firepol  (Solis BioDyne)

Journal: Scientific Reports

Article Title: The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons

doi: 10.1038/srep15317

Figure Lengend Snippet: Integrons detected by long-range PCR. ( a ) 1.5 kb partially sequenced integron by long-range PCR product. ( b ) 1.1 kb partially sequenced integron by long-range PCR. Cylindrical boxes show individual genes that are size dependent, i.e. larger box is longer gene; dotted arrows indicate the direction of transcription; and gradient blue color the end of the acquired sequence. Gene and structural features: attI , primary recombination site; dfrA17 and dfrA12 , dihydrofolate reductase; attC , recombination site; aadA5 and aadA2 , aminoglycoside adenylyltransferase; and orfF , hypothetical protein.

Article Snippet: Each PCR reaction (25 μl) contained 1× HOT FIREPol PCR mix (Solis BioDyne, Estonia); 200 nM uniquely tagged forward and reverse primers; 1 μl of sample DNA and water.

Techniques: Polymerase Chain Reaction, Sequencing

Journal: PLoS ONE

Article Title: Network Analysis Reveals Ecological Links between N-Fixing Bacteria and Wood-Decaying Fungi

doi: 10.1371/journal.pone.0088141

Figure Lengend Snippet: Third part of three ( Figs. 3 , 4 and 5): Phylogenetic tree of nifH protein sequences. 50% majority rule consensus tree of 13,500 PhyloBayes [52] post burn-in trees, unrooted. Black values at internodes = Bayesian Posterior Probability (if > 0.5). Pink values = MEGA5 [56] Maximum Parsimony (MP) bootstrap support (if > 50). Green values = GARLI [54] Maximum Likelihood bootstrap support (if > 50). Terminal triangles represent monophyletic clades with MOTUs solely of one tree species origin, collapsed but keeping the internal distance (substitutions per site, see scale bar), in light pink = 50–79 MP bootstrap support, dark pink = 80–100 MP bootstrap support. Green color indicates MOTUs solely from Fagus origin, red color Picea origin and dark blue color mixed origin (with bars showing ratio of [green] vs. [red]). Terminal labels with sequences from this study: MOTU ID (SMOTU = singleton MOTU), total number of sequences, FASY = from Fagus , PIAB = from Picea , followed by number of sequences in the same order, then forest management type(s) (AC.Conif = managed spruce forests, AC.Decid = managed beech forests, Extensiv = extensively managed beech forests) and number of sequences in same order. Terminal labels with sequences from other sources: near BLAST hit, summary of ecological data of sequences in that MOTU. The width of visible terminal branches represents the number of sequences (size correct up to 10 sequences). To the right, amino acid sequence logos and Kyte-Doolittle hydophobicity alignments for labeled nodes on the tree. The small tree shape (based on screenshot from Archaeopteryx v.0.972 [66] ) shows the position within the complete phylogenetic tree.

Article Snippet: Each composite DNA extract was amplified separately by PCR in triplicate 20 µl reaction mixtures containing 4 µl FIREPol 5x Master Mix (Solis BioDyne, Tartu, Estonia), 10 µM of each primer and approximately 20 ng template DNA.

Techniques: Sequencing, Labeling

Journal: PLoS ONE

Article Title: Network Analysis Reveals Ecological Links between N-Fixing Bacteria and Wood-Decaying Fungi

doi: 10.1371/journal.pone.0088141

Figure Lengend Snippet: Second part of three ( Figs. 3 , 4 and 5 ): Phylogenetic tree of nifH protein sequences. 50% majority rule consensus tree of 13,500 PhyloBayes [52] post burn-in trees, unrooted. Black values at internodes = Bayesian Posterior Probability (if > 0.5). Pink values = MEGA5 [56] Maximum Parsimony (MP) bootstrap support (if > 50). Green values = GARLI [54] Maximum Likelihood bootstrap support (if > 50). Terminal triangles represent monophyletic clades with MOTUs solely of one tree species origin, collapsed but keeping the internal distance (substitutions per site, see scale bar), in light pink = 50–79 MP bootstrap support, dark pink = 80–100 MP bootstrap support. Green color indicates MOTUs solely from Fagus origin, red color Picea origin and dark blue color mixed origin (with bars showing ratio of [green] vs. [red]). Terminal labels with sequences from this study: MOTU ID (SMOTU = singleton MOTU), total number of sequences, FASY = from Fagus , PIAB = from Picea , followed by number of sequences in the same order, then forest management type(s) (AC.Conif = managed spruce forests, AC.Decid = managed beech forests, Extensiv = extensively managed beech forests) and number of sequences in same order. Terminal labels with sequences from other sources: near BLAST hit, summary of ecological data of sequences in that MOTU. The width of visible terminal branches represents the number of sequences (size correct up to 10 sequences). To the right, amino acid sequence logos and Kyte-Doolittle hydophobicity alignments for labeled nodes on the tree. The small tree shape (based on screenshot from Archaeopteryx v.0.972 [66] ) shows the position within the complete phylogenetic tree.

Article Snippet: Each composite DNA extract was amplified separately by PCR in triplicate 20 µl reaction mixtures containing 4 µl FIREPol 5x Master Mix (Solis BioDyne, Tartu, Estonia), 10 µM of each primer and approximately 20 ng template DNA.

Techniques: Sequencing, Labeling

Journal: PLoS ONE

Article Title: Network Analysis Reveals Ecological Links between N-Fixing Bacteria and Wood-Decaying Fungi

doi: 10.1371/journal.pone.0088141

Figure Lengend Snippet: First part of three (Figs. 3, 4 and 5 ): Phylogenetic tree of nifH protein sequences. 50% majority rule consensus tree of 13,500 PhyloBayes [52] post burn-in trees, unrooted. Black values at internodes = Bayesian Posterior Probability (if > 0.5). Pink values = MEGA5 [56] Maximum Parsimony (MP) bootstrap support (if > 50). Green values = GARLI [54] Maximum Likelihood bootstrap support (if > 50). Terminal triangles represent monophyletic clades with MOTUs solely of one tree species origin, collapsed but keeping the internal distance (substitutions per site, see scale bar), in light pink = 50–79 MP bootstrap support, dark pink = 80–100 MP bootstrap support. Green color indicates MOTUs solely from Fagus origin, red color Picea origin and dark blue color mixed origin (with bars showing ratio of [green] vs. [red]). Terminal labels with sequences from this study: MOTU ID (SMOTU = singleton MOTU), total number of sequences, FASY = from Fagus , PIAB = from Picea , followed by number of sequences in the same order, then forest management type(s) (AC.Conif = managed spruce forests, AC.Decid = managed beech forests, Extensiv = extensively managed beech forests) and number of sequences in same order. Terminal labels with sequences from other sources: near BLAST hit, summary of ecological data of sequences in that MOTU. MOTUs that contain nucleotide sequences flagged as potential chimeras appear in italics and with the term PotChim (only present in Fig. 3, Supergrade). The width of visible terminal branches represents the number of sequences (size correct up to 10 sequences). To the right, amino acid sequence logos and Kyte-Doolittle hydophobicity alignments for labeled nodes on the tree. The small tree shape (based on screenshot from Archaeopteryx v.0.972 [66] ) shows the position within the complete phylogenetic tree.

Article Snippet: Each composite DNA extract was amplified separately by PCR in triplicate 20 µl reaction mixtures containing 4 µl FIREPol 5x Master Mix (Solis BioDyne, Tartu, Estonia), 10 µM of each primer and approximately 20 ng template DNA.

Techniques: Sequencing, Labeling

Journal: PLoS ONE

Article Title: Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding

doi: 10.1371/journal.pone.0257971

Figure Lengend Snippet: Leptospira variant identification using metabarcoded primers amplifying the glmU locus from three mock community samples using Oxford Nanopore sequencing. Mock community “a” contains a DNA ratio of 1:1 for all serovars, mock community “b” contains a DNA ratio of 5:1 for Hardjo type Bovis, Ballum, Pomona: Balcanica (NZ), Tarassovi, Copenhageni and, mock community “c” contains a DNA ratio of 1:5 for Hardjo type Bovis, Ballum, Pomona: Balcanica (NZ), Tarassovi, Copenhageni. Red dashed lines on each taxon represent the expected proportion of sequences based on the composition of each mock community. Each experiment was performed in triplicate using independently mixed mock communities each time.

Article Snippet: Conventional PCR assays were performed with FIREPol master mix (Solis BioDyne) using primers specific for the glmU and gyrB loci [ ].

Techniques: Variant Assay, Nanopore Sequencing

Journal: PLoS ONE

Article Title: Detection of treponemes in digital dermatitis lesions of captive European bison (Bison bonasus)

doi: 10.1371/journal.pone.0255921

Figure Lengend Snippet: Histological appearance of interdigital skin of European bison ( Bison bonasus ) with digital dermatitis. Left hind foot of animal no. 7. A: The dermatitis is characterized by epithelial acanthosis, ballooning degeneration of keratinocytes and elongated, dermal papillae containing mixed cellular infiltrate (arrows) protruding to the surface. Large amounts of basophilic bacteria are infiltrating the superficial epidermis (arrowhead). H E, bar 100 μm. Rectangle shows selected area for in situ hybridization on a parallel section. B: Bacteria visualized as bright green organisms (*) infiltrating the superficial epidermis. Fluorescent in situ hybridization. Bar 25 μm. C: Treponema organisms (arrows) infiltrating deep into the epidermis whereas other bacteria (arrowheads) are seen superficially. Double fluorescent in situ hybridization with probe for genus Treponema (Cy3 labelled) and for domain Bacterium (fluorescein labelled). Bar 25 μm.

Article Snippet: Specific nested PCR assays for T . medium , T . phagedenis , and T . pedis , were performed on swab and pooled biopsy samples according to Evans et al. [ ] using FIREPol® Master Mix Ready to load with 12.5 mM MgCl2 (Solis Biodyne, Tartu, Estonia).

Techniques: In Situ Hybridization