Journal: Nature chemical biology

Article Title: Diabetes reversal by inhibition of the low molecular weight tyrosine phosphatase

doi: 10.1038/nchembio.2344

Figure Lengend Snippet: (a) Surface representation of human LMPTP-A showing phosphate (P) non-covalently bound in the active-site. Residues are colored according to magnitude of shift in the HSQC 15 N- 1 H spectrum upon Compd. 18 titration (red>orange>green). Gray residues had negligible shifts or could not be assigned. (b) Crystal structure of bovine LMPTP W49Y/N50E bound to orthovanadate and Compd. 18 (cyan and blue sticks; Q=quinoline; Pip=piperidine; BN=benzonitrile; L=linker), with selected side-chains (yellow=carbon; red=oxygen; blue=nitrogen; pink=vanadium) and H-bonds/ionic interactions (dashed green/gray lines) shown. (c) Inhibition of phosphatase activity of LMPTP-A/mutants by Compd. 18 using 0.4 mM OMFP substrate. Mean±SD % activity is shown. Data is representative of 3 independent experiments. (d) Compd. 18 modeled into the crystal structure of phosphate-bound human LMPTP, based on an overlay with the bovine ternary complex crystal structure (RMSD=0.33 Å). Selected residues are colored by NMR shift as in (a) . Dashed red line depicts predicted clash between apical oxygen (“A”) of phosphate and Q. (e–f) Structural rationale for SAR data, with atoms at 66% of their true radii. (e) “Side” view of pocket, rotated ~90° about a horizontal axis. The molecular surface has been sliced through the active-site to reveal the tight fit of Q in the pocket. Atoms with a formal charge (±) are labeled. BN is highly polarized, as indicated (δ±); arrows labeled “S” indicate solvent exposure of ring substitutions. (f) “Top” view looking down at the active-site pocket filled by Q. Arrow above atom N1 locates the “saddle-point” at pocket exit.

Article Snippet: cDNAs encoding mouse and human LMPTP-A (protein reference sequences NP_067305.2 and NP_004291.1) and bovine LMPTP (protein reference sequence NP_776403.1) were codon-optimized for E. coli , synthesized, and cloned into the pGEX-4T vector using BamHI/EcoRI by Genscript.

Techniques: Titration, Inhibition, Activity Assay, Labeling, Solvent

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