Journal: BMC Ecology

Article Title: Identification of roots from grass swards using PCR-RFLP and FFLP of the plastid trn L (UAA) intron

doi: 10.1186/1472-6785-3-8

Figure Lengend Snippet: Key to grass identification at Sourhope using trn L PCR-RFLP. Fragment sizes were determined using nucleotide sequence data of the trn L PCR product of each reference species. Restriction enzyme(s) are followed by the fragment sizes expected from digestion with the enzyme(s). GenBank accession numbers are provided in brackets following the species name.

Article Snippet: The double digest with Nla IV and Dde I was performed in Promega buffer B. Bfa I and Nla IV were obtained from New England Biolabs; Dde I, Hin fI, Hsp 92II and Xmn I from Promega.

Techniques: Sequencing

Journal: PLoS ONE

Article Title: Restriction and Sequence Alterations Affect DNA Uptake Sequence-Dependent Transformation in Neisseria meningitidis

doi: 10.1371/journal.pone.0039742

Figure Lengend Snippet: Transforming DNA plasmids are based on pilG (black) interrupted by an erythromycin resistance insert, ermC , (gray). DUS ( 5′- ATGCCGTCTGAA-3′ ) or reverse complimentary DUS ( 5′-TTCAGACGGCAT-3′ ) are inserted in three different positions A, B and C as marked above the bar. All numbers refer to the nucleotide position following the start codon (1) of pilG. The 137 nucleotide long Bam HI-fragment which is removed in pDV-b, pDV-c versions is shown in white with black stripes. B. Nla IV restriction profile of rpoB and location of selective SNP. The homologous 723 nt long PCR fragment of an internal part of the meningococcal rpoB gene used in transformation contains two Nla IV restriction sites on both sides of the selective SNP responsible for rifampicin resistance in the recipient.

Article Snippet: The hybrid plasmids pOHA-0-DUS and pOHA-Single from a previous study containing the naturally DUS-less neisserial pilus biogenesis gene pilG harbouring a selective marker encoding erythromycin (erm) resistance , were used to make all constructs employed, varying in DUS, Nla IV sites and homologous region as shown in . pOHA-0-DUS and pSingle were trimmed with Bam HI (recognition sequence GGATCC) (New England Biolabs) and recircularised with T4 Ligase (New England Biolabs) or polished with Phusion polymerase (New England Biolabs) following Bam HI restriction and recircularised to generate the plasmids -b, -c and -d versions of pOHA-0-DUS and pOHA13, respectively.

Techniques: Transformation Assay

Journal: PLoS ONE

Article Title: Restriction and Sequence Alterations Affect DNA Uptake Sequence-Dependent Transformation in Neisseria meningitidis

doi: 10.1371/journal.pone.0039742

Figure Lengend Snippet: The Y axis shows the number of resistant (erythromycin) CFU/total 10 10 CFU on a log scale. Along the X-axis are the different DNA substrates (10 ng/ml) with altered numbers of Nla IV restriction sites shown. pDV4-a harbours two and three Nla IV restriction sites more than pDV4-b and pDV4-c, respectively. For further details of the restriction profiles and DUS locations in the transforming DNA plasmids please consult and . Statistically significant differences in transformation frequencies between the Nla IV null mutant and wildtype backgrounds are indicated above the columns, ***equals p≤0.001 in a two tailed paired student’s t-test.

Article Snippet: The hybrid plasmids pOHA-0-DUS and pOHA-Single from a previous study containing the naturally DUS-less neisserial pilus biogenesis gene pilG harbouring a selective marker encoding erythromycin (erm) resistance , were used to make all constructs employed, varying in DUS, Nla IV sites and homologous region as shown in . pOHA-0-DUS and pSingle were trimmed with Bam HI (recognition sequence GGATCC) (New England Biolabs) and recircularised with T4 Ligase (New England Biolabs) or polished with Phusion polymerase (New England Biolabs) following Bam HI restriction and recircularised to generate the plasmids -b, -c and -d versions of pOHA-0-DUS and pOHA13, respectively.

Techniques: Transformation Assay, Mutagenesis, Two Tailed Test

Journal: PLoS ONE

Article Title: Restriction and Sequence Alterations Affect DNA Uptake Sequence-Dependent Transformation in Neisseria meningitidis

doi: 10.1371/journal.pone.0039742

Figure Lengend Snippet: The Y axis shows the number of rifampicin-resistant CFU/total CFU 10 9 on a log scale. Along the X-axis are shown the two different DNA substrates (5 ng/ml), rpoB PCR fragment and rpoB PCR fragment pre-digested with Nla IV. For further details on the transforming DNA please consult and . The transformation frequencies in the wildtype and in the Nla IV null mutant backgrounds are not statistically significant from each other.

Article Snippet: The hybrid plasmids pOHA-0-DUS and pOHA-Single from a previous study containing the naturally DUS-less neisserial pilus biogenesis gene pilG harbouring a selective marker encoding erythromycin (erm) resistance , were used to make all constructs employed, varying in DUS, Nla IV sites and homologous region as shown in . pOHA-0-DUS and pSingle were trimmed with Bam HI (recognition sequence GGATCC) (New England Biolabs) and recircularised with T4 Ligase (New England Biolabs) or polished with Phusion polymerase (New England Biolabs) following Bam HI restriction and recircularised to generate the plasmids -b, -c and -d versions of pOHA-0-DUS and pOHA13, respectively.

Techniques: Transformation Assay, Mutagenesis

Journal: PLoS ONE

Article Title: Restriction and Sequence Alterations Affect DNA Uptake Sequence-Dependent Transformation in Neisseria meningitidis

doi: 10.1371/journal.pone.0039742

Figure Lengend Snippet: The Y axis shows the number of erythromycin-resistant CFU/total CFU 10 8 on a log scale. Along the X-axis are shown the transforming DNA (1 µg/ml) that differ in Nla IV restriction profiles and DUS location. For further details on the DNA plasmid templates please consult and . Statistically significant values are indicated above the columns, **equals p≤0.05 and ***equals p≤0.001 in a two-tailed paired student’s t tests.

Article Snippet: The hybrid plasmids pOHA-0-DUS and pOHA-Single from a previous study containing the naturally DUS-less neisserial pilus biogenesis gene pilG harbouring a selective marker encoding erythromycin (erm) resistance , were used to make all constructs employed, varying in DUS, Nla IV sites and homologous region as shown in . pOHA-0-DUS and pSingle were trimmed with Bam HI (recognition sequence GGATCC) (New England Biolabs) and recircularised with T4 Ligase (New England Biolabs) or polished with Phusion polymerase (New England Biolabs) following Bam HI restriction and recircularised to generate the plasmids -b, -c and -d versions of pOHA-0-DUS and pOHA13, respectively.

Techniques: Plasmid Preparation, Two Tailed Test

Journal: PLoS ONE

Article Title: Restriction and Sequence Alterations Affect DNA Uptake Sequence-Dependent Transformation in Neisseria meningitidis

doi: 10.1371/journal.pone.0039742

Figure Lengend Snippet: Fold-differences and statistical significance values (paired two tailed student’s t tests) in comparing the performances of individual plasmids harbouring DUS in the C (pDV1) or A (pDV4) positions in transformation of the Nla IV mutant and wt backgrounds.

Article Snippet: The hybrid plasmids pOHA-0-DUS and pOHA-Single from a previous study containing the naturally DUS-less neisserial pilus biogenesis gene pilG harbouring a selective marker encoding erythromycin (erm) resistance , were used to make all constructs employed, varying in DUS, Nla IV sites and homologous region as shown in . pOHA-0-DUS and pSingle were trimmed with Bam HI (recognition sequence GGATCC) (New England Biolabs) and recircularised with T4 Ligase (New England Biolabs) or polished with Phusion polymerase (New England Biolabs) following Bam HI restriction and recircularised to generate the plasmids -b, -c and -d versions of pOHA-0-DUS and pOHA13, respectively.

Techniques: Two Tailed Test, Transformation Assay, Mutagenesis

Journal: PLoS ONE

Article Title: Restriction and Sequence Alterations Affect DNA Uptake Sequence-Dependent Transformation in Neisseria meningitidis

doi: 10.1371/journal.pone.0039742

Figure Lengend Snippet: Plasmids and bacterial strains.

Article Snippet: The hybrid plasmids pOHA-0-DUS and pOHA-Single from a previous study containing the naturally DUS-less neisserial pilus biogenesis gene pilG harbouring a selective marker encoding erythromycin (erm) resistance , were used to make all constructs employed, varying in DUS, Nla IV sites and homologous region as shown in . pOHA-0-DUS and pSingle were trimmed with Bam HI (recognition sequence GGATCC) (New England Biolabs) and recircularised with T4 Ligase (New England Biolabs) or polished with Phusion polymerase (New England Biolabs) following Bam HI restriction and recircularised to generate the plasmids -b, -c and -d versions of pOHA-0-DUS and pOHA13, respectively.

Techniques: Clone Assay, Plasmid Preparation, Isolation, Mutagenesis