Journal: Scientific Reports

Article Title: High affinity nanobodies block SARS-CoV-2 spike receptor binding domain interaction with human angiotensin converting enzyme

doi: 10.1038/s41598-020-79036-0

Figure Lengend Snippet: Protein sequences for novel nanobodies that bind to the SARS-CoV-2 spike protein receptor binding domain. Single letter amino acid codes. Clustal Omega algorithm used for alignment. Blue highlights indicate sequence diversity with NIH-CoVnb-112, highlighted in gray, set as the reference sequence for comparison. For comparison, seven previously reported nanobody sequences have clearly distinct sequences: Ty1 , VHH72 , H11-D4 , MR3 , Sb#14 , Sb23 , and W25UACh and possess shorter CDR3 domains (represented in NIH-CoVnb-112 by amino acids 99–120).

Article Snippet: Sequences were trimmed to include only the VHH coding region and the protein coding sequences aligned using the Clustal Omega algorithm included in SnapGene software (GSL Biotech LLC).

Techniques: Binding Assay, Sequencing, Comparison

Journal: Microbiology Resource Announcements

Article Title: Whole-genome sequence of Psychrobacter sp. strain AH5, isolated from salted bluespot mullet ( Valamugil seheli )

doi: 10.1128/mra.00829-24

Figure Lengend Snippet: Neighbor-joining phylogenetic tree showing the placement of the strain Psychrobacter sp. AH5 within the genus. The nucleotide sequence was concatenated and subsequently aligned using Clustal Omega (v1.2.2, default settings) in Geneious Prime (Dotmatics, 2024.0.5). Bootstrap values are indicated at the nodes of the branches. The AH5 strain whose genome is reported in this announcement is highlighted in bold font.

Article Snippet: The phylogenetic tree was constructed with the neighbor-joining method using the Clustal Omega program (v1.2.2, default settings) in Geneious Prime (Dotmatics, 2024.0.5) and subsequently aligned using MUSCLE (v3.8.425).

Techniques: Sequencing

Journal: mBio

Article Title: Saccharomyces cerevisiae Requires CFF1 To Produce 4-Hydroxy-5-Methylfuran-3(2H)-One, a Mimic of the Bacterial Quorum-Sensing Autoinducer AI-2

doi: 10.1128/mBio.03303-20

Figure Lengend Snippet: Cff1p homologs restore MHF production to cff1Δ S. cerevisiae . (A) Light output from the V. harveyi TL-26 reporter strain in response to cell-free fluids from cff1Δ S. cerevisiae expressing CFF1 homologs from B. cinerea (green), T. versicolor (red), S. cerevisiae (black), and a vector control (gray). (B) Light output from the V. harveyi TL-26 reporter strain in response to cell-free fluids prepared from cff1Δ S. cerevisiae carrying the designated CFF1 homologs and alleles. The vector control is designated V. Cell-free fluids were added at 10% (vol/vol). (C) Alignment of putative Cff1p homologs, trimmed to the first and final amino acids of S. cerevisiae Cff1p. Only one species per genus is shown. Alignment was performed using Clustal Omega . Negatively charged residues are shown in red, small hydrophobic residues in orange, aromatic hydrophobic residues in yellow, polar uncharged residues in green, and positively charged residues in blue. Shown above the alignment are consensus sequences for regions containing amino acids that are conserved in >75% of the aligned proteins. Arrow designates location of conserved glutamate residue. RLU and Max AI-2 as in Fig. 1 . In A and B, error bars represent standard deviations of biological replicates, n = 3.

Article Snippet: These sequences were aligned using Clustal Omega ( ) in SnapGene software (GSL Biotech).

Techniques: Expressing, Plasmid Preparation