Journal: Journal of molecular evolution

Article Title: Early Divergence of the C-Terminal Variable Region of Troponin T via A Pair of Mutually Exclusive Alternatively Spliced Exons Followed by A Selective Fixation in Vertebrate Heart

doi: 10.1007/s00239-022-10075-z

Figure Lengend Snippet: The phylogenetic tree of amino acid sequences of Drosophila exons 10A- and 10B-like mutually exclusive exon pairs of arthropod TnT with exon 16 and exon 17 of representative vertebrate fast TnT genes and the ancestral exon (exon 11) of C. elegans TnT as references constructed with maximum-likelihood method using MegAlign Pro software demonstrates the emergence of this mechanism early before the divergence of vertebrates and invertebrates. Gap penalty was set at 30. The numbers above the branches are percentage bootstrap values for the associated nodes. NA: No bootstrap value, indicating a poor support of the branch. The colors of fonts indicate exon 16-like (Blue), exon 17-like (Red), cardiac (Purple) and slow (Green) isoforms. While crustacean and insect TnTs have both evolved with the paired mutually exclusive alternatively spliced exons, the insect exons have clearly diverged into Drosophila 10A-like and Drosophila 10B-like. The evolutionary linage also indicates that exon 16 of vertebrate fast skeletal muscle TnT and Drosophila 10A-like exon in arthropod TnT are more closely related to the ancestral exon (exon 11) of C. elegans tnt-3 gene. Accession numbers of the sequences analyzed are listed in Supplement Table S2.

Article Snippet: Phylogenetic analysis Amino acid sequence alignments were done with DNAStar Lasergene MegAlign Pro software (Lasergene, Inc, Madison, WI) using ClustalW method.

Techniques: Construct, Software

Journal: Journal of molecular evolution

Article Title: Early Divergence of the C-Terminal Variable Region of Troponin T via A Pair of Mutually Exclusive Alternatively Spliced Exons Followed by A Selective Fixation in Vertebrate Heart

doi: 10.1007/s00239-022-10075-z

Figure Lengend Snippet: The phylogenetic tree of amino acid sequences of exon 16 and exon 17 of representative vertebrate fast TnT genes and counterpart exons of vertebrate cardiac and slow TnT genes constructed with maximum-likelihood method using DNAStar MegAlign Pro software demonstrates their phylogenetic lineages with exons 10A and 10B of Drosophila TpnT gene as references. Gap penalty was set at 30. The numbers below the branches are percentage bootstrap values for the associated nodes. NA: No bootstrap value, indicating a poor support of the branch. The colors of fonts indicate exon 16-like (Blue), exon 17-like (Red), cardiac (Purple) and slow (Green) isoforms. The exon of vertebrate cardiac TnT gene that emerged from duplication of the fast skeletal muscle TnT gene (Chong and Jin 2009) shows closer relationship to the exon 17 of fast TnT gene, indicating the selective fixation of one of the inherited alternative exons in vertebrate heart, which was conserved in vertebrate slow TnT gene duplicated from the cardiac gene (Chong and Jin 2009). The pattern of divergence further indicates that this structure in cardiac TnT has diverged further while it is more conserved in slow TnT. Accession numbers of the sequences analyzed are listed in Supplement Table S2.

Article Snippet: Phylogenetic analysis Amino acid sequence alignments were done with DNAStar Lasergene MegAlign Pro software (Lasergene, Inc, Madison, WI) using ClustalW method.

Techniques: Construct, Software

Journal:

Article Title: Involvement of an Inducible Fructose Phosphotransferase Operon in Streptococcus gordonii Biofilm Formation

doi: 10.1128/JB.185.21.6241-6254.2003

Figure Lengend Snippet: (A) Alignment of the promoter region of S. gordonii fruR with the fruR homologs in S. pneumoniae (accession no. NP345362), S. mitis, S. mutans (accession no. NC004350), S. pyogenes (accession no. 002737), and S. agalactiae (accession no. NC004116) determined by using the AlignX program in the Vector NTI software (Informax). Streptococcal sequences without accession numbers were obtained from the unfinished microbial genome database (www.ncbi.nlm.nih.gov). Nucleotides that are identical and conserved are indicated by dark grey and light grey backgrounds, respectively, and start codons are enclosed in boxes. In S. gordonii, direct repeat regions (DR) are indicated by horizontal arrows, while the CRE, putative ribosome binding site (rbs), putative −35, and putative −10 regions are underlined. (B) Phylogenetic tree of S. gordonii FruR and other bacterial sugar PTS regulatory proteins. The phylogenetic relatedness dendrogram was constructed on the basis of amino acid sequence similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm (32). The reliability of the topology was estimated by performing 100 bootstrap trials, and the bootstrap values are expressed in percentages at branch points (www.genebee.msu.su). Accession numbers follow the species names, and sequences without accession numbers were obtained from the unfinished microbial genome sequence database (www.ncbi.nlm.nih.gov).

Article Snippet: The phylogenetic relatedness dendrogram was constructed on the basis of amino acid sequence similarities by using the AlignX program in the Vector NTI software (Informax Inc.), which utilizes the neighbor-joining algorithm ( 32 ).

Techniques: Plasmid Preparation, Software, Binding Assay, Construct, Sequencing

Journal: Scientific Reports

Article Title: Comparative proteomic analysis of edible bird’s nest from different origins

doi: 10.1038/s41598-023-41851-6

Figure Lengend Snippet: Quantitative analysis of EBN’s proteins. ( A ) Scatter diagram of Protein concentration ranged by iBAQ intensity from low to high. Protein was detected in all samples marked with black, and protein was detected in some samples marked with gray. ( B ) Scatter diagram of protein concentration and the difference between samples. Proteins with disulfide bonds were highlighted in blue. ( C – E ) Histogram of the iBAQ intensity of CHIA, KRT4, and PIGR in EBN samples. ( F , G ) Principal component analysis based on protein composition and quantitation. A, B, C, and D refer to Grass EBN , Imperial EBN , White EBN , and Feather EBN respectively. ( H ) Hierarchical clustering based on label-free proteome quantification. The size of the dots below refers to the iBAQ intensity of each detection. A1/A2/A3, B1/B2/B3, C1/C2/C3 and D1/D2/D3 refer to N = 3 per group.A1/A2/A3, B1/B2/B3, C1/C2/C3 and D1/D2/D3 represent Grass EBN, Imperial EBN, White EBN and Feather EBN in that order.

Article Snippet: Briefly, protein sequences were done BLAST against Gallus gallus 's reference proteome (proteome id: UP000000539_9031, with swiss-prot’s annotation) and the best match with e-value under 10 –5 was chosen as the homologous reference proteins.

Techniques: Protein Concentration, Quantitation Assay