Structured Review

Pacific Biosciences dna sequences
Variation in the amino acid motif structure of the <t>CagY</t> MRR regulates T4SS function by altering α 5 β 1 integrin binding. Shown is Western blot detection of the CagY MRR in whole-cell bacterial lysates of H. pylori J166 (A) or PMSS1 (C) isogenic strains, each bearing unique cagY alleles, or their Δ cagY deletion mutants. The corresponding amino acid structure of the MRR is shown schematically as a series of A (orange) or B (yellow) motifs, each 31 to 39 residues, based on <t>DNA</t> sequence analysis as described previously ( 61 ). IL-8 induction (white bars) and integrin adhesion (black bars) relative to WT are shown for H. pylori J166 (B) and PMSS1 (D), which correspond to strains shown in panels A and C, respectively. (E) Western blot detection and schematic of the CagY MRR (derived as in panels A and C) from KUS13A, KUS13B, and isogenic variants in which cagY was deleted (Δ cagY ) or replaced with that from the variant strain (i.e., KUS13A with cagY 13B or KUS13B with cagY 13A ). (F) IL-8 induction (white bars) and integrin adhesion (black bars) relative to WT for the strains shown in panel E. Quantitative results represent the mean ± SEM from at least 3 independent experiments. *, P
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Images

1) Product Images from "CagY-Dependent Regulation of Type IV Secretion in Helicobacter pylori Is Associated with Alterations in Integrin Binding"

Article Title: CagY-Dependent Regulation of Type IV Secretion in Helicobacter pylori Is Associated with Alterations in Integrin Binding

Journal: mBio

doi: 10.1128/mBio.00717-18

Variation in the amino acid motif structure of the CagY MRR regulates T4SS function by altering α 5 β 1 integrin binding. Shown is Western blot detection of the CagY MRR in whole-cell bacterial lysates of H. pylori J166 (A) or PMSS1 (C) isogenic strains, each bearing unique cagY alleles, or their Δ cagY deletion mutants. The corresponding amino acid structure of the MRR is shown schematically as a series of A (orange) or B (yellow) motifs, each 31 to 39 residues, based on DNA sequence analysis as described previously ( 61 ). IL-8 induction (white bars) and integrin adhesion (black bars) relative to WT are shown for H. pylori J166 (B) and PMSS1 (D), which correspond to strains shown in panels A and C, respectively. (E) Western blot detection and schematic of the CagY MRR (derived as in panels A and C) from KUS13A, KUS13B, and isogenic variants in which cagY was deleted (Δ cagY ) or replaced with that from the variant strain (i.e., KUS13A with cagY 13B or KUS13B with cagY 13A ). (F) IL-8 induction (white bars) and integrin adhesion (black bars) relative to WT for the strains shown in panel E. Quantitative results represent the mean ± SEM from at least 3 independent experiments. *, P
Figure Legend Snippet: Variation in the amino acid motif structure of the CagY MRR regulates T4SS function by altering α 5 β 1 integrin binding. Shown is Western blot detection of the CagY MRR in whole-cell bacterial lysates of H. pylori J166 (A) or PMSS1 (C) isogenic strains, each bearing unique cagY alleles, or their Δ cagY deletion mutants. The corresponding amino acid structure of the MRR is shown schematically as a series of A (orange) or B (yellow) motifs, each 31 to 39 residues, based on DNA sequence analysis as described previously ( 61 ). IL-8 induction (white bars) and integrin adhesion (black bars) relative to WT are shown for H. pylori J166 (B) and PMSS1 (D), which correspond to strains shown in panels A and C, respectively. (E) Western blot detection and schematic of the CagY MRR (derived as in panels A and C) from KUS13A, KUS13B, and isogenic variants in which cagY was deleted (Δ cagY ) or replaced with that from the variant strain (i.e., KUS13A with cagY 13B or KUS13B with cagY 13A ). (F) IL-8 induction (white bars) and integrin adhesion (black bars) relative to WT for the strains shown in panel E. Quantitative results represent the mean ± SEM from at least 3 independent experiments. *, P

Techniques Used: Binding Assay, Western Blot, Sequencing, Derivative Assay, Variant Assay

2) Product Images from "Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment"

Article Title: Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment

Journal: Scientific Reports

doi: 10.1038/s41598-018-20018-8

Inactivation of sceliphrolactam biosynthetic gene sceN using CRISPR/Cas9-based method. ( A ) Schematic illustration of the CRISPR/Cas9-mediated cleavage of genomic DNA and homology directed repair (HDR) to delete part of sceN . ( B ) PCR results confirmed the deletion of 883 base pairs of sceN using sgRNA2 as guide. A full-sized image of the DNA gel is included in the supporting information. ( C ) HPLC analysis of the ∆sceN mutant strain to show the abolishment of sceliphrolactam production. The sceliphrolactam peak is indicated by the arrow. The wavelength (λ) was set at 330 nm for the HPLC detector (Inset: on-line absorption spectrum of sceliphrolactam).
Figure Legend Snippet: Inactivation of sceliphrolactam biosynthetic gene sceN using CRISPR/Cas9-based method. ( A ) Schematic illustration of the CRISPR/Cas9-mediated cleavage of genomic DNA and homology directed repair (HDR) to delete part of sceN . ( B ) PCR results confirmed the deletion of 883 base pairs of sceN using sgRNA2 as guide. A full-sized image of the DNA gel is included in the supporting information. ( C ) HPLC analysis of the ∆sceN mutant strain to show the abolishment of sceliphrolactam production. The sceliphrolactam peak is indicated by the arrow. The wavelength (λ) was set at 330 nm for the HPLC detector (Inset: on-line absorption spectrum of sceliphrolactam).

Techniques Used: CRISPR, Polymerase Chain Reaction, High Performance Liquid Chromatography, Mutagenesis

( A ) Schematic illustration of the CRISPR/Cas9-mediated and dual sgRNA-guided DNA cleavage to fuse the sceQ and sceR genes. ( B ) DNA sequencing result confirmed the fusion of the two genes upon the deletion of 14 base pairs (sequence in red). ( C ) HPLC analysis comparing the production of sceliphrolactam between the sceQ-R fusion mutant and the wild type Streptomyces sp. SD85. The sceliphrolactam peak is indicated by the arrow. The wavelength (λ) was set at 330 nm for the HPLC detector.
Figure Legend Snippet: ( A ) Schematic illustration of the CRISPR/Cas9-mediated and dual sgRNA-guided DNA cleavage to fuse the sceQ and sceR genes. ( B ) DNA sequencing result confirmed the fusion of the two genes upon the deletion of 14 base pairs (sequence in red). ( C ) HPLC analysis comparing the production of sceliphrolactam between the sceQ-R fusion mutant and the wild type Streptomyces sp. SD85. The sceliphrolactam peak is indicated by the arrow. The wavelength (λ) was set at 330 nm for the HPLC detector.

Techniques Used: CRISPR, DNA Sequencing, Sequencing, High Performance Liquid Chromatography, Mutagenesis

3) Product Images from "HLA Typing for the Next Generation"

Article Title: HLA Typing for the Next Generation

Journal: PLoS ONE

doi: 10.1371/journal.pone.0127153

Basic stages of the Single Molecule Real-Time (SMRT) DNA sequencing method. SMRTbell adaptors are ligated onto the ends of a blunt-ended PCR amplicon to facilitate continuous sequencing of both strands of the amplicon. The entire sequence generated may include multiple copies of the sense and anti-sense strands of the PCR amplicon in a single read known as the Continuous Long Read (CLR). The post-sequencing bioinformatic post-processes are able to break down the CLR into shorter sub-reads, which encompass the sequence of one strand of the amplicon. These sub-reads can then be compared and used to create a consensus sequence.
Figure Legend Snippet: Basic stages of the Single Molecule Real-Time (SMRT) DNA sequencing method. SMRTbell adaptors are ligated onto the ends of a blunt-ended PCR amplicon to facilitate continuous sequencing of both strands of the amplicon. The entire sequence generated may include multiple copies of the sense and anti-sense strands of the PCR amplicon in a single read known as the Continuous Long Read (CLR). The post-sequencing bioinformatic post-processes are able to break down the CLR into shorter sub-reads, which encompass the sequence of one strand of the amplicon. These sub-reads can then be compared and used to create a consensus sequence.

Techniques Used: DNA Sequencing, Polymerase Chain Reaction, Amplification, Sequencing, Generated

4) Product Images from "Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment"

Article Title: Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment

Journal: Scientific Reports

doi: 10.1038/s41598-018-20018-8

Inactivation of sceliphrolactam biosynthetic gene sceN using CRISPR/Cas9-based method. ( A ) Schematic illustration of the CRISPR/Cas9-mediated cleavage of genomic DNA and homology directed repair (HDR) to delete part of sceN . ( B ) PCR results confirmed the deletion of 883 base pairs of sceN using sgRNA2 as guide. A full-sized image of the DNA gel is included in the supporting information. ( C ) HPLC analysis of the ∆sceN mutant strain to show the abolishment of sceliphrolactam production. The sceliphrolactam peak is indicated by the arrow. The wavelength (λ) was set at 330 nm for the HPLC detector (Inset: on-line absorption spectrum of sceliphrolactam).
Figure Legend Snippet: Inactivation of sceliphrolactam biosynthetic gene sceN using CRISPR/Cas9-based method. ( A ) Schematic illustration of the CRISPR/Cas9-mediated cleavage of genomic DNA and homology directed repair (HDR) to delete part of sceN . ( B ) PCR results confirmed the deletion of 883 base pairs of sceN using sgRNA2 as guide. A full-sized image of the DNA gel is included in the supporting information. ( C ) HPLC analysis of the ∆sceN mutant strain to show the abolishment of sceliphrolactam production. The sceliphrolactam peak is indicated by the arrow. The wavelength (λ) was set at 330 nm for the HPLC detector (Inset: on-line absorption spectrum of sceliphrolactam).

Techniques Used: CRISPR, Polymerase Chain Reaction, High Performance Liquid Chromatography, Mutagenesis

( A ) Schematic illustration of the CRISPR/Cas9-mediated and dual sgRNA-guided DNA cleavage to fuse the sceQ and sceR genes. ( B ) DNA sequencing result confirmed the fusion of the two genes upon the deletion of 14 base pairs (sequence in red). ( C ) HPLC analysis comparing the production of sceliphrolactam between the sceQ-R fusion mutant and the wild type Streptomyces sp. SD85. The sceliphrolactam peak is indicated by the arrow. The wavelength (λ) was set at 330 nm for the HPLC detector.
Figure Legend Snippet: ( A ) Schematic illustration of the CRISPR/Cas9-mediated and dual sgRNA-guided DNA cleavage to fuse the sceQ and sceR genes. ( B ) DNA sequencing result confirmed the fusion of the two genes upon the deletion of 14 base pairs (sequence in red). ( C ) HPLC analysis comparing the production of sceliphrolactam between the sceQ-R fusion mutant and the wild type Streptomyces sp. SD85. The sceliphrolactam peak is indicated by the arrow. The wavelength (λ) was set at 330 nm for the HPLC detector.

Techniques Used: CRISPR, DNA Sequencing, Sequencing, High Performance Liquid Chromatography, Mutagenesis

Related Articles

Sequencing:

Article Title: Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment
Article Snippet: .. The DNA sequences for the sceliphrolactam biosynthetic gene cluster obtained from illumina and PacBio sequencing are identical and have been deposited in GenBank (Accession number: KX230849). .. For Illumina MiSeq sequencing, a total of 3,906,106 reads were obtained with an average read length of 145.17 bases.

Article Title: Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment
Article Snippet: .. The DNA sequences for the sceliphrolactam biosynthetic gene cluster obtained from illumina and PacBio sequencing are identical and have been deposited in GenBank (Accession number: ). .. For Illumina MiSeq sequencing, a total of 3,906,106 reads were obtained with an average read length of 145.17 bases.

Article Title: pYR4 From a Norwegian Isolate of Yersinia ruckeri Is a Putative Virulence Plasmid Encoding Both a Type IV Pilus and a Type IV Secretion System
Article Snippet: .. Here, we report and analyze the complete DNA sequence of pYR4, a plasmid from a highly pathogenic Norwegian Y. ruckeri isolate, sequenced using PacBio SMRT technology. .. Like the well-known pYV plasmid of human pathogenic Yersiniae , pYR4 is a member of the IncFII family.

Article Title: Structure and evolution of the filaggrin gene repeated region in primates
Article Snippet: .. Therefore, to overcome these difficulties and determine the complete nucleotide sequences of FLG , we combined two different sequencing platforms: PacBio RS II and Illumina MiSeq. .. The long reads ( > 8 kb) generated by PacBio RS II were used to determine the overall structure of the repeat regions as an initial reference.

Article Title: CagY-Dependent Regulation of Type IV Secretion in Helicobacter pylori Is Associated with Alterations in Integrin Binding
Article Snippet: .. The DNA sequences of cagY from H. pylori PMSS1 and KUS13A and -B were determined using single-molecule real-time sequencing (Pacific Biosciences, Menlo Park, CA). .. Briefly, cagY was amplified as previously described , and purified PCR products were submitted to the DNA Technologies Core at the UC Davis Genome Center.

Article Title: High resolution assembly and characterization of genomes of Canadian isolates of Salmonella Enteritidis
Article Snippet: .. Apart from our use of genome maps [ ] and additional Sanger sequencing to ensure the completeness of the genomes assembled using the hybrid approach as described above, we also compared the entire nucleotide sequence of one of our isolates with a sequence of the same isolate generated with the Pacific Biosciences single molecule sequencing protocol followed by error correction of the assembled long reads at the Genome Quebec Sequencing Centre, Montreal. .. The two molecules had 99.98% nucleotide match and a complete agreement of their in silico maps (Ogunremi et al., manuscript in preparation).

Article Title: HLA Typing for the Next Generation
Article Snippet: .. The DNA sequences derived from Pacific Biosciences’ SMRT sequencing technologies underwent post-processing using the SMRT analysis tool v2.1, and were assigned HLA types using Anthony Nolan in-house Bioinformatics methods. .. The PacBio methodology provides a number of sequences for analysis for each sample.

Generated:

Article Title: High resolution assembly and characterization of genomes of Canadian isolates of Salmonella Enteritidis
Article Snippet: .. Apart from our use of genome maps [ ] and additional Sanger sequencing to ensure the completeness of the genomes assembled using the hybrid approach as described above, we also compared the entire nucleotide sequence of one of our isolates with a sequence of the same isolate generated with the Pacific Biosciences single molecule sequencing protocol followed by error correction of the assembled long reads at the Genome Quebec Sequencing Centre, Montreal. .. The two molecules had 99.98% nucleotide match and a complete agreement of their in silico maps (Ogunremi et al., manuscript in preparation).

Plasmid Preparation:

Article Title: pYR4 From a Norwegian Isolate of Yersinia ruckeri Is a Putative Virulence Plasmid Encoding Both a Type IV Pilus and a Type IV Secretion System
Article Snippet: .. Here, we report and analyze the complete DNA sequence of pYR4, a plasmid from a highly pathogenic Norwegian Y. ruckeri isolate, sequenced using PacBio SMRT technology. .. Like the well-known pYV plasmid of human pathogenic Yersiniae , pYR4 is a member of the IncFII family.

Derivative Assay:

Article Title: HLA Typing for the Next Generation
Article Snippet: .. The DNA sequences derived from Pacific Biosciences’ SMRT sequencing technologies underwent post-processing using the SMRT analysis tool v2.1, and were assigned HLA types using Anthony Nolan in-house Bioinformatics methods. .. The PacBio methodology provides a number of sequences for analysis for each sample.

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  • 92
    Pacific Biosciences rs ii sequencing dna
    Total genomic and plasmid extractions of strains were subjected to electrophoresis ( a ) and probed with pthA probe (using primer pthAF/R DIG as the probe), Xc-A306-p33 and Xc-A306-p64 plasmid specific probes by Southern hybridization ( b , c and d , respectively). Lanes 1 and 17 = <t>DNA</t> Molecular Weight Marker III DIG labeled; 2 = Erwinia stewartii SW2; 3 = Xc-A306 plasmid extraction (pXc-A306); 4 = Xc-A306 genomic DNA restricted with EcoRI (Xc-A306 EcoRI); 5 = <t>pXc-03-1638-1-1;</t> 6 = Xc-03-1638-1-1 EcoRI); 7 = pXc-A2090; 8 = Xc-A2090 EcoRI; 9 = pXc-A1660; 10 = Xc-A2090 EcoRI; 11 = pXc-AEtrog; 12 = Xc-AEtrog EcoRI; 13 = pXc-A100-Japan; 14 = Xc-A100 Japan EcoRI; 15 = pXc-A109 India; 16 = Xc-A109 India EcoRI. A = Ethidium bromide stained gel (agarose 0.7%). b Southern blot of gel in A with pthA probe. c Southern blot of gel in A with Xc-p33 probe (using primer SPCF33F/R DIG as the probe). d Southern blot of gel in A with Xc-p64 probe (using primer SPCF64F/R DIG as the probe)
    Rs Ii Sequencing Dna, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 92/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 16 article reviews
    Price from $9.99 to $1999.99
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    Pacific Biosciences smrt dna sequencing
    Basic stages of the Single Molecule Real-Time <t>(SMRT)</t> <t>DNA</t> sequencing method. SMRTbell adaptors are ligated onto the ends of a blunt-ended PCR amplicon to facilitate continuous sequencing of both strands of the amplicon. The entire sequence generated may include multiple copies of the sense and anti-sense strands of the PCR amplicon in a single read known as the Continuous Long Read (CLR). The post-sequencing bioinformatic post-processes are able to break down the CLR into shorter sub-reads, which encompass the sequence of one strand of the amplicon. These sub-reads can then be compared and used to create a consensus sequence.
    Smrt Dna Sequencing, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 90/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/smrt dna sequencing/product/Pacific Biosciences
    Average 90 stars, based on 21 article reviews
    Price from $9.99 to $1999.99
    smrt dna sequencing - by Bioz Stars, 2020-09
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    94
    Pacific Biosciences sanger dna sequencing
    Highly conserved chitinase-like and trypsin-like protease genes among B . bassiana <t>JEF-007</t> and other Bb isolates. ( A ) chitinase-like protein gene and ( B ) trypsin-like protease gene. PacBio sequencing <t>DNA</t> and predicted RNA data were aligned to investigate similarity and the existence of introns. Sanger sequences of PCR DNA were aligned among the B . bassiana isolates, and similarity results are provided. 3D protein structures of JEF-007 were generated using RaptorX.
    Sanger Dna Sequencing, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 94/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Total genomic and plasmid extractions of strains were subjected to electrophoresis ( a ) and probed with pthA probe (using primer pthAF/R DIG as the probe), Xc-A306-p33 and Xc-A306-p64 plasmid specific probes by Southern hybridization ( b , c and d , respectively). Lanes 1 and 17 = DNA Molecular Weight Marker III DIG labeled; 2 = Erwinia stewartii SW2; 3 = Xc-A306 plasmid extraction (pXc-A306); 4 = Xc-A306 genomic DNA restricted with EcoRI (Xc-A306 EcoRI); 5 = pXc-03-1638-1-1; 6 = Xc-03-1638-1-1 EcoRI); 7 = pXc-A2090; 8 = Xc-A2090 EcoRI; 9 = pXc-A1660; 10 = Xc-A2090 EcoRI; 11 = pXc-AEtrog; 12 = Xc-AEtrog EcoRI; 13 = pXc-A100-Japan; 14 = Xc-A100 Japan EcoRI; 15 = pXc-A109 India; 16 = Xc-A109 India EcoRI. A = Ethidium bromide stained gel (agarose 0.7%). b Southern blot of gel in A with pthA probe. c Southern blot of gel in A with Xc-p33 probe (using primer SPCF33F/R DIG as the probe). d Southern blot of gel in A with Xc-p64 probe (using primer SPCF64F/R DIG as the probe)

    Journal: BMC Genomics

    Article Title: Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains

    doi: 10.1186/s12864-017-4408-9

    Figure Lengend Snippet: Total genomic and plasmid extractions of strains were subjected to electrophoresis ( a ) and probed with pthA probe (using primer pthAF/R DIG as the probe), Xc-A306-p33 and Xc-A306-p64 plasmid specific probes by Southern hybridization ( b , c and d , respectively). Lanes 1 and 17 = DNA Molecular Weight Marker III DIG labeled; 2 = Erwinia stewartii SW2; 3 = Xc-A306 plasmid extraction (pXc-A306); 4 = Xc-A306 genomic DNA restricted with EcoRI (Xc-A306 EcoRI); 5 = pXc-03-1638-1-1; 6 = Xc-03-1638-1-1 EcoRI); 7 = pXc-A2090; 8 = Xc-A2090 EcoRI; 9 = pXc-A1660; 10 = Xc-A2090 EcoRI; 11 = pXc-AEtrog; 12 = Xc-AEtrog EcoRI; 13 = pXc-A100-Japan; 14 = Xc-A100 Japan EcoRI; 15 = pXc-A109 India; 16 = Xc-A109 India EcoRI. A = Ethidium bromide stained gel (agarose 0.7%). b Southern blot of gel in A with pthA probe. c Southern blot of gel in A with Xc-p33 probe (using primer SPCF33F/R DIG as the probe). d Southern blot of gel in A with Xc-p64 probe (using primer SPCF64F/R DIG as the probe)

    Article Snippet: PacBio RS II sequencing DNA sample for Xc-03-1638-1-1 was sequenced using PacBio single molecule real-time (SMRT) technology.

    Techniques: Plasmid Preparation, Electrophoresis, Hybridization, Molecular Weight, Marker, Labeling, Staining, Southern Blot

    Validation of rs12470652 identified by T-SMS. SMRT® View screenshot of secondary data analysis from SMRT® Portal (A and B). Validation of the LHCGR rs12470652 heterozygous variant discovered using T-SMS by Sanger DNA sequencing. The figure depicts the process of biomarker identification by SMS (A and B) and validation by conventional Sanger sequencing (C) .

    Journal: BMC Genomics

    Article Title: Targeted single molecule sequencing methodology for ovarian hyperstimulation syndrome

    doi: 10.1186/s12864-015-1451-2

    Figure Lengend Snippet: Validation of rs12470652 identified by T-SMS. SMRT® View screenshot of secondary data analysis from SMRT® Portal (A and B). Validation of the LHCGR rs12470652 heterozygous variant discovered using T-SMS by Sanger DNA sequencing. The figure depicts the process of biomarker identification by SMS (A and B) and validation by conventional Sanger sequencing (C) .

    Article Snippet: SMS was carried out using single molecule, real-time DNA sequencing (SMRT® Pacific Biosciences®), average raw read length = 1178 nucleotides, 5% of the amplicons > 6000 nucleotides).

    Techniques: Variant Assay, DNA Sequencing, Biomarker Assay, Sequencing

    Basic stages of the Single Molecule Real-Time (SMRT) DNA sequencing method. SMRTbell adaptors are ligated onto the ends of a blunt-ended PCR amplicon to facilitate continuous sequencing of both strands of the amplicon. The entire sequence generated may include multiple copies of the sense and anti-sense strands of the PCR amplicon in a single read known as the Continuous Long Read (CLR). The post-sequencing bioinformatic post-processes are able to break down the CLR into shorter sub-reads, which encompass the sequence of one strand of the amplicon. These sub-reads can then be compared and used to create a consensus sequence.

    Journal: PLoS ONE

    Article Title: HLA Typing for the Next Generation

    doi: 10.1371/journal.pone.0127153

    Figure Lengend Snippet: Basic stages of the Single Molecule Real-Time (SMRT) DNA sequencing method. SMRTbell adaptors are ligated onto the ends of a blunt-ended PCR amplicon to facilitate continuous sequencing of both strands of the amplicon. The entire sequence generated may include multiple copies of the sense and anti-sense strands of the PCR amplicon in a single read known as the Continuous Long Read (CLR). The post-sequencing bioinformatic post-processes are able to break down the CLR into shorter sub-reads, which encompass the sequence of one strand of the amplicon. These sub-reads can then be compared and used to create a consensus sequence.

    Article Snippet: The potential impact of using SMRT DNA sequencing in the future to generate such high-resolution HLA typing on many of these areas of medicine are likely to be considerable.

    Techniques: DNA Sequencing, Polymerase Chain Reaction, Amplification, Sequencing, Generated

    Highly conserved chitinase-like and trypsin-like protease genes among B . bassiana JEF-007 and other Bb isolates. ( A ) chitinase-like protein gene and ( B ) trypsin-like protease gene. PacBio sequencing DNA and predicted RNA data were aligned to investigate similarity and the existence of introns. Sanger sequences of PCR DNA were aligned among the B . bassiana isolates, and similarity results are provided. 3D protein structures of JEF-007 were generated using RaptorX.

    Journal: Scientific Reports

    Article Title: Genomic Analysis of the Insect-Killing Fungus Beauveria bassiana JEF-007 as a Biopesticide

    doi: 10.1038/s41598-018-30856-1

    Figure Lengend Snippet: Highly conserved chitinase-like and trypsin-like protease genes among B . bassiana JEF-007 and other Bb isolates. ( A ) chitinase-like protein gene and ( B ) trypsin-like protease gene. PacBio sequencing DNA and predicted RNA data were aligned to investigate similarity and the existence of introns. Sanger sequences of PCR DNA were aligned among the B . bassiana isolates, and similarity results are provided. 3D protein structures of JEF-007 were generated using RaptorX.

    Article Snippet: The Sanger DNA sequencing of the JEF-007 chitinase-like protein was identical to the PacBio sequencing data.

    Techniques: Sequencing, Polymerase Chain Reaction, Generated

    Diverse sequences of metalloprotease-like protein, eukaryotic aspartyl protease, and protein kinase genes in B. bassiana JEF-007 and other Bb isolates. ( A ) metalloprotease-like protein gene, ( B ) eukaryotic aspartyl protease gene, and ( C ) protein kinase gene. PacBio sequencing DNA and predicted RNA data were aligned to investigate similarity and the existence of introns. Sanger sequences of PCR DNA were aligned among the B. bassiana isolates, and similarity results are provided. Circles represent B. bassiana isolates including insertion (●) and deletion ( ) fragments, compared to JEF-007. JEF-007 eukaryotic aspartyl protease gene was predicted to have two introns.

    Journal: Scientific Reports

    Article Title: Genomic Analysis of the Insect-Killing Fungus Beauveria bassiana JEF-007 as a Biopesticide

    doi: 10.1038/s41598-018-30856-1

    Figure Lengend Snippet: Diverse sequences of metalloprotease-like protein, eukaryotic aspartyl protease, and protein kinase genes in B. bassiana JEF-007 and other Bb isolates. ( A ) metalloprotease-like protein gene, ( B ) eukaryotic aspartyl protease gene, and ( C ) protein kinase gene. PacBio sequencing DNA and predicted RNA data were aligned to investigate similarity and the existence of introns. Sanger sequences of PCR DNA were aligned among the B. bassiana isolates, and similarity results are provided. Circles represent B. bassiana isolates including insertion (●) and deletion ( ) fragments, compared to JEF-007. JEF-007 eukaryotic aspartyl protease gene was predicted to have two introns.

    Article Snippet: The Sanger DNA sequencing of the JEF-007 chitinase-like protein was identical to the PacBio sequencing data.

    Techniques: Sequencing, Polymerase Chain Reaction