santa Clara, CA) using the program: 3 minutes at 95°C for DNA polymerase activation, then 40 cycles each consisting of 20 seconds at 95°C for denaturation and 20 seconds at 54°C annealing/extension temperature. .. A DNA ladder (GeneRuler 100 bp DNA ladder, Thermo Scientific) was run alongside samples for verification of amplicon size.

    Marker:

    Article Title: Detection of Free-Living Amoebae Using Amoebal Enrichment in a Wastewater Treatment Plant of Gauteng Province, South Africa
    Article Snippet: DNA was analyzed in a horizontal 1% (w/v) agarose slab gel (FP Agarose from Promega) with ethidium bromide (0.5 µ g/mL) in a TAE (40 mM Tris acetate; 2 mM EDTA, pH 8.3) buffered system. .. 5 µ L of 100 bp DNA marker (Fermentas O'GeneRuler DNA ladder, Canada) was loaded into the first well of the gel and into the remaining wells 10 µ L each sample (including positive and negative controls) mixed with 3 µ L of loading dye (Fermentas Orange × 6 Loading Dye, Canada). .. Statistical analysis was carried out to compare amoebae recovered using live or heat-killed E. coli at different temperatures (room temperature, 32°C, and 37°C) and concentration techniques (centrifugation or filtration).

    Article Title: Morphologic, Genetic, and Biochemical Characterization of Helicobacter Magdeburgensis, a Novel Species Isolated from the Intestine of Laboratory Mice
    Article Snippet: The electrophoresis was for 2 hours at 100V. .. The 1-kb or 100-bp DNA ladder (Fermentas GeneRuler) was used as the size marker (M) in all gels. .. Bacterial cells were harvested and fixed in a sterile solution containing 5% formaldehyde, 2% glutaraldehyde in cacodylate buffer (0.1 m cacodylate, 0.01 m CaCl2 , 0.01 m MgCl2 , 0.09 m sucrose, pH 6.9) for 1 hour on ice.

    Staining:

    Article Title: Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification
    Article Snippet: Results of LAMP were observed by naked-eye, under UV light or after gel electrophoresis in 2 % agarose gels stained with ethidium bromide (0.5 µg/ml). .. The length of LAMP products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA).

    Article Title: Is There a Correlation between Helicobacter Pylori and Enterohepatic Helicobacter Species and Gallstone Cholecystitis?
    Article Snippet: For this reason, PCR products were applied to the gel in parallel with DNA ladders (GeneRuler™ 100 bp Plus DNA Ladder Fermentas, Germany) to determine reaction product sizes. .. For this reason, PCR products were applied to the gel in parallel with DNA ladders (GeneRuler™ 100 bp Plus DNA Ladder Fermentas, Germany) to determine reaction product sizes.

    Article Title: Base-Pair Resolution Genome-Wide Mapping Of Active RNA polymerases using Precision Nuclear Run-On (PRO-seq)
    Article Snippet: Gel loading dye, Orange G 6× (NEB, cat. no. B7022S) 100 bp DNA ladder (Life Technologies, cat. no. 15628-019) 10 bp DNA ladder (Life Technologies, cat. no. 10821-015). .. Gel loading dye, Orange G 6× (NEB, cat. no. B7022S) 100 bp DNA ladder (Life Technologies, cat. no. 15628-019) 10 bp DNA ladder (Life Technologies, cat. no. 10821-015).

    Article Title: Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification
    Article Snippet: The PCR products were separated in 2 % agarose gel stained with ethidium bromide (0.5 µg/ml). .. The length of PCR products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA).

    Article Title: Polymorphism of the melatonin receptor 1A (MNTR1A) gene and association with seasonality of reproductive activity in a local Greek sheep breed
    Article Snippet: Eight microliters of each PCR product was digested for 3 h at 37 °C, with 8 units of Rsa I (Thermo Scientific, Dreieich, Germany), in a reaction of 20 μl total volume, containing 2 μl of 10× buffer Tango and 9.2 μl nuclease-free water. .. Restriction patterns were visualized in a 2.5 % agarose gel, stained with ethidium bromide and the fragments were sized according to a 100 bp DNA ladder (GeneRuler 100 bp, Fermentas, Vilnius, Lithuania). .. Statistical analysis was carried out using the SPSS package (ver.

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  • 99
    Thermo Fisher kb dna ladder
    Genotyping Exoc3l2 tm1a(KOMP)Wtsi KO 1st chimeras with construct-specific primers. A. The Exoc3l2 tm1a(KOMP)Wtsi KO 1st construct with conditional potential. The targeted exon is flanked by a loxP (loxP2) and a synthetic loxP3 site. The final blue box represents the terminal exon of the Exoc3l2 gene encoded by the construct. B. Combining primers designed to target loxP2 (F loxP2 ) and the target exon (R Target ) was predicted to amplify a <t>PCR</t> product of 637 bp. The primer F loxP3 targeted the synthetic loxP3 region and in combination with the R Flank1 primer it was predicted to produce a 136 bp product from KO 1st templates. The F Target and R Target primers amplify a sequence of 105 bp from the targeted exon, common to all samples. C. PCR using the F loxP2 and R Target primers confirmed the KO 1st genotype in <t>DNA</t> samples extracted from KO 1st chimera biopsies and amplified no product in samples extracted from Wt biopsies. D. PCR using the F loxP3 and R Flank1 primers with KO 1st and Wt biopsies also produced a PCR product close to the predicted size in KO 1st chimera samples and no product in Wt samples. PCR with F Target and R Target primers amplified a product close to the predicted size in all samples. E. Sanger sequencing of the PCR products from C. confirmed the KO 1st specific identity of the amplified product. F. Sanger sequencing of the 136 bp PCR product amplified using the F loxP3 and R Flank1 primers confirmed the correct position of the junction between the synthetic loxP3 sequence and the Wt sequence. Black dots were placed under bases of low quality, but the specific base peaks at these positions were identical to those predicted for this sequence. PCR was performed with an annealing temperature of 56°C and products were separated on 1% agarose gels containing GelRed stain. Each of the two KO 1st lanes in C and D represent PCR products derived from two distinct KO 1st chimeric mice. Abbreviations : B2: B2 Gateway (Gateway cloning strategy element) | CR: Critical region of Exoc3l2 (identified by KOMP) | En2/SA: Engrailed-2/Splice acceptor | IRES: Internal ribosome entry site | lacZ: Lactose operon Z (β-galactosidase gene) | pA: SV40 polyadenylation site | P: Human beta actin promoter | neo: Neomycin resistance gene | KO 1st : Knockout first chimera.
    Kb Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 71 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/kb dna ladder/product/Thermo Fisher
    Average 99 stars, based on 71 article reviews
    Price from $9.99 to $1999.99
    kb dna ladder - by Bioz Stars, 2019-10
    99/100 stars
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    98
    Thermo Fisher generuler 100 bp plus dna ladder
    Agarose gel electrophoresis of successful RCA amplification of members of Sporothrix schenckii - Ophiostoma stenoceras complex from a sample containing host/vegetable and fungal <t>DNA</t> . (A) Sbra-RCA padlock probe; (B) Ssch-RCA padlock probe; (C) Sglo-RCA padlock probe; (D) Slur-RCA padlock probe; (E) Smex-RCA padlock probe; and (F) Spa-RCA padlock probe. Gel lanes 1–7 on the left correspond to non-spiked samples (negative control): 1, soil; 2, Sphagnum moss; 3, Rose spp.; 4, BALB/c spleen; 5, BALB/c lungs; 6, BALB/c tail; 7, BALB/c feces. Gel lanes 1–7 on the right correspond to spiked samples (species as indicated): 1, spiked soil; 2, spiked Sphagnum moss; 3, spiked Rose spp.; 4, spiked BALB/c spleen; 5, spiked BALB/c lungs; 6, spiked BALB/c tail; 7, spiked BALB/c feces. +, positive control using DNA from culture; -, negative control (blank). Amplicons were sized by comparison with bands of known size from the GeneRuler 100 bp Plus DNA Ladder (M) (Thermo Fisher Scientific, USA). The results show an efficient replication of samples spiked with pathogen DNA. On the other hand, RCA failed to replicate the DNA originated solely from environmental or clinical samples (non-spiked), which remained negative. It can thus be assumed that the padlock probes can selectively replicate pathogen DNA, confirming the high specificity of our RCA-based assay.
    Generuler 100 Bp Plus Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/generuler 100 bp plus dna ladder/product/Thermo Fisher
    Average 98 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    generuler 100 bp plus dna ladder - by Bioz Stars, 2019-10
    98/100 stars
      Buy from Supplier

    Image Search Results


    Genotyping Exoc3l2 tm1a(KOMP)Wtsi KO 1st chimeras with construct-specific primers. A. The Exoc3l2 tm1a(KOMP)Wtsi KO 1st construct with conditional potential. The targeted exon is flanked by a loxP (loxP2) and a synthetic loxP3 site. The final blue box represents the terminal exon of the Exoc3l2 gene encoded by the construct. B. Combining primers designed to target loxP2 (F loxP2 ) and the target exon (R Target ) was predicted to amplify a PCR product of 637 bp. The primer F loxP3 targeted the synthetic loxP3 region and in combination with the R Flank1 primer it was predicted to produce a 136 bp product from KO 1st templates. The F Target and R Target primers amplify a sequence of 105 bp from the targeted exon, common to all samples. C. PCR using the F loxP2 and R Target primers confirmed the KO 1st genotype in DNA samples extracted from KO 1st chimera biopsies and amplified no product in samples extracted from Wt biopsies. D. PCR using the F loxP3 and R Flank1 primers with KO 1st and Wt biopsies also produced a PCR product close to the predicted size in KO 1st chimera samples and no product in Wt samples. PCR with F Target and R Target primers amplified a product close to the predicted size in all samples. E. Sanger sequencing of the PCR products from C. confirmed the KO 1st specific identity of the amplified product. F. Sanger sequencing of the 136 bp PCR product amplified using the F loxP3 and R Flank1 primers confirmed the correct position of the junction between the synthetic loxP3 sequence and the Wt sequence. Black dots were placed under bases of low quality, but the specific base peaks at these positions were identical to those predicted for this sequence. PCR was performed with an annealing temperature of 56°C and products were separated on 1% agarose gels containing GelRed stain. Each of the two KO 1st lanes in C and D represent PCR products derived from two distinct KO 1st chimeric mice. Abbreviations : B2: B2 Gateway (Gateway cloning strategy element) | CR: Critical region of Exoc3l2 (identified by KOMP) | En2/SA: Engrailed-2/Splice acceptor | IRES: Internal ribosome entry site | lacZ: Lactose operon Z (β-galactosidase gene) | pA: SV40 polyadenylation site | P: Human beta actin promoter | neo: Neomycin resistance gene | KO 1st : Knockout first chimera.

    Journal: PLoS ONE

    Article Title: Failure to Genotype: A Cautionary Note on an Elusive loxP Sequence

    doi: 10.1371/journal.pone.0165012

    Figure Lengend Snippet: Genotyping Exoc3l2 tm1a(KOMP)Wtsi KO 1st chimeras with construct-specific primers. A. The Exoc3l2 tm1a(KOMP)Wtsi KO 1st construct with conditional potential. The targeted exon is flanked by a loxP (loxP2) and a synthetic loxP3 site. The final blue box represents the terminal exon of the Exoc3l2 gene encoded by the construct. B. Combining primers designed to target loxP2 (F loxP2 ) and the target exon (R Target ) was predicted to amplify a PCR product of 637 bp. The primer F loxP3 targeted the synthetic loxP3 region and in combination with the R Flank1 primer it was predicted to produce a 136 bp product from KO 1st templates. The F Target and R Target primers amplify a sequence of 105 bp from the targeted exon, common to all samples. C. PCR using the F loxP2 and R Target primers confirmed the KO 1st genotype in DNA samples extracted from KO 1st chimera biopsies and amplified no product in samples extracted from Wt biopsies. D. PCR using the F loxP3 and R Flank1 primers with KO 1st and Wt biopsies also produced a PCR product close to the predicted size in KO 1st chimera samples and no product in Wt samples. PCR with F Target and R Target primers amplified a product close to the predicted size in all samples. E. Sanger sequencing of the PCR products from C. confirmed the KO 1st specific identity of the amplified product. F. Sanger sequencing of the 136 bp PCR product amplified using the F loxP3 and R Flank1 primers confirmed the correct position of the junction between the synthetic loxP3 sequence and the Wt sequence. Black dots were placed under bases of low quality, but the specific base peaks at these positions were identical to those predicted for this sequence. PCR was performed with an annealing temperature of 56°C and products were separated on 1% agarose gels containing GelRed stain. Each of the two KO 1st lanes in C and D represent PCR products derived from two distinct KO 1st chimeric mice. Abbreviations : B2: B2 Gateway (Gateway cloning strategy element) | CR: Critical region of Exoc3l2 (identified by KOMP) | En2/SA: Engrailed-2/Splice acceptor | IRES: Internal ribosome entry site | lacZ: Lactose operon Z (β-galactosidase gene) | pA: SV40 polyadenylation site | P: Human beta actin promoter | neo: Neomycin resistance gene | KO 1st : Knockout first chimera.

    Article Snippet: The PCR was performed on a MiniOpticon PCR System (BioRad Laboratories, Solna, Sweden) or a 2720 Thermal Cycler (Applied Biosystems, Thermo Fisher Scientific) with the following protocol: one cycle of 95°C for 3 min; 39 cycles of 95°C for 30 sec; 56, 60, 65 or 70°C for 30 sec; 72°C for 1 min; and one cycle of 72°C for 7 min. PCR products and the GeneRuler 100 bp or 1 kb DNA ladder (Thermo Fisher Scientific) were diluted in DNA Gel Loading Dye (6X; Thermo Fisher Scientific) and separated by electrophoresis on 1% or 2.5% agarose gels, prepared in 40 mM Tris, 20 mM acetate and 1 mM EDTA (TAE buffer) with 1‱ GelRed fluorescent DNA stain (Biotium, Hayward, CA, USA).

    Techniques: Gene Knockout, Construct, Polymerase Chain Reaction, Sequencing, Amplification, Produced, Staining, Derivative Assay, Mouse Assay, Clone Assay, Knock-Out

    Targeting alternative flank positions or altering the PCR annealing temperature does not render templates containing the synthetic loxP3 region susceptible to amplification. A. PCR using the F loxP3 and R Flank1 primers correctly distinguished the genotypes of a KO 1st chimera (band at 136 bp) from a Wt mouse, using DNA isolated from brain tissue. B. Binding sites and predicted PCR product sizes for five primer pairs that target Wt sequences flanking the synthetic loxP3 region in KO 1st templates and an eleven bp Wt-specific sequence in Wt templates. C. PCR was performed with the samples from A. and the primer pairs indicated in B. with the annealing temperature (Ta) set to 60°C, 65°C or 70°C. Products were separated on 2.5% agarose gels containing GelRed stain. DNA samples from the same KO 1st chimeric mouse and Wt mouse were used throughout this figure. Abbreviations: P = primers only.

    Journal: PLoS ONE

    Article Title: Failure to Genotype: A Cautionary Note on an Elusive loxP Sequence

    doi: 10.1371/journal.pone.0165012

    Figure Lengend Snippet: Targeting alternative flank positions or altering the PCR annealing temperature does not render templates containing the synthetic loxP3 region susceptible to amplification. A. PCR using the F loxP3 and R Flank1 primers correctly distinguished the genotypes of a KO 1st chimera (band at 136 bp) from a Wt mouse, using DNA isolated from brain tissue. B. Binding sites and predicted PCR product sizes for five primer pairs that target Wt sequences flanking the synthetic loxP3 region in KO 1st templates and an eleven bp Wt-specific sequence in Wt templates. C. PCR was performed with the samples from A. and the primer pairs indicated in B. with the annealing temperature (Ta) set to 60°C, 65°C or 70°C. Products were separated on 2.5% agarose gels containing GelRed stain. DNA samples from the same KO 1st chimeric mouse and Wt mouse were used throughout this figure. Abbreviations: P = primers only.

    Article Snippet: The PCR was performed on a MiniOpticon PCR System (BioRad Laboratories, Solna, Sweden) or a 2720 Thermal Cycler (Applied Biosystems, Thermo Fisher Scientific) with the following protocol: one cycle of 95°C for 3 min; 39 cycles of 95°C for 30 sec; 56, 60, 65 or 70°C for 30 sec; 72°C for 1 min; and one cycle of 72°C for 7 min. PCR products and the GeneRuler 100 bp or 1 kb DNA ladder (Thermo Fisher Scientific) were diluted in DNA Gel Loading Dye (6X; Thermo Fisher Scientific) and separated by electrophoresis on 1% or 2.5% agarose gels, prepared in 40 mM Tris, 20 mM acetate and 1 mM EDTA (TAE buffer) with 1‱ GelRed fluorescent DNA stain (Biotium, Hayward, CA, USA).

    Techniques: Polymerase Chain Reaction, Amplification, Gene Knockout, Isolation, Binding Assay, Sequencing, Staining

    Predicted secondary structure of the synthetic loxP3 region. A. The 80 base synthetic loxP3 region was submitted to the RNAstructure Webserver; DNA was selected as the nucleic acid type and the default data settings were preserved. The RNAstructure MaxExpect result generated by the Webserver is presented; this represents a structure formed due to high probability base pairing. The centrally located 34 bases is the loxP sequence (highlighted in pink), of which the first and last 13 bases are palindromic sequences. This facilitates intrastrand base-pairing permitting the formation of a hairpin loop structure. An additional stem structure (stem 1 ) is predicted due to intrastrand base-pairing between the synthetic DNA sequences that flank the loxP site (highlighted in grey). The probability of base-pairing is illustrated by colour coding. B. A linear view of the 80 bases of the synthetic loxP3 region is annotated with the position of the stem and loop structures. C. Primers that bind sequences that are capable of intrastrand base-pairing may compete with intrastrand base-pairing, stabilizing the template and permitting PCR to proceed. In contrast, primers that bind in the regions flanking the synthetic loxP3 region cannot prevent secondary structure formation and consequently PCR of these templates may be impaired.

    Journal: PLoS ONE

    Article Title: Failure to Genotype: A Cautionary Note on an Elusive loxP Sequence

    doi: 10.1371/journal.pone.0165012

    Figure Lengend Snippet: Predicted secondary structure of the synthetic loxP3 region. A. The 80 base synthetic loxP3 region was submitted to the RNAstructure Webserver; DNA was selected as the nucleic acid type and the default data settings were preserved. The RNAstructure MaxExpect result generated by the Webserver is presented; this represents a structure formed due to high probability base pairing. The centrally located 34 bases is the loxP sequence (highlighted in pink), of which the first and last 13 bases are palindromic sequences. This facilitates intrastrand base-pairing permitting the formation of a hairpin loop structure. An additional stem structure (stem 1 ) is predicted due to intrastrand base-pairing between the synthetic DNA sequences that flank the loxP site (highlighted in grey). The probability of base-pairing is illustrated by colour coding. B. A linear view of the 80 bases of the synthetic loxP3 region is annotated with the position of the stem and loop structures. C. Primers that bind sequences that are capable of intrastrand base-pairing may compete with intrastrand base-pairing, stabilizing the template and permitting PCR to proceed. In contrast, primers that bind in the regions flanking the synthetic loxP3 region cannot prevent secondary structure formation and consequently PCR of these templates may be impaired.

    Article Snippet: The PCR was performed on a MiniOpticon PCR System (BioRad Laboratories, Solna, Sweden) or a 2720 Thermal Cycler (Applied Biosystems, Thermo Fisher Scientific) with the following protocol: one cycle of 95°C for 3 min; 39 cycles of 95°C for 30 sec; 56, 60, 65 or 70°C for 30 sec; 72°C for 1 min; and one cycle of 72°C for 7 min. PCR products and the GeneRuler 100 bp or 1 kb DNA ladder (Thermo Fisher Scientific) were diluted in DNA Gel Loading Dye (6X; Thermo Fisher Scientific) and separated by electrophoresis on 1% or 2.5% agarose gels, prepared in 40 mM Tris, 20 mM acetate and 1 mM EDTA (TAE buffer) with 1‱ GelRed fluorescent DNA stain (Biotium, Hayward, CA, USA).

    Techniques: Generated, Sequencing, Polymerase Chain Reaction

    Failure to amplify templates containing the synthetic loxP3 region using flanking primers. A. Primers targeting Wt sequences upstream (F Flank1 ) and downstream (R Flank1 ) of the synthetic loxP3 region were predicted to amplify a PCR product of 453 bp from the KO 1st construct and 386 bp from Wt sequences. The 80 bp synthetic loxP3 region replaces eleven Wt-specific bps; therefore, this represents a unique identifier for amplicons derived from Wt alleles. B. PCR with these primers is predicted to produce 453 bp and 386 bp products from KO 1st chimeras and a single 386 bp product from Wt samples. C. A single product is amplified from KO 1st chimeras and Wt mice samples using the F Flank1 with R Flank1 primers. PCR was performed with an annealing temperature of 56°C and products were separated on a 1% agarose gel containing GelRed stain. D. Sanger sequencing of the PCR products from C confirms that only amplicons containing the Wt-specific identifier were produced. E. PCR with F loxP3 and R Flank1 primers using DNA isolated from four F1 progeny (derived from crossing male and female KO 1st chimeras) identified two individuals as positive for the KO 1st template. F . PCR with F Flank1 with R Flank1 primers failed to distinguish the KO 1st positive F1 progeny from Wt samples. PCR was performed with an annealing temperature of 60°C and products were separated on a 2.5% agarose gel containing GelRed stain. The two KO 1st lanes in C represent PCR products derived from the same two distinct KO 1st chimeric mice presented in Fig 1 . The Wt and KO 1st chimera DNA samples in F are isolated from brain tissue; these samples are also used in Fig 3 . Abbreviations : KO 1st : Knockout first chimera, F1: Filial hybrid 1, P: Primers only.

    Journal: PLoS ONE

    Article Title: Failure to Genotype: A Cautionary Note on an Elusive loxP Sequence

    doi: 10.1371/journal.pone.0165012

    Figure Lengend Snippet: Failure to amplify templates containing the synthetic loxP3 region using flanking primers. A. Primers targeting Wt sequences upstream (F Flank1 ) and downstream (R Flank1 ) of the synthetic loxP3 region were predicted to amplify a PCR product of 453 bp from the KO 1st construct and 386 bp from Wt sequences. The 80 bp synthetic loxP3 region replaces eleven Wt-specific bps; therefore, this represents a unique identifier for amplicons derived from Wt alleles. B. PCR with these primers is predicted to produce 453 bp and 386 bp products from KO 1st chimeras and a single 386 bp product from Wt samples. C. A single product is amplified from KO 1st chimeras and Wt mice samples using the F Flank1 with R Flank1 primers. PCR was performed with an annealing temperature of 56°C and products were separated on a 1% agarose gel containing GelRed stain. D. Sanger sequencing of the PCR products from C confirms that only amplicons containing the Wt-specific identifier were produced. E. PCR with F loxP3 and R Flank1 primers using DNA isolated from four F1 progeny (derived from crossing male and female KO 1st chimeras) identified two individuals as positive for the KO 1st template. F . PCR with F Flank1 with R Flank1 primers failed to distinguish the KO 1st positive F1 progeny from Wt samples. PCR was performed with an annealing temperature of 60°C and products were separated on a 2.5% agarose gel containing GelRed stain. The two KO 1st lanes in C represent PCR products derived from the same two distinct KO 1st chimeric mice presented in Fig 1 . The Wt and KO 1st chimera DNA samples in F are isolated from brain tissue; these samples are also used in Fig 3 . Abbreviations : KO 1st : Knockout first chimera, F1: Filial hybrid 1, P: Primers only.

    Article Snippet: The PCR was performed on a MiniOpticon PCR System (BioRad Laboratories, Solna, Sweden) or a 2720 Thermal Cycler (Applied Biosystems, Thermo Fisher Scientific) with the following protocol: one cycle of 95°C for 3 min; 39 cycles of 95°C for 30 sec; 56, 60, 65 or 70°C for 30 sec; 72°C for 1 min; and one cycle of 72°C for 7 min. PCR products and the GeneRuler 100 bp or 1 kb DNA ladder (Thermo Fisher Scientific) were diluted in DNA Gel Loading Dye (6X; Thermo Fisher Scientific) and separated by electrophoresis on 1% or 2.5% agarose gels, prepared in 40 mM Tris, 20 mM acetate and 1 mM EDTA (TAE buffer) with 1‱ GelRed fluorescent DNA stain (Biotium, Hayward, CA, USA).

    Techniques: Polymerase Chain Reaction, Gene Knockout, Construct, Derivative Assay, Amplification, Mouse Assay, Agarose Gel Electrophoresis, Staining, Sequencing, Produced, Isolation, Knock-Out

    Agarose gel electrophoresis of successful RCA amplification of members of Sporothrix schenckii - Ophiostoma stenoceras complex from a sample containing host/vegetable and fungal DNA . (A) Sbra-RCA padlock probe; (B) Ssch-RCA padlock probe; (C) Sglo-RCA padlock probe; (D) Slur-RCA padlock probe; (E) Smex-RCA padlock probe; and (F) Spa-RCA padlock probe. Gel lanes 1–7 on the left correspond to non-spiked samples (negative control): 1, soil; 2, Sphagnum moss; 3, Rose spp.; 4, BALB/c spleen; 5, BALB/c lungs; 6, BALB/c tail; 7, BALB/c feces. Gel lanes 1–7 on the right correspond to spiked samples (species as indicated): 1, spiked soil; 2, spiked Sphagnum moss; 3, spiked Rose spp.; 4, spiked BALB/c spleen; 5, spiked BALB/c lungs; 6, spiked BALB/c tail; 7, spiked BALB/c feces. +, positive control using DNA from culture; -, negative control (blank). Amplicons were sized by comparison with bands of known size from the GeneRuler 100 bp Plus DNA Ladder (M) (Thermo Fisher Scientific, USA). The results show an efficient replication of samples spiked with pathogen DNA. On the other hand, RCA failed to replicate the DNA originated solely from environmental or clinical samples (non-spiked), which remained negative. It can thus be assumed that the padlock probes can selectively replicate pathogen DNA, confirming the high specificity of our RCA-based assay.

    Journal: Frontiers in Microbiology

    Article Title: Rapid Identification of Emerging Human-Pathogenic Sporothrix Species with Rolling Circle Amplification

    doi: 10.3389/fmicb.2015.01385

    Figure Lengend Snippet: Agarose gel electrophoresis of successful RCA amplification of members of Sporothrix schenckii - Ophiostoma stenoceras complex from a sample containing host/vegetable and fungal DNA . (A) Sbra-RCA padlock probe; (B) Ssch-RCA padlock probe; (C) Sglo-RCA padlock probe; (D) Slur-RCA padlock probe; (E) Smex-RCA padlock probe; and (F) Spa-RCA padlock probe. Gel lanes 1–7 on the left correspond to non-spiked samples (negative control): 1, soil; 2, Sphagnum moss; 3, Rose spp.; 4, BALB/c spleen; 5, BALB/c lungs; 6, BALB/c tail; 7, BALB/c feces. Gel lanes 1–7 on the right correspond to spiked samples (species as indicated): 1, spiked soil; 2, spiked Sphagnum moss; 3, spiked Rose spp.; 4, spiked BALB/c spleen; 5, spiked BALB/c lungs; 6, spiked BALB/c tail; 7, spiked BALB/c feces. +, positive control using DNA from culture; -, negative control (blank). Amplicons were sized by comparison with bands of known size from the GeneRuler 100 bp Plus DNA Ladder (M) (Thermo Fisher Scientific, USA). The results show an efficient replication of samples spiked with pathogen DNA. On the other hand, RCA failed to replicate the DNA originated solely from environmental or clinical samples (non-spiked), which remained negative. It can thus be assumed that the padlock probes can selectively replicate pathogen DNA, confirming the high specificity of our RCA-based assay.

    Article Snippet: We included a lane loaded with GeneRuler 100 bp Plus DNA Ladder (Thermo Fisher Scientific, USA).

    Techniques: Agarose Gel Electrophoresis, Amplification, Negative Control, Positive Control

    Agarose gel electrophoresis of successful RCA of (A) Sbra-RCA padlock probe; (B) Ssch-RCA padlock probe; (C) Sglo-RCA padlock probe; (D) Slur-RCA padlock probe; (E) Smex-RCA padlock probe; and (F) Spa-RCA padlock probe . Gel lanes: 1, S. brasiliensis (CBS 132990); 2, S. schenckii (CBS 359.36); 3, S. globosa (CBS 120340); 4, S. luriei (CBS 937.72); 5, S. mexicana (CBS 120341); 6, S. pallida (CBS 302.73); 7, negative control. Amplicons were sized by comparison with bands of known size from the GeneRuler 100 bp Plus DNA Ladder (Thermo Fisher Scientific, USA). Direct visual detection of replicated DNA in RCA reactions with SYBR Green I (lower lanes). Tubes were imaged under ultraviolet light. Tube lanes: 1, S. brasiliensis (CBS 132990); 2, S. schenckii (CBS 359.36); 3, S. globosa (CBS 120340); 4, S. luriei (CBS 937.72); 5, S. mexicana (CBS 120341); 6, S. pallida (CBS 302.73); 7, negative control. Each padlock probe is specified.

    Journal: Frontiers in Microbiology

    Article Title: Rapid Identification of Emerging Human-Pathogenic Sporothrix Species with Rolling Circle Amplification

    doi: 10.3389/fmicb.2015.01385

    Figure Lengend Snippet: Agarose gel electrophoresis of successful RCA of (A) Sbra-RCA padlock probe; (B) Ssch-RCA padlock probe; (C) Sglo-RCA padlock probe; (D) Slur-RCA padlock probe; (E) Smex-RCA padlock probe; and (F) Spa-RCA padlock probe . Gel lanes: 1, S. brasiliensis (CBS 132990); 2, S. schenckii (CBS 359.36); 3, S. globosa (CBS 120340); 4, S. luriei (CBS 937.72); 5, S. mexicana (CBS 120341); 6, S. pallida (CBS 302.73); 7, negative control. Amplicons were sized by comparison with bands of known size from the GeneRuler 100 bp Plus DNA Ladder (Thermo Fisher Scientific, USA). Direct visual detection of replicated DNA in RCA reactions with SYBR Green I (lower lanes). Tubes were imaged under ultraviolet light. Tube lanes: 1, S. brasiliensis (CBS 132990); 2, S. schenckii (CBS 359.36); 3, S. globosa (CBS 120340); 4, S. luriei (CBS 937.72); 5, S. mexicana (CBS 120341); 6, S. pallida (CBS 302.73); 7, negative control. Each padlock probe is specified.

    Article Snippet: We included a lane loaded with GeneRuler 100 bp Plus DNA Ladder (Thermo Fisher Scientific, USA).

    Techniques: Agarose Gel Electrophoresis, Negative Control, SYBR Green Assay

    Representative agarose gel electrophoresis of the analytical sensitivity of RCA . Species-specific padlock probes were used for RCA of 10-fold dilutions of CAL amplicon from (A) S. brasiliensis (CBS 132990) and (B) S. globosa (CBS 120340). The in-gel detection limit was 3 × 10 6 copies of CAL for all probes. Gel lanes: 1, 3 × 10 11 copies; 2, 3 × 10 10 copies; 3, 3 × 10 9 copies; 4, 3 × 10 8 copies; 5, 3 × 10 7 copies; 6, 3 × 10 6 copies; 7, 3 × 10 5 copies; 8, 3 × 10 4 copies; 9, 3 × 10 3 copies; 10, 300 copies; 11, 30 copies; 12, 3 copies; 13, negative control. Marker (M): GeneRuler 100 bp Plus DNA Ladder (Thermo Fisher Scientific, USA).

    Journal: Frontiers in Microbiology

    Article Title: Rapid Identification of Emerging Human-Pathogenic Sporothrix Species with Rolling Circle Amplification

    doi: 10.3389/fmicb.2015.01385

    Figure Lengend Snippet: Representative agarose gel electrophoresis of the analytical sensitivity of RCA . Species-specific padlock probes were used for RCA of 10-fold dilutions of CAL amplicon from (A) S. brasiliensis (CBS 132990) and (B) S. globosa (CBS 120340). The in-gel detection limit was 3 × 10 6 copies of CAL for all probes. Gel lanes: 1, 3 × 10 11 copies; 2, 3 × 10 10 copies; 3, 3 × 10 9 copies; 4, 3 × 10 8 copies; 5, 3 × 10 7 copies; 6, 3 × 10 6 copies; 7, 3 × 10 5 copies; 8, 3 × 10 4 copies; 9, 3 × 10 3 copies; 10, 300 copies; 11, 30 copies; 12, 3 copies; 13, negative control. Marker (M): GeneRuler 100 bp Plus DNA Ladder (Thermo Fisher Scientific, USA).

    Article Snippet: We included a lane loaded with GeneRuler 100 bp Plus DNA Ladder (Thermo Fisher Scientific, USA).

    Techniques: Agarose Gel Electrophoresis, Amplification, Negative Control, Marker

    Analytical specificity of LAMP for MS detection. Visible colour change in MS-positive samples, greenish fluorescence under UV light and specific ladder-like patter after gel electrophoresis. Descriptions M molecular length marker GeneRuler™ 100 bp DNA Ladder Plus (Thermo-scientific, Waltham, Massachusetts, USA), 1 M. gallisepticum (ATCC 19610), 2 M. meleagridis (ATCC 25284), 3 M. iowae (ATCC 33552) , 4 M. synoviae strain (ATCC 25204), 5 M. anatis (ATCC 25524), 6 M. anseris (ATCC 49234) and 7 M. cloacale (ATCC 35276)

    Journal: Archives of Microbiology

    Article Title: Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification

    doi: 10.1007/s00203-014-1063-2

    Figure Lengend Snippet: Analytical specificity of LAMP for MS detection. Visible colour change in MS-positive samples, greenish fluorescence under UV light and specific ladder-like patter after gel electrophoresis. Descriptions M molecular length marker GeneRuler™ 100 bp DNA Ladder Plus (Thermo-scientific, Waltham, Massachusetts, USA), 1 M. gallisepticum (ATCC 19610), 2 M. meleagridis (ATCC 25284), 3 M. iowae (ATCC 33552) , 4 M. synoviae strain (ATCC 25204), 5 M. anatis (ATCC 25524), 6 M. anseris (ATCC 49234) and 7 M. cloacale (ATCC 35276)

    Article Snippet: The length of LAMP products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA).

    Techniques: Mass Spectrometry, Fluorescence, Nucleic Acid Electrophoresis, Marker

    Analysis of field MS isolates by LAMP. a Ladder-like pattern in MS-positive samples after gel electrophoresis, b visible colour change in MS-positive samples, c greenish fluorescence under UV light. Descriptions M molecular length marker GeneRuler™ 100 bp DNA Ladder Plus (Thermo-scientific, Waltham, Massachusetts, USA), 1–18 field MS isolates, NC negative control—DNA extracted from non-inoculated growth medium, PC positive control DNA of reference M. synoviae strain (ATCC 25204)

    Journal: Archives of Microbiology

    Article Title: Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification

    doi: 10.1007/s00203-014-1063-2

    Figure Lengend Snippet: Analysis of field MS isolates by LAMP. a Ladder-like pattern in MS-positive samples after gel electrophoresis, b visible colour change in MS-positive samples, c greenish fluorescence under UV light. Descriptions M molecular length marker GeneRuler™ 100 bp DNA Ladder Plus (Thermo-scientific, Waltham, Massachusetts, USA), 1–18 field MS isolates, NC negative control—DNA extracted from non-inoculated growth medium, PC positive control DNA of reference M. synoviae strain (ATCC 25204)

    Article Snippet: The length of LAMP products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA).

    Techniques: Mass Spectrometry, Nucleic Acid Electrophoresis, Fluorescence, Marker, Negative Control, Positive Control

    Analytical sensitivity of LAMP and PCR for MS detection. a PCR detection of vlhA fragment. The product length is 375 bp and was indicated with an arrow . b LAMP. Visible colour change in MS-positive samples, greenish fluorescence under UV light and specific ladder-like patter after gel electrophoresis. Descriptions M molecular length marker GeneRuler™ 100 bp DNA Ladder Plus (Thermo-scientific, Waltham, Massachusetts, USA), 10-fold dilutions of reference M. synoviae strain (ATCC 25204): 1 10 6 CFU/ml, 2 10 5 CFU/ml, 3 10 4 CFU/ml, 4 10 3 CFU/ml, 5 10 2 CFU/ml, 6 10 1 CFU/ml, 7 10 0 CFU/ml, 8 10 −1 CFU/ml, 9 10 −2 CFU/ml, and NC negative control—DNA extracted from non-inoculated growth medium

    Journal: Archives of Microbiology

    Article Title: Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification

    doi: 10.1007/s00203-014-1063-2

    Figure Lengend Snippet: Analytical sensitivity of LAMP and PCR for MS detection. a PCR detection of vlhA fragment. The product length is 375 bp and was indicated with an arrow . b LAMP. Visible colour change in MS-positive samples, greenish fluorescence under UV light and specific ladder-like patter after gel electrophoresis. Descriptions M molecular length marker GeneRuler™ 100 bp DNA Ladder Plus (Thermo-scientific, Waltham, Massachusetts, USA), 10-fold dilutions of reference M. synoviae strain (ATCC 25204): 1 10 6 CFU/ml, 2 10 5 CFU/ml, 3 10 4 CFU/ml, 4 10 3 CFU/ml, 5 10 2 CFU/ml, 6 10 1 CFU/ml, 7 10 0 CFU/ml, 8 10 −1 CFU/ml, 9 10 −2 CFU/ml, and NC negative control—DNA extracted from non-inoculated growth medium

    Article Snippet: The length of LAMP products was compared to 100-bp DNA Ladder Plus GeneRuler™ (Thermo-scientific, Waltham, Massachusetts, USA).

    Techniques: Polymerase Chain Reaction, Mass Spectrometry, Fluorescence, Nucleic Acid Electrophoresis, Marker, Negative Control