Journal: Scientific Reports

Article Title: Novel gene similar to nitrite reductase (NO forming) plays potentially important role in the latency of tuberculosis

doi: 10.1038/s41598-021-99346-1

Figure Lengend Snippet: ( A – B ) Identification of conserved domains of genes in Mycobacterium tuberculosis ( A ) Conserved sequences obtained after alignment of gene sequences coding for nitrite reductase of different bacteria by ClustalW2 software ( http://www.ebi.ac.uk/Tools/msa/clustalo/ ). ( B ) Gene sequences containing conserved domain Cu-oxidase and Cu-oxidase-3 of Mtb H37Ra nitrite reductase. Data was extracted from CD search software.

Article Snippet: The TOF/TOF mass spectra analysis of the purified protein was compared with the genome database of Mtb H37Ra from UniProt and the protein band was identified as Polyphenol oxidase OS Mtb strain ATCC 25,177 H37Ra OX 419,947 GN yfiH PE 3 with a molecular weight of 26 kDa (identified as MRA2164 ) (Table ) and peptide sequence was provided in Table .

Techniques: Bacteria, Software

Journal: PLoS ONE

Article Title: Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome

doi: 10.1371/journal.pone.0122979

Figure Lengend Snippet: Arrow heads indicate the variably sized products in ATCC H37Ra and ATCC H37Rv genomes. Gene 4 and Gene 8 shares partial homology with laboratory strains and showed the presence of a differently sized product in ATCC H37Rv and ATCC H37Ra. (B) The alignment of Gene 4 against reference genomes showed an insertion of 175bp sequence in Gene 4 of OSDD strains with respect to reference strains. (C) The alignment of Gene 8 against reference genomes showed a deletion of 1,352bp sequence in Gene 8 of OSDD strains.

Article Snippet: Detailed insights into the genomic loci of Gene 4 alignment with reference strains showed partial overlapping of Gene 4 with hypothetical proteins in Mtb ATCC H37Rv and Mtb ATCC H37Ra thereby resulting in the formation of differentially sized gene products (Figures A and B in ).

Techniques: Sequencing

Journal: PLoS ONE

Article Title: Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome

doi: 10.1371/journal.pone.0122979

Figure Lengend Snippet: Summary of gene clusters absent from Mtb ATCC H37Ra and Mtb ATCC H37Rv.

Article Snippet: Detailed insights into the genomic loci of Gene 4 alignment with reference strains showed partial overlapping of Gene 4 with hypothetical proteins in Mtb ATCC H37Rv and Mtb ATCC H37Ra thereby resulting in the formation of differentially sized gene products (Figures A and B in ).

Techniques:

Journal: medRxiv

Article Title: A Streamlined Point-of-Care CRISPR Test for Tuberculosis Detection Directly from Sputum

doi: 10.1101/2025.02.19.25322517

Figure Lengend Snippet: A. Cas13a detecting BCG genomic DNA spiked into sputum:TE matrix and Cas12a detecting internal control. Sp is sputum and gBCG is genomic BCG. Units are genomes/µL. Cas13a reporter is FAM and Cas12a reporter is HEX. B. Comparison of fresh Cas13a (left) or lyophilizer Cas13a (right) assays detecting synthetic internal control (IC) and BCG genome. Synthetic targets were mixed at a concentration of 10 4 and 10 3 copies/µL, respectively. C. Lateral Flow read-out of Cas13a detecting dual targets IS6110+IS1081 (top) and Cas12a detecting internal control (bottom) in BCG spiked into sputum:TE matrix. Appearance of the top line is a positive readout. Faint lines are interpreted as negative. Disappearance of the bottom line is not necessary. D. Range finding experiment demonstrating the dynamic range of fresh Cas13a dual detection assay. Cas13a detecting BCG and Cas12a detecting internal control. BCG culture (left) and BCG spiked into sputum:TE (right). gBCG is genomic BCG and units are genomes/µL. All other units are CFU/mL. E. Testing fresh Cas13a and Cas12a coupled assay against TB-negative clinical sputum samples. Numbers indicate patient number. F. Limit of detection (LoD) for H37Rv. LOD = 69.0 (51.0 – 86.9). G. Limit of detection (LoD) for BCG. LOD = 80.5 (59.4 – 101.6). In A, B, D, and E, error bars: SD based on n=3 technical replicates. C shows a single representative sample. F (N=20) and G (N=21), was plotted using ggplot2 in R.

Article Snippet: Quantitative Mtb genomic DNA was ordered from ATCC (25177DQ).

Techniques: Control, Comparison, Concentration Assay, Detection Assay

Journal: International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

Article Title: Mycobacterium tuberculosis sterilizing activity of faropenem, pyrazinamide and linezolid combination and failure to shorten the therapy duration

doi: 10.1016/j.ijid.2021.01.062

Figure Lengend Snippet: Mycobacterium tuberculosis time-to-positive and kill curves in the HFS-TB. (A) On day 56, except the ZL two-drug combination, there was no growth unit recorded by the mycobacterial growth tube indicator system (MGIT) machine in any of the hollow fiber model of tuberculosis (HFS-TB) units treated with any of the FZL experimental regimens as well as the standard therapy, hence sterilization. (B) As opposed to the TTP results, there was no Mtb colony recorded on agar plates inoculated with samples from the HFS-TB treated with the ZL combination. However, the bacterial burden could have simply been below the limits of detection (0.69 log 10 CFU/mL) because MGIT liquid culture is more sensitive than solid agar culture. All three FZL combinations as well as the standard therapy sterilized the HFS-TB by day 28. Abbreviations: HFS-TB, hollow fiber model of tuberculosis; F, faropenem; Z, pyrazinamide; L, linezolid; TTP, time-to-positive; ZL, two-drug combination; F 1 ZL, F administered once daily plus ZL; F 2 ZL, F administered twice-daily plus once daily ZL; F 2 Z hi L, F 2 ZL with high-dose Z.

Article Snippet: The Mycobacterium tuberculosis ( Mtb ) laboratory strain H37Ra (ATCC #25177) was used in the experiments, with culture media and bacterial growth conditions described in previous publications ( ; ).

Techniques: