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  • 99
    Thermo Fisher random hexamer primers
    Trans -splicing for nad5 and cox1 gene expressions in the Marophrys mitochondrial genome. ( A ) Reverse transcription PCR using a set of primers specific to nad5 _a and nad5 _b loci (left) and that specific to cox1 _a and cox1 _b loci (right). The DNA fragment was amplified from the <t>cDNA</t> template which most likely contained the spliced product connecting the two <t>RNA</t> fragments transcribed from the two separate loci together (lanes labelled with “cDNA”). On the other hand, no specific amplification was observed in the PCR using the genomic DNA template due to the configuration of the two separate loci in the mtDNA (lanes labelled with “gDNA”). ( B-C ) Model for nad5 mRNA trans -splicing. ( B ) Primary structures of nad5 _a and nad5 _b loci. mtDNA, exons, and introns are shown in thin black lines, boxed, and thick lines, respectively. The 5′ exon and subsequent intronic region are colored in red, while the 3′ exon and its preceding intronic region are indicated in blue. The two loci are located on the different strands, and thus transcribed independently from each other. ( C ) Putative group I intron-like secondary structure of nad5 _a and nad5 _b transcripts. Five stem-loop structures conserved among group I intron ribozymes (P3, P4, P6, P7, and P8) can be formed within the nad5 _a transcript and between the nad5 _a and nad5 _b transcripts. This secondary structure was predicted by RNAweasel followed by manual inspection and modification. Watson–Crick base pairings and a wobble bond in the five stem-loop structures are indicated by the black lines and a circle, respectively. The typical secondary structure of group I intron ribozymes is schematically shown as an inset. ( D ) Mature nad5 mRNA.
    Random Hexamer Primers, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 23348 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher taqman gene expression assays
    Knockdown of SRSF3 decreased the expression of miR-1908 and its host gene, FADS1 A . Microarray data showing decreased expression of FADS1 in SRSF3-silenced U2OS cells with three different siRNAs. B . U2OS cells were transfected with control (CTRL) or SRSF3-specific siRNA for 48 h and then the expression level of FADS1 mRNA was determined by RT-qPCR analysis. C-D . The levels of pri-miR-1908 and mature miR-1908-3p/5p were assessed by RT-qPCR analysis using pri-miR-1908-specific primers and <t>TaqMan</t> <t>miRNA</t> primers, respectively. E . Cells were transfected with control (CTRL) or FADS1-specific siRNA for 48 h and then the levels of pri-miR-1908 and mature miR-1908-3p/5p were assessed by RT-qPCR as described above. F . Cells were transfected with control (CTRL) or Sp1-specific siRNA for 48 h. The expression level of FADS1 mRNA was determined by RT-qPCR analysis and the levels of pri-miR-1908 and mature miR-1908 (3p/5p) were assessed by RT-qPCR analysis as described above. All experiments are performed more than three times and data represent the mean ± S.D. Asterisk (*) indicates statistical significance of p
    Taqman Gene Expression Assays, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 51169 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher oligo
    Knockdown of SRSF3 decreased the expression of miR-1908 and its host gene, FADS1 A . Microarray data showing decreased expression of FADS1 in SRSF3-silenced U2OS cells with three different siRNAs. B . U2OS cells were transfected with control (CTRL) or SRSF3-specific siRNA for 48 h and then the expression level of FADS1 mRNA was determined by RT-qPCR analysis. C-D . The levels of pri-miR-1908 and mature miR-1908-3p/5p were assessed by RT-qPCR analysis using pri-miR-1908-specific primers and <t>TaqMan</t> <t>miRNA</t> primers, respectively. E . Cells were transfected with control (CTRL) or FADS1-specific siRNA for 48 h and then the levels of pri-miR-1908 and mature miR-1908-3p/5p were assessed by RT-qPCR as described above. F . Cells were transfected with control (CTRL) or Sp1-specific siRNA for 48 h. The expression level of FADS1 mRNA was determined by RT-qPCR analysis and the levels of pri-miR-1908 and mature miR-1908 (3p/5p) were assessed by RT-qPCR analysis as described above. All experiments are performed more than three times and data represent the mean ± S.D. Asterisk (*) indicates statistical significance of p
    Oligo, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 33696 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rox reference dye
    Results obtained in cross-reactivity tests performed with DNA isolates from 23 animal species with 5 commercial master mixes. ( A ) QuantiTect® Multiplex PCR <t>NoROX</t> Master Mix (Qiagen), ( B ) TaqMan® Universal PCR Master Mix (Applied Biosystems), ( C ) GoTaq® Probe qPCR Master Mix (Promega), ( D ) PerfeCTa® qPCR ToughMix TM , Low <t>ROX</t> TM (Quanta Biosciences) and E) Takyon TM No Rox Probe MasterMix dTTP Blue (Eurogentec).
    Rox Reference Dye, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2769 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher pcr buffer
    Differentiation of 21 bifidobacterial strains isolated from child feces using <t>rep-PCR</t> procedures. <t>DNA</t> profiles were determined in PCR reaction with (GTG) 5 primer ( a ) and BOX1R oligonucleotide ( b ). Lane: 1, DNA molecular marker, 2, Bifdobacterium NK1.2; 3, NK2.2; 4, NK6.1; 5, NK7.2; 6, NK8.1; 7, NK9.1; 8, NK10.2; 9, NK11.1; 10, NK12; 11, NK13; 12, NK14; 13, NK15; 14, NK16; 15, NK17; 16, MP1; 17, MP5; 18, MP6; 19, WP3; 20, WP4; 21, WP7; 22, WP8
    Pcr Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 29007 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher qrt pcr
    Differentiation of 21 bifidobacterial strains isolated from child feces using <t>rep-PCR</t> procedures. <t>DNA</t> profiles were determined in PCR reaction with (GTG) 5 primer ( a ) and BOX1R oligonucleotide ( b ). Lane: 1, DNA molecular marker, 2, Bifdobacterium NK1.2; 3, NK2.2; 4, NK6.1; 5, NK7.2; 6, NK8.1; 7, NK9.1; 8, NK10.2; 9, NK11.1; 10, NK12; 11, NK13; 12, NK14; 13, NK15; 14, NK16; 15, NK17; 16, MP1; 17, MP5; 18, MP6; 19, WP3; 20, WP4; 21, WP7; 22, WP8
    Qrt Pcr, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 22478 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Trans -splicing for nad5 and cox1 gene expressions in the Marophrys mitochondrial genome. ( A ) Reverse transcription PCR using a set of primers specific to nad5 _a and nad5 _b loci (left) and that specific to cox1 _a and cox1 _b loci (right). The DNA fragment was amplified from the cDNA template which most likely contained the spliced product connecting the two RNA fragments transcribed from the two separate loci together (lanes labelled with “cDNA”). On the other hand, no specific amplification was observed in the PCR using the genomic DNA template due to the configuration of the two separate loci in the mtDNA (lanes labelled with “gDNA”). ( B-C ) Model for nad5 mRNA trans -splicing. ( B ) Primary structures of nad5 _a and nad5 _b loci. mtDNA, exons, and introns are shown in thin black lines, boxed, and thick lines, respectively. The 5′ exon and subsequent intronic region are colored in red, while the 3′ exon and its preceding intronic region are indicated in blue. The two loci are located on the different strands, and thus transcribed independently from each other. ( C ) Putative group I intron-like secondary structure of nad5 _a and nad5 _b transcripts. Five stem-loop structures conserved among group I intron ribozymes (P3, P4, P6, P7, and P8) can be formed within the nad5 _a transcript and between the nad5 _a and nad5 _b transcripts. This secondary structure was predicted by RNAweasel followed by manual inspection and modification. Watson–Crick base pairings and a wobble bond in the five stem-loop structures are indicated by the black lines and a circle, respectively. The typical secondary structure of group I intron ribozymes is schematically shown as an inset. ( D ) Mature nad5 mRNA.

    Journal: Scientific Reports

    Article Title: Horizontally-acquired genetic elements in the mitochondrial genome of a centrohelid Marophrys sp. SRT127

    doi: 10.1038/s41598-019-41238-6

    Figure Lengend Snippet: Trans -splicing for nad5 and cox1 gene expressions in the Marophrys mitochondrial genome. ( A ) Reverse transcription PCR using a set of primers specific to nad5 _a and nad5 _b loci (left) and that specific to cox1 _a and cox1 _b loci (right). The DNA fragment was amplified from the cDNA template which most likely contained the spliced product connecting the two RNA fragments transcribed from the two separate loci together (lanes labelled with “cDNA”). On the other hand, no specific amplification was observed in the PCR using the genomic DNA template due to the configuration of the two separate loci in the mtDNA (lanes labelled with “gDNA”). ( B-C ) Model for nad5 mRNA trans -splicing. ( B ) Primary structures of nad5 _a and nad5 _b loci. mtDNA, exons, and introns are shown in thin black lines, boxed, and thick lines, respectively. The 5′ exon and subsequent intronic region are colored in red, while the 3′ exon and its preceding intronic region are indicated in blue. The two loci are located on the different strands, and thus transcribed independently from each other. ( C ) Putative group I intron-like secondary structure of nad5 _a and nad5 _b transcripts. Five stem-loop structures conserved among group I intron ribozymes (P3, P4, P6, P7, and P8) can be formed within the nad5 _a transcript and between the nad5 _a and nad5 _b transcripts. This secondary structure was predicted by RNAweasel followed by manual inspection and modification. Watson–Crick base pairings and a wobble bond in the five stem-loop structures are indicated by the black lines and a circle, respectively. The typical secondary structure of group I intron ribozymes is schematically shown as an inset. ( D ) Mature nad5 mRNA.

    Article Snippet: The extracted RNA was used to synthesize random hexamer-primed cDNA with SuperScript II reverse transcriptase (Thermo Fisher Scientific).

    Techniques: Polymerase Chain Reaction, Amplification, Modification

    Knockdown of SRSF3 decreased the expression of miR-1908 and its host gene, FADS1 A . Microarray data showing decreased expression of FADS1 in SRSF3-silenced U2OS cells with three different siRNAs. B . U2OS cells were transfected with control (CTRL) or SRSF3-specific siRNA for 48 h and then the expression level of FADS1 mRNA was determined by RT-qPCR analysis. C-D . The levels of pri-miR-1908 and mature miR-1908-3p/5p were assessed by RT-qPCR analysis using pri-miR-1908-specific primers and TaqMan miRNA primers, respectively. E . Cells were transfected with control (CTRL) or FADS1-specific siRNA for 48 h and then the levels of pri-miR-1908 and mature miR-1908-3p/5p were assessed by RT-qPCR as described above. F . Cells were transfected with control (CTRL) or Sp1-specific siRNA for 48 h. The expression level of FADS1 mRNA was determined by RT-qPCR analysis and the levels of pri-miR-1908 and mature miR-1908 (3p/5p) were assessed by RT-qPCR analysis as described above. All experiments are performed more than three times and data represent the mean ± S.D. Asterisk (*) indicates statistical significance of p

    Journal: Oncotarget

    Article Title: MicroRNA-1908-5p contributes to the oncogenic function of the splicing factor SRSF3

    doi: 10.18632/oncotarget.14184

    Figure Lengend Snippet: Knockdown of SRSF3 decreased the expression of miR-1908 and its host gene, FADS1 A . Microarray data showing decreased expression of FADS1 in SRSF3-silenced U2OS cells with three different siRNAs. B . U2OS cells were transfected with control (CTRL) or SRSF3-specific siRNA for 48 h and then the expression level of FADS1 mRNA was determined by RT-qPCR analysis. C-D . The levels of pri-miR-1908 and mature miR-1908-3p/5p were assessed by RT-qPCR analysis using pri-miR-1908-specific primers and TaqMan miRNA primers, respectively. E . Cells were transfected with control (CTRL) or FADS1-specific siRNA for 48 h and then the levels of pri-miR-1908 and mature miR-1908-3p/5p were assessed by RT-qPCR as described above. F . Cells were transfected with control (CTRL) or Sp1-specific siRNA for 48 h. The expression level of FADS1 mRNA was determined by RT-qPCR analysis and the levels of pri-miR-1908 and mature miR-1908 (3p/5p) were assessed by RT-qPCR analysis as described above. All experiments are performed more than three times and data represent the mean ± S.D. Asterisk (*) indicates statistical significance of p

    Article Snippet: For detection of miRNA, TaqMan® gene expression assays were performed using hsa-1908-5p-specific and has-miR-1908-3p specific primers (Applied Biosystems, USA).

    Techniques: Expressing, Microarray, Transfection, Quantitative RT-PCR

    NF-κB is involved in SRSF3-regulated miR-1908 expression A . U2OS cells were transfected with control (CTRL) or SRSF3-specific siRNA. Transfected cells were resuspended into 12-well plates and then transfected with the NF-κB reporter vector. Transactivation of NF-κB was assessed by calculating the luciferase activity. B . To check whether NF-κB regulates the expression of miR-1908, cells were treated with the NF-κB-specific inhibitor BAY11-7082 (10 μM) for 24 h. The level of miR-1908-3p/5p was determined by RT-qPCR analysis using TaqMan primers. C . Cells were transfected with control (CTRL) or SRSF3-specific siRNA for 48 h and then whole cell lysates were prepared. Western blot analyses were performed using adequate specific antibodies. D . Cells were transfected as described above and then cellular fractionation was performed. Western blot analysis was performed to determine the localization of NF-κB (p65) and α-tubulin and lamin B was checked for cytoplasmic and nuclear markers, respectively. E-F . Cells were transfected with control (CTRL) or TAK1-specific siRNA and then the levels of TAK1 and phosphorylated IKKα/β and NF-κB were assessed by Western blot analysis. The level of miR-1908-5p was determined by RT-qPCR analysis. G-H . The protein and mRNA expression levels of NF-κB target genes including HIF1-α, cyclin D1, and slug, were determined by western blot and RT-qPCR analysis, respectively. All experiments are performed more than three times and data represent the mean ± S.D. Asterisk (*) indicates statistical significance of p

    Journal: Oncotarget

    Article Title: MicroRNA-1908-5p contributes to the oncogenic function of the splicing factor SRSF3

    doi: 10.18632/oncotarget.14184

    Figure Lengend Snippet: NF-κB is involved in SRSF3-regulated miR-1908 expression A . U2OS cells were transfected with control (CTRL) or SRSF3-specific siRNA. Transfected cells were resuspended into 12-well plates and then transfected with the NF-κB reporter vector. Transactivation of NF-κB was assessed by calculating the luciferase activity. B . To check whether NF-κB regulates the expression of miR-1908, cells were treated with the NF-κB-specific inhibitor BAY11-7082 (10 μM) for 24 h. The level of miR-1908-3p/5p was determined by RT-qPCR analysis using TaqMan primers. C . Cells were transfected with control (CTRL) or SRSF3-specific siRNA for 48 h and then whole cell lysates were prepared. Western blot analyses were performed using adequate specific antibodies. D . Cells were transfected as described above and then cellular fractionation was performed. Western blot analysis was performed to determine the localization of NF-κB (p65) and α-tubulin and lamin B was checked for cytoplasmic and nuclear markers, respectively. E-F . Cells were transfected with control (CTRL) or TAK1-specific siRNA and then the levels of TAK1 and phosphorylated IKKα/β and NF-κB were assessed by Western blot analysis. The level of miR-1908-5p was determined by RT-qPCR analysis. G-H . The protein and mRNA expression levels of NF-κB target genes including HIF1-α, cyclin D1, and slug, were determined by western blot and RT-qPCR analysis, respectively. All experiments are performed more than three times and data represent the mean ± S.D. Asterisk (*) indicates statistical significance of p

    Article Snippet: For detection of miRNA, TaqMan® gene expression assays were performed using hsa-1908-5p-specific and has-miR-1908-3p specific primers (Applied Biosystems, USA).

    Techniques: Expressing, Transfection, Plasmid Preparation, Luciferase, Activity Assay, Quantitative RT-PCR, Western Blot, Cell Fractionation

    ZnT3 efficiency plot . Quadruplicate ZnT3 qPCR analyses were carried out using the indicated dilutions of a cDNA pool, derived as described in the Methods section. Mean Ct values ± SD are presented for each dilution where the assay signal rose above the detection threshold. PCR reaction efficiency for the ZnT3 TaqMan assay (85%) was calculated from the slope of the line as described in the Methods section.

    Journal: Molecular Neurodegeneration

    Article Title: ZnT3 mRNA levels are reduced in Alzheimer's disease post-mortem brain

    doi: 10.1186/1750-1326-4-53

    Figure Lengend Snippet: ZnT3 efficiency plot . Quadruplicate ZnT3 qPCR analyses were carried out using the indicated dilutions of a cDNA pool, derived as described in the Methods section. Mean Ct values ± SD are presented for each dilution where the assay signal rose above the detection threshold. PCR reaction efficiency for the ZnT3 TaqMan assay (85%) was calculated from the slope of the line as described in the Methods section.

    Article Snippet: Each reaction contained 2 μl cDNA (corresponding to 20 ng reverse transcribed RNA), 0.25 μl TaqMan® gene expression assay for the relevant gene, 2.5 μl TaqMan® universal PCR master mix (Applied Biosystems) and 0.25 μl RNAse free water in a total volume of 5 μl.

    Techniques: Real-time Polymerase Chain Reaction, Derivative Assay, Polymerase Chain Reaction, TaqMan Assay

    FS Modifies NAD(P)H Quinone Oxidoreductase Gene Expression in Buccal Epithelium. Buccal swabs were performed at weeks 0, 4, and 8 during the study. Buccal epithelial cells were harvested for RNA isolation and subsequent qPCR analysis. Antioxidant gene expression levels were determined using Taqman specific primers and probes to Nqo1. Values are reported as fold change from pre-FS. Panel A displays comparison between healthy controls (n = 5) and all cystic fibrosis patients (n = 10). Panel B displays comparison between healthy controls (n = 5), cystic fibrosis patients with low lignans (n = 6), and cystic fibrosis patients with high lignans (n = 4).

    Journal: BMC Complementary and Alternative Medicine

    Article Title: Flaxseed modulates inflammatory and oxidative stress biomarkers in cystic fibrosis: a pilot study

    doi: 10.1186/s12906-015-0651-2

    Figure Lengend Snippet: FS Modifies NAD(P)H Quinone Oxidoreductase Gene Expression in Buccal Epithelium. Buccal swabs were performed at weeks 0, 4, and 8 during the study. Buccal epithelial cells were harvested for RNA isolation and subsequent qPCR analysis. Antioxidant gene expression levels were determined using Taqman specific primers and probes to Nqo1. Values are reported as fold change from pre-FS. Panel A displays comparison between healthy controls (n = 5) and all cystic fibrosis patients (n = 10). Panel B displays comparison between healthy controls (n = 5), cystic fibrosis patients with low lignans (n = 6), and cystic fibrosis patients with high lignans (n = 4).

    Article Snippet: Gene expression analysis Quantitative Reverse Transcription Polymerase Chain Reaction (qPCR) was performed using TaqMan® Probe-Based Gene Expression Assays supplied by Applied Biosystems, Life Technologies (Carlsbad, CA).

    Techniques: Expressing, Isolation, Real-time Polymerase Chain Reaction

    FS Modifies Heme Oxygenase 1 Gene Expression in Buccal Epithelium. Buccal swabs were performed at week 0, 4, and 8 during the study. Buccal epithelial cells were harvested for RNA isolation and subsequent qPCR analysis. Antioxidant gene expression levels were determined using Taqman specific primers and probes to HO-1. Values are reported as fold change from pre-FS. Panel A displays comparison between healthy controls (n = 5) and all cystic fibrosis patients (n = 10). Panel B displays comparison between healthy controls (n = 5), cystic fibrosis patients with low lignans (n = 6), and cystic fibrosis patients with high lignans (n = 4). * signifies p

    Journal: BMC Complementary and Alternative Medicine

    Article Title: Flaxseed modulates inflammatory and oxidative stress biomarkers in cystic fibrosis: a pilot study

    doi: 10.1186/s12906-015-0651-2

    Figure Lengend Snippet: FS Modifies Heme Oxygenase 1 Gene Expression in Buccal Epithelium. Buccal swabs were performed at week 0, 4, and 8 during the study. Buccal epithelial cells were harvested for RNA isolation and subsequent qPCR analysis. Antioxidant gene expression levels were determined using Taqman specific primers and probes to HO-1. Values are reported as fold change from pre-FS. Panel A displays comparison between healthy controls (n = 5) and all cystic fibrosis patients (n = 10). Panel B displays comparison between healthy controls (n = 5), cystic fibrosis patients with low lignans (n = 6), and cystic fibrosis patients with high lignans (n = 4). * signifies p

    Article Snippet: Gene expression analysis Quantitative Reverse Transcription Polymerase Chain Reaction (qPCR) was performed using TaqMan® Probe-Based Gene Expression Assays supplied by Applied Biosystems, Life Technologies (Carlsbad, CA).

    Techniques: Expressing, Isolation, Real-time Polymerase Chain Reaction

    Results obtained in cross-reactivity tests performed with DNA isolates from 23 animal species with 5 commercial master mixes. ( A ) QuantiTect® Multiplex PCR NoROX Master Mix (Qiagen), ( B ) TaqMan® Universal PCR Master Mix (Applied Biosystems), ( C ) GoTaq® Probe qPCR Master Mix (Promega), ( D ) PerfeCTa® qPCR ToughMix TM , Low ROX TM (Quanta Biosciences) and E) Takyon TM No Rox Probe MasterMix dTTP Blue (Eurogentec).

    Journal: Scientific Reports

    Article Title: Sika deer (Cervus nippon)-specific real-time PCR method to detect fraudulent labelling of meat and meat products

    doi: 10.1038/s41598-018-25299-7

    Figure Lengend Snippet: Results obtained in cross-reactivity tests performed with DNA isolates from 23 animal species with 5 commercial master mixes. ( A ) QuantiTect® Multiplex PCR NoROX Master Mix (Qiagen), ( B ) TaqMan® Universal PCR Master Mix (Applied Biosystems), ( C ) GoTaq® Probe qPCR Master Mix (Promega), ( D ) PerfeCTa® qPCR ToughMix TM , Low ROX TM (Quanta Biosciences) and E) Takyon TM No Rox Probe MasterMix dTTP Blue (Eurogentec).

    Article Snippet: In order to use the QuantiTect Multiplex PCR NoROX Master Mix on the ABI 7500 Real-time PCR System, 2 µL ROX Reference Dye (25 µM) (Invitrogen by Life Technologies, Carlsbad, CA, USA) were added to 1.8 mL master mix.

    Techniques: Multiplex Assay, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    Differentiation of 21 bifidobacterial strains isolated from child feces using rep-PCR procedures. DNA profiles were determined in PCR reaction with (GTG) 5 primer ( a ) and BOX1R oligonucleotide ( b ). Lane: 1, DNA molecular marker, 2, Bifdobacterium NK1.2; 3, NK2.2; 4, NK6.1; 5, NK7.2; 6, NK8.1; 7, NK9.1; 8, NK10.2; 9, NK11.1; 10, NK12; 11, NK13; 12, NK14; 13, NK15; 14, NK16; 15, NK17; 16, MP1; 17, MP5; 18, MP6; 19, WP3; 20, WP4; 21, WP7; 22, WP8

    Journal: BMC Microbiology

    Article Title: Comparison of various molecular methods for rapid differentiation of intestinal bifidobacteria at the species, subspecies and strain level

    doi: 10.1186/s12866-016-0779-3

    Figure Lengend Snippet: Differentiation of 21 bifidobacterial strains isolated from child feces using rep-PCR procedures. DNA profiles were determined in PCR reaction with (GTG) 5 primer ( a ) and BOX1R oligonucleotide ( b ). Lane: 1, DNA molecular marker, 2, Bifdobacterium NK1.2; 3, NK2.2; 4, NK6.1; 5, NK7.2; 6, NK8.1; 7, NK9.1; 8, NK10.2; 9, NK11.1; 10, NK12; 11, NK13; 12, NK14; 13, NK15; 14, NK16; 15, NK17; 16, MP1; 17, MP5; 18, MP6; 19, WP3; 20, WP4; 21, WP7; 22, WP8

    Article Snippet: PCR was carried out in the total volume of 20 μl of the reaction mixture containing 1 U (for BOXA1R-PCR) and 2 U (for (GTG)5 -PCR) of Taq DNA polymerase, 200 μM of each deoxynucleoside triphosphate, 1 μM of each primer, 50 ng of bacterial DNA and PCR buffer (Thermo Fisher Scientific, Waltham, USA).

    Techniques: Isolation, Polymerase Chain Reaction, Marker

    Randomly amplified polymorphic DNA (RAPD)-PCR patterns obtained with PER1 primer for 17 bifidobacterial strains. Analysis of the discriminatory power of the procedure applied was performed at a species level ( a ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. animalis NRRL B-41406; 4, B. bifidum DSM 204564; 5, B. breve DSM 20091; 6, B. catenulatum DSM 20224; 7, B. longum NRRL B-41409; 8, B. pseudocatenulatum DSM 20439; 9, B. pseudolongum DSM 20099; at a subspecies level ( b ) - 1, DNA molecular marker; 2, B. animalis subsp. animalis NRRL B-41406; 3, B. animalis subsp. lactis NRRL B-41405; 4, B. longum subsp. infantis ATCC 15697; 5, B. longum subsp. longum NRRL B-41409; 5, B. longum subsp. suis NRRL B-41407; 6, B. pseudolongum subsp. pseudolongum DSM 20099; 7, B. pseudolongum subsp. globosum DSM 20092; and at a strain level ( c ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. adolescentis DSM 20083; 4, B. adolescentis 20086; 5, B. breve DSM 20091; 6, B. breve NRRL B-41408; 7 , B. pseudolongum DSM 20099; 8, B. pseudolongum 20094; 9, B. pseudolongum DSM 20095

    Journal: BMC Microbiology

    Article Title: Comparison of various molecular methods for rapid differentiation of intestinal bifidobacteria at the species, subspecies and strain level

    doi: 10.1186/s12866-016-0779-3

    Figure Lengend Snippet: Randomly amplified polymorphic DNA (RAPD)-PCR patterns obtained with PER1 primer for 17 bifidobacterial strains. Analysis of the discriminatory power of the procedure applied was performed at a species level ( a ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. animalis NRRL B-41406; 4, B. bifidum DSM 204564; 5, B. breve DSM 20091; 6, B. catenulatum DSM 20224; 7, B. longum NRRL B-41409; 8, B. pseudocatenulatum DSM 20439; 9, B. pseudolongum DSM 20099; at a subspecies level ( b ) - 1, DNA molecular marker; 2, B. animalis subsp. animalis NRRL B-41406; 3, B. animalis subsp. lactis NRRL B-41405; 4, B. longum subsp. infantis ATCC 15697; 5, B. longum subsp. longum NRRL B-41409; 5, B. longum subsp. suis NRRL B-41407; 6, B. pseudolongum subsp. pseudolongum DSM 20099; 7, B. pseudolongum subsp. globosum DSM 20092; and at a strain level ( c ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. adolescentis DSM 20083; 4, B. adolescentis 20086; 5, B. breve DSM 20091; 6, B. breve NRRL B-41408; 7 , B. pseudolongum DSM 20099; 8, B. pseudolongum 20094; 9, B. pseudolongum DSM 20095

    Article Snippet: PCR was carried out in the total volume of 20 μl of the reaction mixture containing 1 U (for BOXA1R-PCR) and 2 U (for (GTG)5 -PCR) of Taq DNA polymerase, 200 μM of each deoxynucleoside triphosphate, 1 μM of each primer, 50 ng of bacterial DNA and PCR buffer (Thermo Fisher Scientific, Waltham, USA).

    Techniques: Amplification, Polymerase Chain Reaction, Marker

    BOX-PCR DNA profiles obtained for Bifidobacterium strains used in this work. Analysis of the discriminatory power of this procedure was performed at a species level ( a ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. animalis NRRL B-41406; 4, B. bifidum DSM 204564; 5, B. breve DSM 20091; 6, B. catenulatum DSM 20224; 7, B. longum NRRL B-41409; 8, B. pseudocatenulatum DSM 20439; 9, B. pseudolongum DSM 20099; at a subspecies level ( b ) - 1, DNA molecular marker; 2, B. animalis subsp. animalis NRRL B-41406; 3, B. animalis subsp. lactis NRRL B-41405; 4, B. longum subsp. infantis ATCC 15697; 5, B. longum subsp. longum NRRL B-41409; 5, B. longum subsp. suis NRRL B-41407; 6, B. pseudolongum subsp. pseudolongum DSM 20099; 7, B. pseudolongum subsp. globosum DSM 20092; and at a strain level ( c ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. adolescentis DSM 20083; 4, B. adolescentis 20086; 5, B. breve DSM 20091; 6, B. breve NRRL B-41408; 7 , B. pseudolongum DSM 20099; 8, B. pseudolongum 20094; 9, B. pseudolongum DSM 20095

    Journal: BMC Microbiology

    Article Title: Comparison of various molecular methods for rapid differentiation of intestinal bifidobacteria at the species, subspecies and strain level

    doi: 10.1186/s12866-016-0779-3

    Figure Lengend Snippet: BOX-PCR DNA profiles obtained for Bifidobacterium strains used in this work. Analysis of the discriminatory power of this procedure was performed at a species level ( a ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. animalis NRRL B-41406; 4, B. bifidum DSM 204564; 5, B. breve DSM 20091; 6, B. catenulatum DSM 20224; 7, B. longum NRRL B-41409; 8, B. pseudocatenulatum DSM 20439; 9, B. pseudolongum DSM 20099; at a subspecies level ( b ) - 1, DNA molecular marker; 2, B. animalis subsp. animalis NRRL B-41406; 3, B. animalis subsp. lactis NRRL B-41405; 4, B. longum subsp. infantis ATCC 15697; 5, B. longum subsp. longum NRRL B-41409; 5, B. longum subsp. suis NRRL B-41407; 6, B. pseudolongum subsp. pseudolongum DSM 20099; 7, B. pseudolongum subsp. globosum DSM 20092; and at a strain level ( c ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. adolescentis DSM 20083; 4, B. adolescentis 20086; 5, B. breve DSM 20091; 6, B. breve NRRL B-41408; 7 , B. pseudolongum DSM 20099; 8, B. pseudolongum 20094; 9, B. pseudolongum DSM 20095

    Article Snippet: PCR was carried out in the total volume of 20 μl of the reaction mixture containing 1 U (for BOXA1R-PCR) and 2 U (for (GTG)5 -PCR) of Taq DNA polymerase, 200 μM of each deoxynucleoside triphosphate, 1 μM of each primer, 50 ng of bacterial DNA and PCR buffer (Thermo Fisher Scientific, Waltham, USA).

    Techniques: Polymerase Chain Reaction, Marker

    (GTG) 5 -PCR patterns of 17 strains belonging to the genus Bifidobacterium . Analysis of the discriminatory power of the procedure applied was performed at a species level ( a ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. animalis NRRL B-41406; 4, B. bifidum DSM 204564; 5, B. breve DSM 20091; 6, B. catenulatum DSM 20224; 7, B. longum NRRL B-41409; 8, B. pseudocatenulatum DSM 20439; 9, B. pseudolongum DSM 20099; at a subspecies level ( b ) - 1, DNA molecular marker; 2, B. animalis subsp. animalis NRRL B-41406; 3, B. animalis subsp. lactis NRRL B-41405; 4, B. longum subsp. infantis ATCC 15697; 5, B. longum subsp. longum NRRL B-41409; 5, B. longum subsp. suis NRRL B-41407; 6, B. pseudolongum subsp. pseudolongum DSM 20099; 7, B. pseudolongum subsp. globosum DSM 20092; and at a strain level ( c ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. adolescentis DSM 20083; 4, B. adolescentis 20086; 5, B. breve DSM 20091; 6, B. breve NRRL B-41408; 7 , B. pseudolongum DSM 20099; 8, B. pseudolongum 20094; 9, B. pseudolongum DSM 20095

    Journal: BMC Microbiology

    Article Title: Comparison of various molecular methods for rapid differentiation of intestinal bifidobacteria at the species, subspecies and strain level

    doi: 10.1186/s12866-016-0779-3

    Figure Lengend Snippet: (GTG) 5 -PCR patterns of 17 strains belonging to the genus Bifidobacterium . Analysis of the discriminatory power of the procedure applied was performed at a species level ( a ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. animalis NRRL B-41406; 4, B. bifidum DSM 204564; 5, B. breve DSM 20091; 6, B. catenulatum DSM 20224; 7, B. longum NRRL B-41409; 8, B. pseudocatenulatum DSM 20439; 9, B. pseudolongum DSM 20099; at a subspecies level ( b ) - 1, DNA molecular marker; 2, B. animalis subsp. animalis NRRL B-41406; 3, B. animalis subsp. lactis NRRL B-41405; 4, B. longum subsp. infantis ATCC 15697; 5, B. longum subsp. longum NRRL B-41409; 5, B. longum subsp. suis NRRL B-41407; 6, B. pseudolongum subsp. pseudolongum DSM 20099; 7, B. pseudolongum subsp. globosum DSM 20092; and at a strain level ( c ) - 1, DNA molecular marker; 2, B. adolescentis DSM 20087; 3, B. adolescentis DSM 20083; 4, B. adolescentis 20086; 5, B. breve DSM 20091; 6, B. breve NRRL B-41408; 7 , B. pseudolongum DSM 20099; 8, B. pseudolongum 20094; 9, B. pseudolongum DSM 20095

    Article Snippet: PCR was carried out in the total volume of 20 μl of the reaction mixture containing 1 U (for BOXA1R-PCR) and 2 U (for (GTG)5 -PCR) of Taq DNA polymerase, 200 μM of each deoxynucleoside triphosphate, 1 μM of each primer, 50 ng of bacterial DNA and PCR buffer (Thermo Fisher Scientific, Waltham, USA).

    Techniques: Polymerase Chain Reaction, Marker