Sequencing:Article Title: Visualizing translation dynamics at atomic detail inside a bacterial cell
Article Snippet: .. Bioinformatic sequence analysis of ribosomal proteins in M. pneumoniae and the comparison with E. coli homologues were performed as follows, with the different steps described in detail below: (i) protein sequences and RefSeq genome annotation for the M. pneumoniae strain M129 (ATCC 29342) were downloaded from NCBI; (ii) protein sequences were also annotated with eggNOG-mapper to obtain COG (Clusters of Orthologous Groups) IDs , ; (iii) for the annotated ribosomal proteins, the corresponding COG multiple sequence alignments from representative bacterial species were downloaded from the eggNOG database ; (iv) as M. pneumoniae M129 is not among the representative species, its protein sequences were added to the multiple sequence alignments with MAFFT software ; (v) for each COG multiple sequence alignment, the number of amino acids in every representative species (including M. pneumoniae M129) present at positions before the N terminus and after the C terminus positions of E. coli K-12 substr. ..
Article Title: Visualizing translation dynamics at atomic detail inside a bacterial cell
Article Snippet: .. Bioinformatic sequence analysis of ribosomal proteins in M. pneumoniae and the comparison with E. coli homologs, described in details in the Supplementary Methods, were performed as follows: i) protein sequences and RefSeq genome annotation for M. pneumoniae strain M129 (ATCC 29342) were downloaded from NCBI; ii) protein sequences were additionally annotated with eggNOG-mapper to obtain COG IDs (Clusters of Orthologous Groups) , ; iii) for the annotated ribosomal proteins, the corresponding COG multiple sequence alignments from representative bacterial species were downloaded from the eggNOG database ; iv) as M. pneumoniae M129 is not among the representative species, its protein sequences were added to the multiple sequence alignments with MAFFT software ; v) for each COG multiple sequence alignment, the number of amino acids in every representative species (including M. pneumoniae M129) present at positions before the N-terminus and after the C-terminus positions of E. coli K-12 substr. ..
Comparison:Article Title: Visualizing translation dynamics at atomic detail inside a bacterial cell
Article Snippet: .. Bioinformatic sequence analysis of ribosomal proteins in M. pneumoniae and the comparison with E. coli homologues were performed as follows, with the different steps described in detail below: (i) protein sequences and RefSeq genome annotation for the M. pneumoniae strain M129 (ATCC 29342) were downloaded from NCBI; (ii) protein sequences were also annotated with eggNOG-mapper to obtain COG (Clusters of Orthologous Groups) IDs , ; (iii) for the annotated ribosomal proteins, the corresponding COG multiple sequence alignments from representative bacterial species were downloaded from the eggNOG database ; (iv) as M. pneumoniae M129 is not among the representative species, its protein sequences were added to the multiple sequence alignments with MAFFT software ; (v) for each COG multiple sequence alignment, the number of amino acids in every representative species (including M. pneumoniae M129) present at positions before the N terminus and after the C terminus positions of E. coli K-12 substr. ..
Article Title: Visualizing translation dynamics at atomic detail inside a bacterial cell
Article Snippet: .. Bioinformatic sequence analysis of ribosomal proteins in M. pneumoniae and the comparison with E. coli homologs, described in details in the Supplementary Methods, were performed as follows: i) protein sequences and RefSeq genome annotation for M. pneumoniae strain M129 (ATCC 29342) were downloaded from NCBI; ii) protein sequences were additionally annotated with eggNOG-mapper to obtain COG IDs (Clusters of Orthologous Groups) , ; iii) for the annotated ribosomal proteins, the corresponding COG multiple sequence alignments from representative bacterial species were downloaded from the eggNOG database ; iv) as M. pneumoniae M129 is not among the representative species, its protein sequences were added to the multiple sequence alignments with MAFFT software ; v) for each COG multiple sequence alignment, the number of amino acids in every representative species (including M. pneumoniae M129) present at positions before the N-terminus and after the C-terminus positions of E. coli K-12 substr. ..
Software:Article Title: Visualizing translation dynamics at atomic detail inside a bacterial cell
Article Snippet: .. Bioinformatic sequence analysis of ribosomal proteins in M. pneumoniae and the comparison with E. coli homologues were performed as follows, with the different steps described in detail below: (i) protein sequences and RefSeq genome annotation for the M. pneumoniae strain M129 (ATCC 29342) were downloaded from NCBI; (ii) protein sequences were also annotated with eggNOG-mapper to obtain COG (Clusters of Orthologous Groups) IDs , ; (iii) for the annotated ribosomal proteins, the corresponding COG multiple sequence alignments from representative bacterial species were downloaded from the eggNOG database ; (iv) as M. pneumoniae M129 is not among the representative species, its protein sequences were added to the multiple sequence alignments with MAFFT software ; (v) for each COG multiple sequence alignment, the number of amino acids in every representative species (including M. pneumoniae M129) present at positions before the N terminus and after the C terminus positions of E. coli K-12 substr. ..
Article Title: Visualizing translation dynamics at atomic detail inside a bacterial cell
Article Snippet: .. Bioinformatic sequence analysis of ribosomal proteins in M. pneumoniae and the comparison with E. coli homologs, described in details in the Supplementary Methods, were performed as follows: i) protein sequences and RefSeq genome annotation for M. pneumoniae strain M129 (ATCC 29342) were downloaded from NCBI; ii) protein sequences were additionally annotated with eggNOG-mapper to obtain COG IDs (Clusters of Orthologous Groups) , ; iii) for the annotated ribosomal proteins, the corresponding COG multiple sequence alignments from representative bacterial species were downloaded from the eggNOG database ; iv) as M. pneumoniae M129 is not among the representative species, its protein sequences were added to the multiple sequence alignments with MAFFT software ; v) for each COG multiple sequence alignment, the number of amino acids in every representative species (including M. pneumoniae M129) present at positions before the N-terminus and after the C-terminus positions of E. coli K-12 substr. ..
Cell Culture:Article Title: Total Flavonoids from Camellia oleifera Alleviated Mycoplasma pneumoniae -Induced Lung Injury via Inhibition of the TLR2-Mediated NF-κB and MAPK Pathways
Article Snippet: .. Briefly, M. pneumoniae strain M129 (ATCC 29342) was cultured in PPLO broth (BD Biosciences) supplemented with 20% FBS, 0.25% glucose, 0.4% yeast extract (Oxoid), penicillin G (1000 U/mL), and phenol red (0.005%) at pH 7.6 and 37 °C for 5–7 days, until the pH indicator transitioned from red to orange. .. The M. pneumoniae pellet was obtained by centrifugation, resuspended in Tris-buffered saline with 1 mM ethylenediaminetetraacetic, and further dissolved by Triton X-114 (Solarbio, Beijing, China) to a final concentration of 2%.
Article Title: Total Flavonoids from Camellia oleifera Alleviated Mycoplasma pneumoniae -Induced Lung Injury via Inhibition of the TLR2-Mediated NF-κB and MAPK Pathways.
Article Snippet: .. Briefly, M. pneumoniae strain M129 (ATCC 29342) was cultured in PPLO broth (BD Biosciences) supplemented with 20% FBS, 0.25% glucose, 0.4% yeast extract (Oxoid), penicillin G (1000 U/mL), and phenol red (0.005%) at pH 7.6 and 37 ◦C for 5–7 days, until the pH indicator transitioned from red to orange. .. The M. Molecules 2023, 28, 7077 11 of 15 pneumoniae pellet was obtained by centrifugation, resuspended in Tris-buffered saline with 1 mM ethylenediaminetetraacetic, and further dissolved by Triton X-114 (Solarbio, Beijing, China) to a final concentration of 2%.
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