t denticola atcc 35405 t genomic dna  (ATCC)

Journal: Microbiology Spectrum

Article Title: Functional Characterization of Small Alarmone Synthetase and Small Alarmone Hydrolase Proteins from Treponema denticola

doi: 10.1128/spectrum.05100-22

Figure Lengend Snippet: Domain structure and conserved motifs within Treponema denticola encoding putative small alarmone synthetase (Tde-SAS). (A) Schematic diagram showing the domain structure and conserved motifs present within Tde-SAS and Tde-SAS 1–246 (N-terminal catalytic domain). (B) Sequence alignment of the four tetratricopeptide repeat (TPR) motifs (TPR1 to TPR4) in the C-terminal TPR domain of Tde-SAS, indicating their respective start and end positions, as identified by TPRpred . (C) Predicted structural arrangement of the four TPR motifs within the Tde-SAS TPR domain (prepared using SwissModel ). The tandem array of four TPR motifs generates a right-handed superhelical structure, with the region immediately C-terminal to TPR4 (colored dark orange/red) forming an extended α-helix. (D) Multiple sequence alignment of the catalytic domain of Tde-SAS (residues 1 to 228 shown) with diverse SAS proteins: C. glutamicum RelS (RelS Cg ; CgRelS), S. aureus RelP/SAS2 (SaRelP), B. subtilis RelP/Ywac/SAS2 (BsRelP), S. aureus RelQ/SAS1 (SaRelQ), and B. subtilis RelQ/YjbM/SAS1 (BsRelQ). The four respective “synthesis” Syn motifs (Syn1 to Syn4) are indicated with brackets. The figure was prepared using ESPript 3.0 .

Article Snippet: The Tde-SAS (TDE_RS08190, formerly TDE1711) and Tde-SAH (TDE_RS08100, formerly TDE1690) genes were PCR amplified from T. denticola ATCC 35405 T genomic DNA and cloned into pET28a (+) (Novagen, Merck Millipore) via BamHI/XhoI to create plasmids pET28a-Tde-SAS and pET28a-Tde-SAH, respectively (Table S1).

Techniques: Sequencing

Journal: PLoS ONE

Article Title: Metagenomic Analysis Reveals Presence of Treponema denticola in a Tissue Biopsy of the Iceman

doi: 10.1371/journal.pone.0099994

Figure Lengend Snippet: Assignment of bacterial rRNA reads of the Icemańs metagenome to different genera and pre-selection of human pathogenic or opportunistic pathogenic bacteria according to the NCBI Genome Project database ( ftp://ftp.ncbi.nih.gov/genomes/genomeprj_archive/lproks_0.txt ).

Article Snippet: For the Treponema denticola ATCC 35405 genome (NCBI GenBank accession AE017226.1), to which most of the Treponema -specific reads were most similar, contiguous consensus sequences were extracted using the mpileup command implemented in samtools .

Techniques:

Journal: PLoS ONE

Article Title: Metagenomic Analysis Reveals Presence of Treponema denticola in a Tissue Biopsy of the Iceman

doi: 10.1371/journal.pone.0099994

Figure Lengend Snippet: ( A ) Human reference genome (ENA Experiment Accession No.: ERX008207) ( B ) Human reads of the Iceman metagenome (ENA Study Accession No.: ERP001144) ( C ) Validated T. denticola reads from the Iceman metagenome. Grey lines indicate all possible misincorporations; G-to-A and C-to-T misincorporations are plotted in blue and red, respectively. The green lines display all possible variants of a nucleotide-to-gap position.

Article Snippet: For the Treponema denticola ATCC 35405 genome (NCBI GenBank accession AE017226.1), to which most of the Treponema -specific reads were most similar, contiguous consensus sequences were extracted using the mpileup command implemented in samtools .

Techniques:

Journal: PLoS ONE

Article Title: Metagenomic Analysis Reveals Presence of Treponema denticola in a Tissue Biopsy of the Iceman

doi: 10.1371/journal.pone.0099994

Figure Lengend Snippet: ( A ) PCR assay targeting the 16S rRNA gene of T. denticola . ( B ) PCR assay targeting the repetitive element IS1126 of Porphyromonas gingivalis . All assays include a PCR negative control (3) and a PCR of the DNA extraction blank (4).

Article Snippet: For the Treponema denticola ATCC 35405 genome (NCBI GenBank accession AE017226.1), to which most of the Treponema -specific reads were most similar, contiguous consensus sequences were extracted using the mpileup command implemented in samtools .

Techniques: Negative Control, DNA Extraction