dntps Thermo Fisher

Journal: AoB Plants

Article Title: Molecular detection and species identification ofAlexandrium (Dinophyceae) causing harmful algal blooms along the Chilean coastline

doi: 10.1093/aobpla/pls033

Figure Lengend Snippet: Amplification of local Alexandrium strains ACC01, ACC02 and ACC07 using species - specific primers; A. tamarense (lanes 1, 2 and 3) and A. catenella (lanes 4, 5 and 6). M = 100-bp DNA size marker. Species-specific amplification in the rDNA region using A. catenella and A. tamarense primers were carried out in a MaxiGene Gradiente thermocycler (Axygen) in 1× PCR buffer, 20–50 ng of genomic DNA template, 3 mM MgCl 2, 100 µM each dNTP, 0.1 µM each primer and 0.4 U of TopTaq DNA polymerase (Fermentas) in a 10-µL reaction volume. Five microlitres of each PCR product were analysed in a 2 % agarose gel. A Fermentas GeneRuller™ 100-bp DNA ladder was used for size estimation of amplified fragments.

Article Snippet: All amplifications were carried out in duplicate with 1× PCR buffer, 20–50 ng of genomic DNA template, 3 mM MgCl2, 100 µM each dNTP, 0.1 µM each primer and 0.4 U of recombinant Taq DNA polymerase (MBI Fermentas, Vilnius, Lithuania) in a 10-µL reaction volume.

Techniques: Amplification, Marker, Polymerase Chain Reaction, Agarose Gel Electrophoresis

Journal: AoB Plants

Article Title: Molecular detection and species identification ofAlexandrium (Dinophyceae) causing harmful algal blooms along the Chilean coastline

doi: 10.1093/aobpla/pls033

Figure Lengend Snippet: Alexandrium tamarense microsatellite amplifications of the three local strains with (A) specific primers ATB8 (lanes 1, 2 and 3) and ATD8 (lanes 4, 5 and 6). Lanes 7 and 8 correspond to controls with primers ATB8 without DNA. (B) Specific amplification with primers ATB1 (lanes 1, 2 and 3) and ATF11 (lanes 6, 7 and 8). Lanes 4–5 and 9–10 are controls without DNA for primer sets ATB1 and ATF11, respectively. M = 100-bp DNA size marker. Species-specific microsatellite amplifications using A. catenella and A. tamarense primers were carried out in a MaxiGene Gradiente thermocycler (Axygen) in 1× PCR buffer, 20–50 ng of genomic DNA template, 3 mM MgCl 2, 100 µM each dNTP, 0.1 µM each primer and 0.4 U of TopTaq DNA polymerase (Fermentas) in a 10-µL reaction volume. Five microlitres of each PCR product were analysed in a 2 % agarose gel. A Fermentas GeneRuller TM 100-bp DNA ladder was used for size estimation of amplified fragments.

Article Snippet: All amplifications were carried out in duplicate with 1× PCR buffer, 20–50 ng of genomic DNA template, 3 mM MgCl2, 100 µM each dNTP, 0.1 µM each primer and 0.4 U of recombinant Taq DNA polymerase (MBI Fermentas, Vilnius, Lithuania) in a 10-µL reaction volume.

Techniques: Amplification, Marker, Polymerase Chain Reaction, Agarose Gel Electrophoresis

Journal: Nature structural & molecular biology

Article Title: Oxidative guanine base damage regulates human telomerase activity

doi: 10.1038/nsmb.3319

Figure Lengend Snippet: Telomerase elongation of primers with a terminal 8-oxoG. ( a ) Telomerase reactions were conducted using primers containing three (3R) or four (4R) TTAGGG repeats, with a 3′ terminal G or 8-oxoG ( Supplementary Table 1 , oligos #3, 4, 6 and 7). Reactions contained high (lanes 1 – 4) or cellular (lanes 5 – 8) dNTP concentrations and 0.3 μM 32 P-α-dGTP. Telomerase products were separated on denaturing gels. The LC was 32 P end-labeled 36-mer oligonucleotide. Arrow points to a product from degraded primer. Numbers with plus sign indicate number of added repeats. ( b ) and ( c ) Products were normalized to the LC and used to calculate processivity and relative activity. Bars represent the mean ± sd from three independent reactions. ** p

Article Snippet: Briefly, reactions (20 μl) contained 1x human telomerase buffer, 1 μM oligonucleotide substrate, 0.3 μM of 3,000 Ci/mmol 32 P-α-dGTP or 32 P-α-dTTP (Perkin Elmer) and dNTP (Invitrogen) mix as indicated in the figure legend.

Techniques: Liquid Chromatography, Labeling, Activity Assay

Journal: Nature structural & molecular biology

Article Title: Oxidative guanine base damage regulates human telomerase activity

doi: 10.1038/nsmb.3319

Figure Lengend Snippet: 8-oxoG restores telomerase activity on quadruplex folded overhangs ( a ) Telomerase reactions were conducted using primers containing three (3R) or four (4R) TTAGGG repeats, with a middle G or 8-oxoG in the terminal repeat ( Supplementary Table 1 , oligos #3, 5, 6 and 8). Reactions contained high (lanes 1–4) or cellular (lanes 5–8) dNTP concentrations and 0.3 μM 32 P-α-dGTP. Products were separated on denaturing gels. The LC was a 32 P end-labeled 36-mer oligonucleotide. Numbers with plus sign indicate number of added repeats. ( b ) and ( c ) Products were normalized to the LC, and used to calculate processivity ( b ) and relative activity ( c ). Bars represent the mean ± sd from three independent reactions. * p

Article Snippet: Briefly, reactions (20 μl) contained 1x human telomerase buffer, 1 μM oligonucleotide substrate, 0.3 μM of 3,000 Ci/mmol 32 P-α-dGTP or 32 P-α-dTTP (Perkin Elmer) and dNTP (Invitrogen) mix as indicated in the figure legend.

Techniques: Activity Assay, Liquid Chromatography, Labeling

Journal: Sensors (Basel, Switzerland)

Article Title: Amplified Detection of the Aptamer–Vanillin Complex with the Use of Bsm DNA Polymerase

doi: 10.3390/s18010049

Figure Lengend Snippet: ( a ) Dependence of response (with background subtraction) of modified with Van_74/DP ISFETs to the Bsm DNA polymerase reaction with the addition of different vanillin concentrations. Conditions: mix1 —low molarity selection buffer, 0.2 M ;M dNTP, FP 0.05 pmol/μL, PR 1.6 pmol/μL, Bsm DNA polymerase 0.1 U/μL; mix2 —low molarity selection buffer, 0.2 M M dNTP, FP 1.0 pmol/μL, PR 1.6 pmol/μL, Bsm DNA polymerase 0.1 U/μL, T = 22 °C; ( b ) Real time signal of the ISFET (in ∆ϕ) of modified with Van_74/DP ISFETs to the addition of vanillin (final concentration 1 × 10 −8 ) concentration. Conditions: low molarity selection buffer, 0.2 M M dNTP, PR 1.6 pmol/μL, Bsm DNA polymerase 0.1 U/μL.

Article Snippet: Bsm DNA polymerase, large fragment, Bsm buffer, dNTP solution, TBE electrophoresis buffer, and SYBR Gold dye were all purchased from Thermo Fisher Scientific (Waltham, MA, USA).

Techniques: Modification, Selection, Concentration Assay

Journal: Sensors (Basel, Switzerland)

Article Title: Amplified Detection of the Aptamer–Vanillin Complex with the Use of Bsm DNA Polymerase

doi: 10.3390/s18010049

Figure Lengend Snippet: ( a ) Real time signal of the ISFET (in ∆ϕ, with background subtraction) during the Bsm DNA polymerase reaction in homogenous solution in low molarity selection buffer initiated (30–40 s) by the addition of DP at different concentrations (final concentration is marked on the picture); ( b ) Slope (∆ϕ/∆t) dependence on DP concentration calculated from real time signal curves. Reaction conditions: 0.2 mM dNTP, 0.05 pmol/μL FP, 1.6 pmol/μL PR, 0.1 U/μL BSM DNA polymerase; ( c ) Real time signal of the ISFET (in ∆ϕ, with background subtraction) during the Bsm DNA polymerase reaction in homogenous solution in low molarity selection buffer initiated (30–40 s) by the addition of DP at different concentrations (final concentration is marked on the picture); ( d ) Slope (∆ϕ/∆t) dependence on DP concentration calculated from real time signal curves. Reaction conditions: 0.2 mM dNTP, 1.0 pmol/μL FP, 1.6 pmol/μL PR, 0.1 U/μL BSM DNA polymerase.

Article Snippet: Bsm DNA polymerase, large fragment, Bsm buffer, dNTP solution, TBE electrophoresis buffer, and SYBR Gold dye were all purchased from Thermo Fisher Scientific (Waltham, MA, USA).

Techniques: Selection, Concentration Assay

Journal: Sensors (Basel, Switzerland)

Article Title: Amplified Detection of the Aptamer–Vanillin Complex with the Use of Bsm DNA Polymerase

doi: 10.3390/s18010049

Figure Lengend Snippet: Kinetics of Bsm DNA polymerase reaction (after subtraction of the background) monitored by spectrofluorimeter in different buffers and probes. Conditions: buffer, 0.2 mM dNTP, 0.05 pmol/μL FP, 1.6 pmol/μL PR, 0.1 U/μL BSM DNA polymerase, 0.1 pmol/μL DP/B1.

Article Snippet: Bsm DNA polymerase, large fragment, Bsm buffer, dNTP solution, TBE electrophoresis buffer, and SYBR Gold dye were all purchased from Thermo Fisher Scientific (Waltham, MA, USA).

Techniques:

Journal: Journal of Cancer

Article Title: Association of SMUG1 SNPs in Intron Region and Linkage Disequilibrium with Occurrence of Cervical Carcinoma and HPV Infection in Chinese Population

doi: 10.7150/jca.27103

Figure Lengend Snippet: SMUG1 protein expression in CSCCs with different genotypes of rs3087404 and rs2029167 (Western Blot) (A) AA: rs3087404 genotype is AA; AG: rs3087404 genotype is AG; GG: rs3087404 genotype is GG; (B) AA: rs2029167 genotype is AA; AG: rs2029167 genotype is AG; GG: rs2029167 genotype is GG

Article Snippet: The primers of SMUG1 (mRNA: NM_001243787.1) were 5'-CGCAACTACGTGACTCGCTA-3'; 5'-GTCCCAGCACTGGTCGTTTA- 3'.

Techniques: Expressing, Western Blot

Journal: Journal of Cancer

Article Title: Association of SMUG1 SNPs in Intron Region and Linkage Disequilibrium with Occurrence of Cervical Carcinoma and HPV Infection in Chinese Population

doi: 10.7150/jca.27103

Figure Lengend Snippet: SMUG1 mRNA expression in CSCCs with different genotypes of rs3087404 and rs2029167 (qPCR).

Article Snippet: The primers of SMUG1 (mRNA: NM_001243787.1) were 5'-CGCAACTACGTGACTCGCTA-3'; 5'-GTCCCAGCACTGGTCGTTTA- 3'.

Techniques: Expressing, Real-time Polymerase Chain Reaction

Journal:

Article Title: Photobiological Implications of Folate Depletion and Repletion in Cultured Human Keratinocytes

doi: 10.1016/j.jphotobiol.2010.02.003

Figure Lengend Snippet: Effects of differential folate repletion on inherent DNA damage and uracil misincorporation in 10 day folate depleted HaCaT cells as measured by comet assay with (solid bars) or without (open bars) UDG treatment. Cells cultured for 10 days in folate free

Article Snippet: Briefly, after cell lysis, the slides were washed three times for 5 min each in uracil DNA glycosylase (UDG) buffer (60 mM Tris-HCl, 1 mM EDTA, 0.1 mg/mL BSA, pH 8.0) (Fermentas).

Techniques: Single Cell Gel Electrophoresis, Cell Culture

Journal:

Article Title: Photobiological Implications of Folate Depletion and Repletion in Cultured Human Keratinocytes

doi: 10.1016/j.jphotobiol.2010.02.003

Figure Lengend Snippet: Effects of folate restriction on inherent DNA damage and uracil misincorporation as measured by comet assay with (solid bars) or without (open bars) uracil DNA glycosylase (UDG) treatment. Results are mean ± SEM. *** P

Article Snippet: Briefly, after cell lysis, the slides were washed three times for 5 min each in uracil DNA glycosylase (UDG) buffer (60 mM Tris-HCl, 1 mM EDTA, 0.1 mg/mL BSA, pH 8.0) (Fermentas).

Techniques: Single Cell Gel Electrophoresis

Journal: PLoS ONE

Article Title: Rod Photoreceptor Ribbon Synapses in DBA/2J Mice Show Progressive Age-Related Structural Changes

doi: 10.1371/journal.pone.0044645

Figure Lengend Snippet: C1qA and C1qC gene expression is upregulated in photoreceptor cells of aging DBA/2J mice. (A) Agarose gels showing PCR fragments that represent the gene expression of C1qA, C1qB and C1qC in the retinae of 2 and 6 months old DBA/2J and C57BL/6 control mice. (B) The expression of C1qA, C1qB and C1qC in photoreceptor cells of 2, 6, and 10 months old DBA/2J mice and age-matched C57BL/6 control mice was compared with PCR. For each age, cDNA obtained from three animals was subjected to triplicate PCR amplifications (n = 9). Statistically significant differences are indicated by asterisks (* p

Article Snippet: PCR amplification was performed using 1 µl cDNA as a template in 10 µl PCR buffer (20 mM Tris–HCl pH 8.0, 50 mM KCl, 2.5 mM MgCl2 , 0.2 mM dNTPs, 2.5 mM, 1 U Taq-polymerase; Invitrogen) in a programmable thermocycler (GeneAmp PCR System 9700; Applied Biosystems, Foster City, CA) using primer pairs specific for C1qA (sense: 5′-agctgctggcatccggac-3′, antisense: 5′-ggtcccacttggagatcac-3′), C1qB (sense: 5′-cctgaggaccatcaacagc-3′, antisense: 5′-ctcctcttgctctagcttc-3′), and C1qC (sense: 5′-cgatacaaacagaagcaccag-3′, antisense: 5′-ctggcaaggttgaggttcag-3′) with the following parameters: 94°C for 2 minutes followed by 40 cycles at 94°C for 45 s, 62°C for 60 s, 72°C for 30 s and a final incubation at 72°C for 10 minutes.

Techniques: Expressing, Mouse Assay, Polymerase Chain Reaction

Journal: Frontiers in Endocrinology

Article Title: Analysis of Endocannabinoid System in Rat Testis During the First Spermatogenetic Wave

doi: 10.3389/fendo.2018.00269

Figure Lengend Snippet: Expression of cannabinoid receptors in fetal and post-natal rat testis. Representative fetal testis section from 19.5 days post coitum (dpc) old rats stained with hematoxylin eosin and immunostained for CB1. Arrowheads indicate immunopositive gonocytes. Scale bar: 20 µm (A) . Representative images of RT-PCR analyses showing Cb1 and Actin mRNA expression in rat testes from 1-to-14 days post partum ( dpp ). Cb1 expression was quantified by densitometry analysis, normalized against Actin signals and expressed in OD values (B) . Representative images of RT-PCR analyses showing Cb2 and Actin mRNA expression in rat testes, from 7 to 60 dpp . Cb2 expression was quantified by densitometry analysis, normalized against Actin signals and expressed in OD values (C) . Representative agarose gel image of RT + cDNA (testes from 90 dpp rats), RT− cDNA (testes from 1 to 60 dpp rats) and water (H 2 O) analyzed by PCR using actin primers (D) . All data are reported as the mean ± SEM. Different letters indicate statistically significant differences ( p

Article Snippet: PCR was carried out using 2 µl cDNA and 10 pmol of the appropriate primers in a PCR mix [0.2 mM dNTP, 1× PCR buffer (Invitrogen Life Technologies), 1.5 mM MgCl2 , 1.25 U Taq Polymerase (Invitrogen Life Technologies, Paisley, UK)], using an Applied Biosystem Thermocycler.

Techniques: Expressing, Staining, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, Polymerase Chain Reaction

Journal: Frontiers in Endocrinology

Article Title: Analysis of Endocannabinoid System in Rat Testis During the First Spermatogenetic Wave

doi: 10.3389/fendo.2018.00269

Figure Lengend Snippet: RT-PCR analysis of the main AEA and 2-arachidonoylglycerol metabolizing enzymes in rat testis during the first wave of spermatogenesis. Representative images of RT-PCR analyses showing Nape-pld, Faah, Dagl, Magl , and Actin mRNA expression in rat testes from 7 to 60 days post partum ( dpp ) (A) . Representative agarose gel image of RT + cDNA (testes from 90 dpp rats), RT− cDNA (testes from 7 to 60 dpp rats) and water (H 2 O) analyzed by PCR using actin primers (B) . Gene expression was quantified by densitometry analysis and graphed relatively to germ cells appearance or activities (C) . Values for Nape-pld, Faah, Dagl , and Magl signals were normalized against Actin and are expressed as OD values (D) . All data are expressed as the mean ± SEM. Different letters indicate statistically significant differences ( p

Article Snippet: PCR was carried out using 2 µl cDNA and 10 pmol of the appropriate primers in a PCR mix [0.2 mM dNTP, 1× PCR buffer (Invitrogen Life Technologies), 1.5 mM MgCl2 , 1.25 U Taq Polymerase (Invitrogen Life Technologies, Paisley, UK)], using an Applied Biosystem Thermocycler.

Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing, Agarose Gel Electrophoresis, Polymerase Chain Reaction