Journal: Frontiers in Microbiology

Article Title: Evaluation of MALDI–TOF Mass Spectrometry in Diagnostic and Environmental Surveillance of Legionella Species: A Comparison With Culture and Mip -Gene Sequencing Technique

doi: 10.3389/fmicb.2020.589369

Figure Lengend Snippet: Isolates identification by MALDI Biotyper system according to the manufacturer’s threshold and the revised sub-criteria.

Article Snippet: Concerning the intra-species analysis, the tree reveals the presence of a subclade inside the L. anisa principal clade, formed by two isolates sequences (i.e., mip -17 and mip -49), which share only 96.7% pairwise identity with the L. anisa reference mip sequence (i.e., ATCC 35392).

Techniques:

Journal: Frontiers in Microbiology

Article Title: Evaluation of MALDI–TOF Mass Spectrometry in Diagnostic and Environmental Surveillance of Legionella Species: A Comparison With Culture and Mip -Gene Sequencing Technique

doi: 10.3389/fmicb.2020.589369

Figure Lengend Snippet: Results of the mip- gene sequencing and the number of isolates identified.

Article Snippet: Concerning the intra-species analysis, the tree reveals the presence of a subclade inside the L. anisa principal clade, formed by two isolates sequences (i.e., mip -17 and mip -49), which share only 96.7% pairwise identity with the L. anisa reference mip sequence (i.e., ATCC 35392).

Techniques: Sequencing

Journal: Frontiers in Microbiology

Article Title: Evaluation of MALDI–TOF Mass Spectrometry in Diagnostic and Environmental Surveillance of Legionella Species: A Comparison With Culture and Mip -Gene Sequencing Technique

doi: 10.3389/fmicb.2020.589369

Figure Lengend Snippet: Comparison of the results of the three techniques.

Article Snippet: Concerning the intra-species analysis, the tree reveals the presence of a subclade inside the L. anisa principal clade, formed by two isolates sequences (i.e., mip -17 and mip -49), which share only 96.7% pairwise identity with the L. anisa reference mip sequence (i.e., ATCC 35392).

Techniques: Comparison

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: Maximum likelihood phylogeny and pairwise sequence identity heatmap of Pasteuria spp. taxonomic reference sequences used in primer design and Pasteuria spp. ZOTU taxonomic assignment.

Article Snippet: The pairwise percentage identity of reference Pasteuria spp. sequences in the aligned region of the 16S rRNA gene ranged from a low of 84.7% ( P. ramosa vs P. usgae ) to a high of 99.3% ( P. penetrans to Pasteuria HcP) with an average of 95% identity between all reference sequences.

Techniques: Sequencing

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: Map of distribution of the most abundant Pasteuria spp. ZOTUs across both NSIS2 (circles) and ESFN (triangles) datasets. Plot points are colored by ZOTU and sized as a function of the total number of merged read pairs recovered for that ZOTU µl −1 of product added to the final pool from the corresponding sample.

Article Snippet: The pairwise percentage identity of reference Pasteuria spp. sequences in the aligned region of the 16S rRNA gene ranged from a low of 84.7% ( P. ramosa vs P. usgae ) to a high of 99.3% ( P. penetrans to Pasteuria HcP) with an average of 95% identity between all reference sequences.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: NDMS ordination plot of NSIS2 Pasteuria spp. community composition. Points are colored by soil horizon where L = litter; H = humus; O = peaty material formed under wet, anaerobic conditions; and A = mineral horizon formed at or near the surface showing accumulation and incorporation of organic matter. Points are sized by the total number of merged read pairs µl −1 of PCR product added to the final pool from the corresponding sample. Stress = 0.245235.

Article Snippet: The pairwise percentage identity of reference Pasteuria spp. sequences in the aligned region of the 16S rRNA gene ranged from a low of 84.7% ( P. ramosa vs P. usgae ) to a high of 99.3% ( P. penetrans to Pasteuria HcP) with an average of 95% identity between all reference sequences.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: Environmental variables with a statistically significant relationship to Pasteuria spp. community ordination before or after Benjamini-Hochberg correction.

Article Snippet: The pairwise percentage identity of reference Pasteuria spp. sequences in the aligned region of the 16S rRNA gene ranged from a low of 84.7% ( P. ramosa vs P. usgae ) to a high of 99.3% ( P. penetrans to Pasteuria HcP) with an average of 95% identity between all reference sequences.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: Spearman’s rank correlation of soil properties with statistically significant correlation to Pasteuria spp. community composition.

Article Snippet: The pairwise percentage identity of reference Pasteuria spp. sequences in the aligned region of the 16S rRNA gene ranged from a low of 84.7% ( P. ramosa vs P. usgae ) to a high of 99.3% ( P. penetrans to Pasteuria HcP) with an average of 95% identity between all reference sequences.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: The top three most abundant Pasteuria spp. ZOTUs in the ESFN dataset and respective metazoan ZOTU Spearman’s rank correlations which were statistically significant after Benjamini-Hochberg correction.

Article Snippet: The pairwise percentage identity of reference Pasteuria spp. sequences in the aligned region of the 16S rRNA gene ranged from a low of 84.7% ( P. ramosa vs P. usgae ) to a high of 99.3% ( P. penetrans to Pasteuria HcP) with an average of 95% identity between all reference sequences.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils

doi: 10.3389/fpls.2019.01763

Figure Lengend Snippet: (A) 400x magnification Pratylenchus spp. recovered from ESFN soil with Pasteuria spp. endospore attached (position indicated by red arrow). (B) 1000x magnification of Pratylenchus spp. recovered from ESFN soil with Pasteuria spp. endospore attached (position indicated by red arrow). (C) 1000x magnification of free living non-parasitic nematode recovered from ESFN soil with several Pasteuria spp. endospores attached (positions indicated by red arrows). (D) 1000x magnification of fluorescence image of Pratylenchus spp. recovered from ESFN soil with Pasteuria spp. endospore attached (position indicated by blue arrow), showing anti- Pasteuria penetrans antibody recognition.

Article Snippet: The pairwise percentage identity of reference Pasteuria spp. sequences in the aligned region of the 16S rRNA gene ranged from a low of 84.7% ( P. ramosa vs P. usgae ) to a high of 99.3% ( P. penetrans to Pasteuria HcP) with an average of 95% identity between all reference sequences.

Techniques: Fluorescence

Journal: bioRxiv

Article Title: Heterogeneity in establishment of polyethylene glycol-mediated plasmid transformations for five forest pathogenic Phytophthora species

doi: 10.1101/2024.06.13.598956

Figure Lengend Snippet: Gel electrophoresis of products from a PCR performed on DNA from P. ramorum NA2_17 wildtype (PrWT; wells 3-4), pYF515 transformant (pYF515 PrT; wells 5-7), and pYF2-PsCG transformant (pYF2-PsCG PrT; wells 10-14) cultures using the pYF_Cas9_Diag_F3/R3 primer pair (expected product size is 824 bp). The positive PCR controls are pYF515 plasmid DNA (well 2) and pYF2-PsCG plasmid DNA (well 9). The gel was run at 100 volts for 60 minutes on 0.8% agarose in 0.5X TBE buffer with a 100 bp DNA Ladder (Thermo Fisher Scientific, Waltham, MA, USA). All samples were loaded with Safe-Green™ stain (Applied Biological Materials Inc., Richmond, BC, Canada) at a ratio of 1 μL Safe-Green: 5 μL PCR product.

Article Snippet: The sequencing results from Plasmidsaurus showed the expected sequences for pYF515 (99.8% pairwise identity to original plasmid sequence; S5 Fig) and pYF2-PsCG (99.8% pairwise identity to original plasmid sequence; S6 Fig), but not for either of the two pGFPN samples (52.9% and 62.6% pairwise identity to original plasmid sequence; S7 Fig and S8 Fig, respectively).

Techniques: Nucleic Acid Electrophoresis, Plasmid Preparation, Staining