Journal: Clinical chemistry and laboratory medicine

Article Title: Rapid Screening for Targeted Genetic Variants via High-Resolution Melting Curve Analysis

doi: 10.1515/cclm-2016-0603

Figure Lengend Snippet: HRM curves distinguish genotypes. For each SNP, representative HRM curves of reference (black curves), heterozygous (green curves), and homozygous (red curves) DNA are illustrated. Single nucleotide base pair mutations caused a shift in melting temperature of the target amplicon, allowing for visual separation of genotypes with HRM curves. No homozygous control DNA template was available for CYP3A5*2 (F).

Article Snippet: DNA templates Reference sequence, heterozygous, and homozygous control template DNA samples containing each SNP of interest were obtained from the Coriell Institute for Medical Research (Camden, NJ, USA) after obtaining proper institutional approval.

Techniques: Amplification, Control

Journal: Clinical chemistry and laboratory medicine

Article Title: Rapid Screening for Targeted Genetic Variants via High-Resolution Melting Curve Analysis

doi: 10.1515/cclm-2016-0603

Figure Lengend Snippet: HRM difference plots. Differences in melting curve shape were visualized by subtracting the curves from a reference sequence control curve. Normalized fluorescence minus reference (y-axis) was plotted against temperature (x-axis) for each SNP. Heterozygous (green curves) and homozygous (red curves) samples were clearly delineated from reference samples (black curves). With the described HRM screening approach, both heterozygous and homozygous samples would be collectively called as ‘variant.’

Article Snippet: DNA templates Reference sequence, heterozygous, and homozygous control template DNA samples containing each SNP of interest were obtained from the Coriell Institute for Medical Research (Camden, NJ, USA) after obtaining proper institutional approval.

Techniques: Sequencing, Control, Fluorescence, Variant Assay

Journal: Clinical chemistry and laboratory medicine

Article Title: Rapid Screening for Targeted Genetic Variants via High-Resolution Melting Curve Analysis

doi: 10.1515/cclm-2016-0603

Figure Lengend Snippet: Concordance with Sanger sequencing. A representative example is shown for CYP3A5*3, a substitution of thymine for cytosine. With Sanger sequencing, reference samples displayed thymine at the SNP location (A), homozygous samples displayed cytosine (C), and heterozygous samples displayed peaks for both alleles (B). HRM difference plots show the same unknown samples (cyan curves) alongside DNA controls of known genotype (D–F).

Article Snippet: DNA templates Reference sequence, heterozygous, and homozygous control template DNA samples containing each SNP of interest were obtained from the Coriell Institute for Medical Research (Camden, NJ, USA) after obtaining proper institutional approval.

Techniques: Sequencing

Journal:

Article Title: Isolation and Characterization of Mini-Tn 5 Km2 Insertion Mutants of Enterohemorrhagic Escherichia coli O157:H7 Deficient in Adherence to Caco-2 Cells

doi:

Figure Lengend Snippet: Adherence behavior of O157Sakai (WT), the intimin mutant (Δeae), type III secretion mutant (B9-F9), and EPEC B171-8 (EPEC). B9-F9 is representative of class 1 mutants defective in the type III secretion system. (A) The bacteria were grown at 37°C for 2 h in DMEM-glycerol and then used to infect Caco-2 cell monolayers. Then these infected monolayers were incubated for 1.5 h and washed five times with PBS. After another 0, 1, 2, or 3 h of incubation at 37°C in DMEM-glycerol, the monolayers were again washed three times with PBS, fixed with methanol, and stained with Giemsa solution to visualize the adherent bacterial colonies. Strains and incubation times are shown above and on the left side of photos, respectively. (B) The black bars represent the total number of sites containing adherent EHEC, having either a single bacterium or a cluster of multiple bacteria. The white bars represent the number of clusters containing at least eight bacteria. The data shown are the means and standard errors of the means for 20 microscopic fields. The representative results were obtained from three independent experiments.

Article Snippet: The sites of mini-Tn 5 Km2 on the chromosome were estimated based on sequence homology between the flanking DNA and sequences in a DNA database of O157Sakai or E. coli K-12 genome sequences (K. Makino and H. Shinagawa, unpublished data; Escherichia coli www home page [ http://mol.genes.nig.ac.jp/ecoli/ ] or E. coli database collection [ECDC] [ http://susi.bio.uni-giessen.de/ecdc/ecdc.html ]).

Techniques: Mutagenesis, Bacteria, Infection, Incubation, Staining

Journal:

Article Title: Isolation and Characterization of Mini-Tn 5 Km2 Insertion Mutants of Enterohemorrhagic Escherichia coli O157:H7 Deficient in Adherence to Caco-2 Cells

doi:

Figure Lengend Snippet: Photomicrographs of the intimin mutant and parental wild-type strain in a rhodamine-phalloidin assay for FAS in Caco-2 cells. (A) Caco-2 cells infected by bacteria as described in the Fig. ​Fig.44 legend are shown as follows: in fluorescent views after treatment with anti-O157 LPS rabbit antibody followed by anti-rabbit goat antibody conjugated with fluorescein isothiocyanate (Bacteria), in fluorescent views of actin stained by rhodamine-phalloidin (Actin), and in a superimposed view of bacteria (green) and actin (red) (Super impose). Strains and incubation times are indicated at the left of photos. (B) Quantitative FAS assay of the O157Sakai wild type (WT) and the intimin mutant (Δeae), derived from the experiments whose results are shown in panel A.

Article Snippet: The sites of mini-Tn 5 Km2 on the chromosome were estimated based on sequence homology between the flanking DNA and sequences in a DNA database of O157Sakai or E. coli K-12 genome sequences (K. Makino and H. Shinagawa, unpublished data; Escherichia coli www home page [ http://mol.genes.nig.ac.jp/ecoli/ ] or E. coli database collection [ECDC] [ http://susi.bio.uni-giessen.de/ecdc/ecdc.html ]).

Techniques: Mutagenesis, Infection, Bacteria, Staining, Incubation, Derivative Assay

Journal: BMC Plant Biology

Article Title: Fragments of the key flowering gene GIGANTEA are associated with helitron-type sequences in the Pooideae grass Lolium perenne

doi: 10.1186/1471-2229-9-70

Figure Lengend Snippet: Lolium perenne and Festuca pratensis helitron sequences containing GIGANTEA gene fragment . Helitron sequences conserved between Lp- psGI.1 and/or Lp- psGI.2/.3 and Fp -psGI.1 (thick black bar); helitron sequence unique to Lp- psGI.1 (thin black bar); non-helitron genomic sequence (thin grey bar); putative gene fragments (thick grey bar): a = succinate dehydrogenase, b = non-LTR retroelement, c = ribosomal protein, d = GIGANTEA . Sequence : detail of 3' helitron border illustrating hairpin motif and 3' terminus.

Article Snippet: The L. perenne GeneThresher ® ( Lp GT) DNA sequence library database was obtained on license from ViaLactia Biosciences, Auckland, New Zealand and was described previously [ , ].

Techniques: Sequencing

Journal: BMC Plant Biology

Article Title: Fragments of the key flowering gene GIGANTEA are associated with helitron-type sequences in the Pooideae grass Lolium perenne

doi: 10.1186/1471-2229-9-70

Figure Lengend Snippet: Sequences derived from the L. perenne GeneThresher library ( Lp GT) with homology to flanking regions of the complete helitron sequence Lp -psGI.1 . Identifiers for the LpGT sequences are: 1) FLPB002709C17-g0RSP_20020409, 2) FLPB002048C23-g0RSP_20011109, 3) FLPB002662H10-b0FSP_20020409, 4) FLPB001026M06-g0RSP_20010815, 5) FLPB001057C01-g1RSP_20010815, 6) FLPB001013B03-g0RSP_20010815, 7) FLPB002024D17-b0FSP_20010827, 8) FLPB001091D09-b0FSP_20011203 (see Additional File ).

Article Snippet: The L. perenne GeneThresher ® ( Lp GT) DNA sequence library database was obtained on license from ViaLactia Biosciences, Auckland, New Zealand and was described previously [ , ].

Techniques: Derivative Assay, Sequencing

Journal: BMC Plant Biology

Article Title: Fragments of the key flowering gene GIGANTEA are associated with helitron-type sequences in the Pooideae grass Lolium perenne

doi: 10.1186/1471-2229-9-70

Figure Lengend Snippet: Diagrammatic representation of region of GIGANTEA ( GI ) that has been ancestrally incorporated into a helitron . Black horizontal bar = L. perenne genomic sequence spanning the complete GI coding sequences; predicted exons are indicated by the thick bar. Grey horizontal bar indicates putative complete helitron sequence from Lp- psGI.1; relative position of the GI fragment incorporated into the helitron is indicated by the thick grey bar. Sequence detail shows 3' border of conserved GI region with putative helitron A↓T insertion site at the border.

Article Snippet: The L. perenne GeneThresher ® ( Lp GT) DNA sequence library database was obtained on license from ViaLactia Biosciences, Auckland, New Zealand and was described previously [ , ].

Techniques: Sequencing

Journal: BMC Plant Biology

Article Title: Fragments of the key flowering gene GIGANTEA are associated with helitron-type sequences in the Pooideae grass Lolium perenne

doi: 10.1186/1471-2229-9-70

Figure Lengend Snippet: Percentage sequence similarity comparing the L. perenne ( Lp ) and F. pratensis ( Fp ) pseudo-GIGANTEA (-psGI) regions and the equivalent region of L. perenne GIGANTEA over introns and exons.

Article Snippet: The L. perenne GeneThresher ® ( Lp GT) DNA sequence library database was obtained on license from ViaLactia Biosciences, Auckland, New Zealand and was described previously [ , ].

Techniques: Sequencing

Journal: BMC Plant Biology

Article Title: Fragments of the key flowering gene GIGANTEA are associated with helitron-type sequences in the Pooideae grass Lolium perenne

doi: 10.1186/1471-2229-9-70

Figure Lengend Snippet: Putative helitron hairpin and 3' border motifs identified in the L. perenne GeneThresher ® database with the SEEDTOP search . Five examples of each of the 7 hairpin sequence types are illustrated; the total number of each type identified is given in brackets. Large horizontal brackets indicate hairpins, small horizontal brackets indicate CTRR↓T 3' helitron border. DNA base colour scheme relates to relative sequence conservation across all examples of each putative helitron hairpin and 3' border motif identified, not just the 5 examples of each type illustrated (see Additional File ).

Article Snippet: The L. perenne GeneThresher ® ( Lp GT) DNA sequence library database was obtained on license from ViaLactia Biosciences, Auckland, New Zealand and was described previously [ , ].

Techniques: Sequencing