Journal: Cell reports

Article Title: Oxygen level regulates N-terminal translation elongation of selected proteins through deoxyhypusine hydroxylation

doi: 10.1016/j.celrep.2022.110855

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Methionine , Chem Impex , Cat# 00221-100G.

Techniques: Virus, Recombinant, Membrane

Journal: Cell reports

Article Title: Oxygen level regulates N-terminal translation elongation of selected proteins through deoxyhypusine hydroxylation

doi: 10.1016/j.celrep.2022.110855

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Methionine , Chem Impex , Cat# 00221-100G.

Techniques: Virus, Recombinant, Membrane

Journal: Cell reports

Article Title: Oxygen level regulates N-terminal translation elongation of selected proteins through deoxyhypusine hydroxylation

doi: 10.1016/j.celrep.2022.110855

Figure Lengend Snippet:

Article Snippet: Methionine , Chem Impex , Cat# 00221-100G.

Techniques:

Journal: Applied Microbiology and Biotechnology

Article Title: Comparative genomics of Streptococcus parauberis : new target for molecular identification of serotype III

doi: 10.1007/s00253-020-10683-z

Figure Lengend Snippet: Multiplex PCR products of S. parauberis strains. Lanes: MM, Generuler DNA ladder 1 kb (Fermentas); 1, (subserotype Ia); 2, subserotype Ib; 3, subserotype Ic; 4, serotype II; 5, serotype III; 6 and 7, non-typeable strains; 8, NCDO2020 (serotype IV)

Article Snippet: DNA isolated from pure cultures of the reference strain S. parauberis NCIMB 703043, which belongs to serotype III, was used as a positive control in qPCR reactions.

Techniques: Multiplex Assay

Journal: Applied Microbiology and Biotechnology

Article Title: Comparative genomics of Streptococcus parauberis : new target for molecular identification of serotype III

doi: 10.1007/s00253-020-10683-z

Figure Lengend Snippet: Determination of C q values obtained from the amplification of tenfold dilutions of a purified amplicon of the cps3K gene of the strain NCIMB 703043 obtained by qPCR

Article Snippet: DNA isolated from pure cultures of the reference strain S. parauberis NCIMB 703043, which belongs to serotype III, was used as a positive control in qPCR reactions.

Techniques: Amplification, Purification, Concentration Assay, Intra Assay, Inter Assay

Journal: Applied Microbiology and Biotechnology

Article Title: Comparative genomics of Streptococcus parauberis : new target for molecular identification of serotype III

doi: 10.1007/s00253-020-10683-z

Figure Lengend Snippet: Standard curves obtained by qPCR from the amplification of 10-fold dilutions of purified amplicon obtained using SP3-130F and SP3-130R primers and DNA from the reference strain S. parauberis NCIMB 703043 (black circles) and a clinical isolate of S. parauberis (SK451/04) (gray squares) ( a ) and the corresponding electrophoresis gel showing the band intensities correlating with the number of copies of the cps3K gene ( b ). Lanes: MM, Generuler DNA ladder 1-kb (Fermentas); 1, 2.67 × 10 8 copies; 2, 2.67 × 10 7 copies; 3, 2.67 × 10 6 copies; 4, 2.67 × 10 5 copies; 5, 2.67 × 10 4 copies; 6, 2.67 × 10 3 copies; 7, 2.67 × 10 2 copies

Article Snippet: DNA isolated from pure cultures of the reference strain S. parauberis NCIMB 703043, which belongs to serotype III, was used as a positive control in qPCR reactions.

Techniques: Amplification, Purification, Electrophoresis

Journal: Applied Microbiology and Biotechnology

Article Title: Comparative genomics of Streptococcus parauberis : new target for molecular identification of serotype III

doi: 10.1007/s00253-020-10683-z

Figure Lengend Snippet: Samples tested by qPCR for the detection of S. parauberis serotype III

Article Snippet: DNA isolated from pure cultures of the reference strain S. parauberis NCIMB 703043, which belongs to serotype III, was used as a positive control in qPCR reactions.

Techniques: Concentration Assay

Journal: Journal of Oral Microbiology

Article Title: Streptococcus tigurinus is frequent among gtfR -negative Streptococcus oralis isolates and in the human oral cavity, but highly virulent strains are uncommon

doi: 10.1080/20002297.2017.1307079

Figure Lengend Snippet: Primers and polymerase chain reaction conditions used in this study.

Article Snippet: DNA was extracted from S. oralis SN 16495, SN 17127, SN 28194, SN 31376, SN 37569, SN 37737, SN 39325, SN 40525, SN 45448, SN 48861, SN 50746, SN 51446, SN 54788, SN 58364, SN 58746, SN 59433, SN 60579, SN 63707, S. infantis SN 54787, SN 57625, SN 17128, SN 19640, ‘S. tigurinus’ SN 62386 (all proven and epidemiologically unrelated endocarditis isolates collected by the National Reference Center for Streptococci, Aachen), and from four S. tigurinus reference strains, including type strain AZ_3a, as well as small colony variants (2425, 2426) of parental strain 1366 [ ] kindly provided by A. Zbinden (Zürich).

Techniques: Polymerase Chain Reaction, Sequencing

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: Rapid and Accurate Species Identification of Mitis Group Streptococci Using the MinION Nanopore Sequencer

doi: 10.3389/fcimb.2020.00011

Figure Lengend Snippet: Heatmap of species-level read abundance based on WIMP and Kraken2 pipeline. Heatmaps show the species-level read abundance of simulation nanopore read sets for reference genomes in the RefSeq database. The species-level read abundance was calculated by WIMP (A) and Kraken2 pipeline (B) . Blue indicates low abundance, yellow indicates intermediate, and red indicates high. The results of the Kraken2 database showed the high species-level read abundance for species identified by multilocus sequence analysis (MLSA) among mitis group streptococci bacteria, whilst the results of WIMP showed low species-level read abundance for S. peroris, S. infantis, S. australis , and S. sinensis . S. p, S. pneumoniae ; S. pp, S. pseudopneumoniae ; S. m, S. mitis ; S. o, S. oralis ; S. pero, S. peroris ; S. infa, S. infantis ; S. aust, S. australis ; S. para, S. parasanguinis ; S. sine, S. sinensis ; S. sang, S. sanguinis ; S. gord, S. gordonii ; and S. cri, S. cristatus .

Article Snippet: In addition, to evaluate the specificity of the test, we tested 3 different reference strains isolated by the National BioResource Project ( http://www.nbrp.jp/ ) and the Global Bioresource Center ( https://www.atcc.org/ ), namely S. mitis (JNBP 05639), S. oralis (JNBP 08070), and S. pneumoniae (ATCC 49619).

Techniques: Sequencing

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: Rapid and Accurate Species Identification of Mitis Group Streptococci Using the MinION Nanopore Sequencer

doi: 10.3389/fcimb.2020.00011

Figure Lengend Snippet: Species-level read abundance based on WIMP and Kraken2 pipeline for clinical isolates and reference strains. The stacked bar graphs show the species-level read abundance in MinION sequencing reads (Kilian and Tettelin, ); abundance was calculated based on WIMP (A) and Kraken2 pipeline (B) . S. p, S. pneumoniae ; S. pp, S. pseudopneumoniae ; S. m, S. mitis ; S. o, S. oralis ; others , S. peroris, S. infantis, S. australis, S. parasanguinis, S. sinensis, S. sanguinis, S. gordonii, S. cristatus , and Streptococcus . sp.

Article Snippet: In addition, to evaluate the specificity of the test, we tested 3 different reference strains isolated by the National BioResource Project ( http://www.nbrp.jp/ ) and the Global Bioresource Center ( https://www.atcc.org/ ), namely S. mitis (JNBP 05639), S. oralis (JNBP 08070), and S. pneumoniae (ATCC 49619).

Techniques: Sequencing

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: Uncovering the link between the SpnIII restriction modification system and LuxS in Streptococcus pneumoniae meningitis isolates

doi: 10.3389/fcimb.2023.1177857

Figure Lengend Snippet: S. pneumoniae strains and oligonucleotide primers used in this study.

Article Snippet: The wildtype S. pneumoniae strains used in this study ( ) were provided to us by the German National Reference Center for Streptococci (Aachen) ( ).

Techniques: Sequencing, Mutagenesis

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: Uncovering the link between the SpnIII restriction modification system and LuxS in Streptococcus pneumoniae meningitis isolates

doi: 10.3389/fcimb.2023.1177857

Figure Lengend Snippet: spnIII allele frequencies of 60B and 60CSF recovered post intranasal murine infection. Mice were intranasally challenged with 10 8 CFU S. pneumoniae serotype 15C ST8711 blood isolate (60B) or CSF isolate (60CSF). At 24 h, mice from each group were humanely euthanized and pneumococci in the nasal tissue were harvested. spnIII allele quantification was performed on DNA extracted from the original inoculum and colonies grown from nasopharynx samples. Allele percentages for original inoculum and bacteria recovered from noses are represented. Statistical analysis was performed using two-way analysis of variance and a Tukey post-comparison test; *P < 0.05.

Article Snippet: The wildtype S. pneumoniae strains used in this study ( ) were provided to us by the German National Reference Center for Streptococci (Aachen) ( ).

Techniques: Infection, Bacteria, Comparison