Journal: iScience

Article Title: Flagellin in blood and Bifidobacterium pseudocatenulatum in gut are associated with live birth upon IVF-frozen embryo transfer

doi: 10.1016/j.isci.2025.111933

Figure Lengend Snippet:

Article Snippet: HEK-Dual™-hTLR5 reporter cell line , InvivoGen , Cat. #hkd-htlr5ni.

Techniques: Recombinant, Purification, LAL Assay, Sequencing, Software

Journal: bioRxiv

Article Title: Divergence of the Individual repeats in the leucine-rich repeat domains of human Toll-like receptors explain their diversity and functional adaptations

doi: 10.1101/2024.09.30.615863

Figure Lengend Snippet: Examples of the regular and irregular LRR domains. Left Panels: An example of a regular LRR domain, the porcine ribonuclease inhibitor (PDB:2BNH), the first LRR protein with an experimentally solved structure. The LRR domain of the RNI structure is superimposed over a 3D model of a regular torus. The repeats recognized by an Interpro/Pfam HMM models are highlighted in blue and magenta which are used to characterize different subtypes of LRR repeats – however the classification does not correlate with structural similarity between repeats. 8 repeats out of 17 repeats are recognized by InterPro/Pfam HMMs. The alignment of three consecutive repeats (86-141) with the central LxL pattern are highlighted on the bottom panel. Right panels: Analogous figures for an example of highly irregular LRR domain of hTLR5 (PDB:3J0A). The LRR domain of hTLR5 LRR is superimposed with an ellipsoid based torus which shows a much greater radius and local curvature divergence than the torus used in RI. The repeats recognized by an Interpro/Pfam HMM models are highlighted in blue and magenta with different colors used to identify different subtypes of LRR repeats – however the classification does not correlate with structural similarity between repeats. Only 7 out of 21 repeats are recognized by InterPro/Pfam HMMs in hTLR5. The repeats identified often overlap in position across LRR subtypes and are inconsistent in length ranging from 19-59 with a mean of 30.5. For reference, manual length analysis showed a range of 20-36 with a mean of 25.9. The alignment of three consecutive repeats (498-560) with the central LxL pattern are highlighted on the bottom panel.

Article Snippet: As shown in , for the hTLR5 InterPro/Pfam HMMs ( ) needed 2, out of 16 defined in the database, different HMM models to recognize individual repeats, and even then, more than 1⁄2 of the repeats in most LRR proteins are still not recognized.

Techniques:

Journal: bioRxiv

Article Title: Divergence of the Individual repeats in the leucine-rich repeat domains of human Toll-like receptors explain their diversity and functional adaptations

doi: 10.1101/2024.09.30.615863

Figure Lengend Snippet: Thumbnail figures of the three-dimensional structures of human TLR 1-10, illustrating the distortions from the ideal solenoid structure (RNI). Local curvature moving averages (interval of three, see the Methods section) and repeat lengths are shown the boxes below. Full data available in the supplemental materials. AlphaFold models of the structures of hTLR5, hTLR6, hTLR9 and hTLR10 are shown, as no experimental structures were available as of this writing.

Article Snippet: As shown in , for the hTLR5 InterPro/Pfam HMMs ( ) needed 2, out of 16 defined in the database, different HMM models to recognize individual repeats, and even then, more than 1⁄2 of the repeats in most LRR proteins are still not recognized.

Techniques: