Journal: Viruses

Article Title: Isolation and Characterization of Contemporary Bovine Coronavirus Strains

doi: 10.3390/v16060965

Figure Lengend Snippet: Sample information and RT-qPCR results 1 .

Article Snippet: The whole genome sequence (WGS) of the BC18 strain was obtained using conventional PCR with multiple primers (shown in ) followed by Sanger sequencing at the Comprehensive Cancer Center of The Ohio State University or Oxford nanopore sequencing at Plasmidsaurus ( https://www.plasmidsaurus.com/ , accessed on 25 April 2024).

Techniques:

Journal: Viruses

Article Title: Isolation and Characterization of Contemporary Bovine Coronavirus Strains

doi: 10.3390/v16060965

Figure Lengend Snippet: Analysis of the S protein amino acid variations between four pairs of respiratory strains and enteric strains (each pair of samples was from the same animal. E: strains from enteric samples, R: strain from respiratory samples).

Article Snippet: The whole genome sequence (WGS) of the BC18 strain was obtained using conventional PCR with multiple primers (shown in ) followed by Sanger sequencing at the Comprehensive Cancer Center of The Ohio State University or Oxford nanopore sequencing at Plasmidsaurus ( https://www.plasmidsaurus.com/ , accessed on 25 April 2024).

Techniques:

Journal: Viruses

Article Title: Isolation and Characterization of Contemporary Bovine Coronavirus Strains

doi: 10.3390/v16060965

Figure Lengend Snippet: The 3D structural analyses of the predicted S protein trimers of BCoV strains using protein structure prediction software online ( https://swissmodel.expasy.org/ , accessed on 25 April 2024). The surface model used BC8 and LUN strains as templates and the stick model used all corresponding strains to predict. The location of amino acid residue 617 in the predicted S protein trimer is shown in blue and red in the detailed stick model for Iso 617 in the BC8-E strain and yellow for Thr 617 in the BC18-R strain ( A ). The location of amino acid residue 960 in the predicted S protein trimer is shown in orange, the detailed stick model for Pro 960 in the BC8-E strain is shown in brown, and Leu 960 in the BC18-R strain is shown in purple ( B ). The location of amino acid residue 1180 in the predicted S protein trimer is shown in white, the detailed stick model for Asp 1180 in the BC8-E, AH65-E, ENT-E, and AH187-E strains is shown in black, and Gly 1180 in the AH65-R, LUN-R, and AH187-R strains is shown in a warm pink color ( C ).

Article Snippet: The whole genome sequence (WGS) of the BC18 strain was obtained using conventional PCR with multiple primers (shown in ) followed by Sanger sequencing at the Comprehensive Cancer Center of The Ohio State University or Oxford nanopore sequencing at Plasmidsaurus ( https://www.plasmidsaurus.com/ , accessed on 25 April 2024).

Techniques: Software, Residue

Journal: Heliyon

Article Title: The gut microbiome–Does stool represent right?

doi: 10.1016/j.heliyon.2023.e13602

Figure Lengend Snippet: Comparison of the microbial community diversity of inner-colonic effluent samples collected during high-volume colon irrigation and home-collected stool samples. A. Alpha diversity of microbial strains based on 16S rRNA sequencing and ASV analysis. Left: Stool samples (n = 11) compared to combined data from all effluent samples (n = 35). Right: Comparison between stool (n = 11) and the three different effluent sample types, where: descending (left) colon, “Effluent-1”, n = 13; transverse colon, “Effluent-2”, n = 11; and, ascending (right) colon “Effluent-3”, n = 11. B. Alpha diversity of bacterial strains detected in whole genome sequencing. Sample types are: Stool, n = 20; Descending (left) colon, “Effluent-1”, n = 22; transverse colon, “Effluent-2”, n = 20; and ascending (right) colon (“Effluent-3”) n = 20. For both A and B, Results are presented as Shannon index. NS indicates p > 0.05; *p ≤ 0.05, **p ≤ 0.01; ***p ≤ 0.001, and ****p ≤ 0.0001. C and D. Beta diversity based on 16S rRNA sequencing and ASV analysis and represented by PCoA weighted Unifrac analysis. Inner-colonic effluent samples are represented in the different panels both as combined (C, n = 35) and separated into three inner-colonic sample types (D), representing the ascending (left) colon, “Effluent-1”, n = 13; transverse colon, “Effluent-2”, n = 11; and descending (right) colon, “Effluent-3”, n = 11. For stool samples, n = 11. E. Beta diversity based on whole genome sequencing and represented by PCoA with Bray-Curtis distances where: descending (left) colon, “Effluent-1”, n = 22; transverse colon, “Effluent-2” n = 20; and ascending (right) colon, “Effluent-3”, n = 20. For stool samples, n = 20.

Article Snippet: Overall, 20 stool samples and 62 colon effluent samples were collected and sent for 16S rRNA amplicon sequencing at Microbiome Insights Inc. (Vancouver, Canada) and whole genome sequencing (WGS) at SeqMatic (Fremont, CA, USA).

Techniques: Sequencing

Journal: Genome Research

Article Title: Unraveling the hidden complexity of cancer through long-read sequencing

doi: 10.1101/gr.280041.124

Figure Lengend Snippet: Summary of software tools for analyzing long reads in cancer

Article Snippet: A more specific study comparing optical maps of breast cancer cell line SKBR3 with long-read whole-genome sequencing (LR-WGS) found that 74% of insertions and 80% of deletions detected with Bionano can be confirmed with PacBio and ONT, but lower concordance for inversions and duplications ( ).

Techniques: Software, Variant Assay, Sequencing, Methylation, DNA Methylation Assay, RNA modification