Journal: Frontiers in Chemistry

Article Title: Ligand and structure-based approaches for the exploration of structure–activity relationships of fusidic acid derivatives as antibacterial agents

doi: 10.3389/fchem.2022.1094841

Figure Lengend Snippet: The inhibition zone test of FA and its derivatives against bacterial strains.

Article Snippet: S. aureus (ATCC 6538), S. albus (ATCC 29213), S. epidermidis (ATCC 12228), S. typhimurium (CMCC 50115), and E. coli (CMCC 44102) were cultured in a liquid medium, Mueller–Hinton Agar (MHA), at 37°C.

Techniques: Inhibition

Journal: Frontiers in Chemistry

Article Title: Ligand and structure-based approaches for the exploration of structure–activity relationships of fusidic acid derivatives as antibacterial agents

doi: 10.3389/fchem.2022.1094841

Figure Lengend Snippet: MICs of FA and its derivatives against the bacterial strains.

Article Snippet: S. aureus (ATCC 6538), S. albus (ATCC 29213), S. epidermidis (ATCC 12228), S. typhimurium (CMCC 50115), and E. coli (CMCC 44102) were cultured in a liquid medium, Mueller–Hinton Agar (MHA), at 37°C.

Techniques:

Journal: Microbiology Spectrum

Article Title: Microbiome Alterations Driven by Trypanosoma cruzi Infection in Two Disjunctive Murine Models

doi: 10.1128/spectrum.00199-23

Figure Lengend Snippet: Functional analysis from metagenomic data. The main results were obtained by Humann3, and the R package, Maaslin2, using a multivariate mixed-effects model. (a and d) Metabolic pathways involving genes with differential abundances between infected and noninfected mice for BALB/c (a) and C57BL/6 (d) mice. Heatmaps were created with MicrobioSee using Ward’s linkage method for hierarchical cluster analysis. The metabolic pathways to which the different processes belong are represented by different colored dots indicated in the legend. (b) Abundance of reads related to the superpathway of fatty acid biosynthesis as observed for noninfected (NI) and infected BALB/c mice. A Student t test was used to compare these groups. (c) Bar plot obtained from HUMAnN 3.0 for butyrate kinase that was modified in terms of abundance of reads during T. cruzi infection. The figure includes the regrouping of bacterial species and the classification of the samples by evaluation point. *, P < 0.05. BALB/c infected mice, n = 5; BALB/c noninfected mice, n = 5; C57BL/6 infected mice, n = 5; C57BL/6 noninfected mice, n = 5.

Article Snippet: The Trypanosoma cruzi strain Tulahuen (ATCC 30208), a discrete typing unit (DTU) VI, was used for infection experiments.

Techniques: Functional Assay, Infection, Modification

Journal: bioRxiv

Article Title: Proximity-dependent biotinylation and identification of flagellar proteins in Trypanosoma cruzi

doi: 10.1101/2023.02.16.528900

Figure Lengend Snippet: ( A ) Live confocal images of SMP1-1-GFP localized to the flagellum of T. cruzi epimastigotes and an intracellular amastigote; white oval denotes position of amastigote body. ( B ) Strategy for generating stable T. cruzi lines expressing TurboID in the flagellum using SMP1-1 as the endogenous bait protein or in the cytoplasm of epimastigotes and amastigotes, where addition of exogenous biotin will mediate biotinylation (red star) of proteins in close proximity to TurboID in both settings. FLAG-epitope is included to facilitate TurboID localization in transfectants. ( C ) Flow chart outlining the experimental protocol used for identification of biotinylated proteins in epimastigotes ( left ) and intracellular amastigotes ( right ). For both life stages, wild-type (‘WT’ ), cytoplasmic-TurboID (‘ C’ ) and flagellar-TurboID (‘ F’ ) parasites (from left to right in the illustration) were exposed to biotin and the biotinylated protein fraction in protein lysates captured on streptavidin-agarose beads and subjected to mass spectrometry for identification and subsequent proteomic analysis.

Article Snippet: Trypanosoma cruzi Tulahuén LacZ clone C4 was obtained from the American Type Culture Collection (ATCC, PRA-330; ATCC, Manassas, Virginia, USA).

Techniques: Expressing, FLAG-tag, Mass Spectrometry

Journal: bioRxiv

Article Title: Proximity-dependent biotinylation and identification of flagellar proteins in Trypanosoma cruzi

doi: 10.1101/2023.02.16.528900

Figure Lengend Snippet: ( A,C ) Fluorescence microscopy images of fixed T. cruzi epimastigotes ( A ) or amastigotes ( C ) expressing SMP1-1-FLAG-TurboID (F-Turbo) ( top ) or FLAG-TurboID (C-Turbo) ( bottom ) stained for FLAG epitope (anti-FLAG)( pink ). In ( C ), white arrows indicate the position of the amastigote flagellum. ( B,D ) Biotinylated proteins in lysates of WT, F-Turbo, and C-Turbo T. cruzi epimastigote ( B ) and amastigotes ( D ) detected with streptavidin-Dylight800.

Article Snippet: Trypanosoma cruzi Tulahuén LacZ clone C4 was obtained from the American Type Culture Collection (ATCC, PRA-330; ATCC, Manassas, Virginia, USA).

Techniques: Fluorescence, Microscopy, Expressing, Staining, FLAG-tag

Journal: bioRxiv

Article Title: Proximity-dependent biotinylation and identification of flagellar proteins in Trypanosoma cruzi

doi: 10.1101/2023.02.16.528900

Figure Lengend Snippet: Principal component analysis (PCA) of biotinylome data plotted for WT ( no TurboID control ), flagellar-TurboID ( F-Turbo ) and cytosolic-TurboID ( C-Turbo ) for T. cruzi epimastigotes ( A ) and intracellular amastigotes ( C ). The two independent F-Turbo groups in the epimastigote PCA plot are represented in green (triangles and squares). Volcano plots ( B,D ) with fold-change (F-Turbo vs C-Turbo; x-axis) and adjusted p-value (q-value; y-axis) for T. cruzi epimastigote ( B ) and amastigote ( D ) proteomic data. Horizontal lines represent a q-value of 0.01 and the two vertical lines indicate the cut-offs for fold change (2-fold). The top right quadrants in each plot ( B,D ) contain proteins that are significantly enriched in F-Turbo proteomes (q<0.01, >2-fold change). Known trypanosomatid flagellar proteins ( purple circles) and hypothetical proteins (green circles ) are shown for the F-Turbo enriched proteins. ( E ) Venn diagram depicting the number of proteins identified as enriched in the F-Turbo samples of T. cruzi epimastigote and amastigote stages. (F ) Interpro domains assigned by DAVID that are significantly enriched in F-Turbo samples (i.e. proteins found in the upper right quadrant of each volcano plot) in epimastigotes, amastigotes and those common to both life stages; p -value is a modified Fisher exact, for protein enrichment analysis.

Article Snippet: Trypanosoma cruzi Tulahuén LacZ clone C4 was obtained from the American Type Culture Collection (ATCC, PRA-330; ATCC, Manassas, Virginia, USA).

Techniques: Modification, Protein Enrichment

Journal: bioRxiv

Article Title: Proximity-dependent biotinylation and identification of flagellar proteins in Trypanosoma cruzi

doi: 10.1101/2023.02.16.528900

Figure Lengend Snippet:

Article Snippet: Trypanosoma cruzi Tulahuén LacZ clone C4 was obtained from the American Type Culture Collection (ATCC, PRA-330; ATCC, Manassas, Virginia, USA).

Techniques:

Journal: bioRxiv

Article Title: Proximity-dependent biotinylation and identification of flagellar proteins in Trypanosoma cruzi

doi: 10.1101/2023.02.16.528900

Figure Lengend Snippet: Endogenous tagging reveals flagellar localization of candidate flagellar proteins: calpain 1.3-smFLAG (TcCLB.506563.200), CARP3-smFLAG (TcCLB.506681.40), or hypothetical protein-FLAG (TcCLB.510329.180) in T. cruzi epimastigotes ( A ) or intracellular amastigotes ( B ).In all cases, the FLAG tag was detected in fixed parasites using an anti-FLAG antibody and secondary antibody ( green ) and the flagellum was detected using anti-FCaBP and secondary antibody ( magenta ). The FLAG signal in the flagellum is indicated ( yellow arrow ).

Article Snippet: Trypanosoma cruzi Tulahuén LacZ clone C4 was obtained from the American Type Culture Collection (ATCC, PRA-330; ATCC, Manassas, Virginia, USA).

Techniques: FLAG-tag