Journal: The Journal of Biological Chemistry

Article Title: A brain-gut excitatory peptide/CCHamide homolog regulates satiation and motivational state transitions in the Aplysia feeding circuit

doi: 10.1016/j.jbc.2026.111257

Figure Lengend Snippet: Gene expression mapping and cloning of the Aplysia EP/CCHa precursor . A , a genome sequence from Aplysia Tools (HiC_scaffold_6:45471172–46843127) transcribes an mRNA (TRINITY_DN9791_c1_g1_i6). It encodes a previously uncharacterized protein, which is similar to EP/CCHa from other lophotrochozoans. B , a PCR product for apEP/CCHa precursor (apEP/CCHa pre) gene with a length of 426 bp. Lane 1: DNA marker (M); Lane 2 and lane 3: the target gene. C , the complete protein sequence of apEP/CCHa precursor illustrating the signal peptide ( green ) and a predicted peptide ( red ). The predicted mature peptide undergoes two post-translational modifications: amidation of the terminal glycine residue at the C-terminus ( purple ) and the formation of a disulfide bond between the two cysteine residues ( blue ). The dibasic cleavage site (KR) is highlight in yellow .

Article Snippet: A , comparison of selected EP/CCHa peptides from protostomes using BioEdit (ClustalW Multiple Alignments-Graphic View).

Techniques: Gene Expression, Cloning, Sequencing, Marker, Residue

Journal: The Journal of Biological Chemistry

Article Title: A brain-gut excitatory peptide/CCHamide homolog regulates satiation and motivational state transitions in the Aplysia feeding circuit

doi: 10.1016/j.jbc.2026.111257

Figure Lengend Snippet: Comparison of EP/CCHa peptides from protostomes . A , comparison of selected EP/CCHa peptides from protostomes using BioEdit (ClustalW Multiple Alignments-Graphic View). “#” indicates that the peptide has been verified. B , a frequency plot for these sequences using Weblogo v2.8.2 ( http://weblogo.berkeley.edu/logo.cgi ). C-terminal amidation and the formation of a disulfide bond between two cysteine residues are highly conserved across protostome species. See for the information about the sequences. -S-S-: disulfide bridge; -NH 2 : the C-terminal amidation. Note that EP/CCHa peptides purified and chemically identified from Eisenia foetida and Pheretima vittata are the only ones characterized by non-amidated C-termini.

Article Snippet: A , comparison of selected EP/CCHa peptides from protostomes using BioEdit (ClustalW Multiple Alignments-Graphic View).

Techniques: Comparison, Purification

Journal: The Journal of Biological Chemistry

Article Title: A brain-gut excitatory peptide/CCHamide homolog regulates satiation and motivational state transitions in the Aplysia feeding circuit

doi: 10.1016/j.jbc.2026.111257

Figure Lengend Snippet: Distribution of peripheral apEP/CCHa-positive cells . A , the esophagus and posterior buccal cavity (pharynx) lining, with the luminal side facing upward. B and C , EP/CCHa-positive cells ( arrows ) in the esophagus and pharynx, anterior to DLF. B , bright-field view and C , fluorescent view showing immunostaining. D , caudal crop and stomatogastric ring, shown with the outside surface facing upward. E , two large apEP/CCHa-positive neurons and positive fibers in the stomatogastric ring. DLF: Dorsal longitudinal fold, D: dorsal, V: ventral, A: anterior, P: posterior. Images were taken from a light fluorescent microscope, except panels B and C , which were taken from a confocal microscope.

Article Snippet: A , comparison of selected EP/CCHa peptides from protostomes using BioEdit (ClustalW Multiple Alignments-Graphic View).

Techniques: Immunostaining, Microscopy

Journal: The Journal of Biological Chemistry

Article Title: A brain-gut excitatory peptide/CCHamide homolog regulates satiation and motivational state transitions in the Aplysia feeding circuit

doi: 10.1016/j.jbc.2026.111257

Figure Lengend Snippet: Bioinformatics and cloning of two putative EP/CCHaRs in Aplysia . A , prediction of 7 TM domains of putative apEP/CCHaRs: apEP/CCHaR1 and apEP/CCHaR2 using TMHMM 2.0. Conserved motifs in transmembrane domains 3 (TM3: D/ERY) and TM7 (NPXXXY) are shown. The amino acids different from the motifs are shown in red . B , the PCR products of two putative apEP/CCHaRs: apEP/CCHaR1 (1302 bp), apEP/CCHaR2 (1755 bp). C , a phylogenetic tree of the two Aplysia receptors with multiple molluscan class A GPCR sequences from Jiang et al . (see the results and for information of these sequences) using MEGA X. A class-B GPCR, Crassostrea gigas parathyroid hormone peptide receptor, was used as an outgroup. The tree suggests that apEP/CCHaR1 and apEP/CCHaR2 are likely Aplysia EP/CCHa receptors. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Numbers at the nodes are bootstrap values as percentage. Only bootstrap values greater than 50 are shown.

Article Snippet: A , comparison of selected EP/CCHa peptides from protostomes using BioEdit (ClustalW Multiple Alignments-Graphic View).

Techniques: Cloning

Journal: The Journal of Biological Chemistry

Article Title: A brain-gut excitatory peptide/CCHamide homolog regulates satiation and motivational state transitions in the Aplysia feeding circuit

doi: 10.1016/j.jbc.2026.111257

Figure Lengend Snippet: Phylogeny of bilaterian EP/CCHa, ET and BN-type peptide receptors, including Aplysia californica receptors, apEP/CCHaR1 and apEP/CCHaR2 . The tree was constructed using MEGA X with 10,000 replicates using JTT + G model (see the results and for information about these sequences). “∗” indicates that the receptor has been verified. “Neuropeptide S receptor Plakobranchus ocellatus ” was used as an outgroup. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Numbers at the nodes are bootstrap values as a percentage. Only bootstrap values greater than 50 are shown. NMBR = BB1 receptor; GRPR = BB2 receptor; BRS3 = BB3 receptor.

Article Snippet: A , comparison of selected EP/CCHa peptides from protostomes using BioEdit (ClustalW Multiple Alignments-Graphic View).

Techniques: Construct

Journal: The Journal of Biological Chemistry

Article Title: Cardiac Troponin T, a Sarcomeric AKAP, Tethers Protein Kinase A at the Myofilaments *

doi: 10.1074/jbc.M110.148684

Figure Lengend Snippet: Cardiac TnT contains a highly conserved PKA docking site. A, schematic illustration shows the location of the PKA binding site and cardiac-specific cTnI-Ser23-Ser24 phosphorylation sites (star). Drawing of the troponin complex is based on the crystal structure of the troponin core domain (50). N-terminal region of cTnT (residues 1–204) was not solved in the crystal structure. Rectangles represent helical structures. cTnC is colored red, cTnI is green, and cTnT is blue. B, ClustalW multiple sequence alignment of cTnT with nine other AKAPs. Conserved residues responsible for tethering PKA are shown in white. The high homology between cTnT and Ht31 is also shown (boxed). C, surface representation of cTnT (PDB 1J1D) helix 203–224 shows the position of hydrophobic residues (red) involved in PKA docking.

Article Snippet: In silico analysis of the cTnT amino acid sequence using the ClustalW multiple alignment algorithm (part of the MacVector 11 sequence analysis suite) identified a fragment of an amphipathic α-helix (spanning residues 212–224) as a putative PKA-R binding site ( ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIGURE 2. caption a7 Cardiac TnT contains a highly conserved PKA docking site.

Techniques: Binding Assay, Sequencing

Journal: The Journal of investigative dermatology

Article Title: Identification of a human skin commensal bacterium that selectively kills Cutibacterium acnes

doi: 10.1016/j.jid.2019.12.026

Figure Lengend Snippet: Functional screen to identify antimicrobial CoNS species that target C. acnes. (A) Schematic for the high-throughput antimicrobial functional screen, outlining the collection and selection of CoNS strains from two distinct healthy skin sites and assays to detect antimicrobial activity against C. acnes via coculture on agar or growth in sterile conditioned supernatant of CoNS. (B,C) Growth of C. acnes C2 after 24 h incubation in 50% sterile filtered supernatant of the CoNS strain library (B) or growth of C. acnes C2 with CoNS coculture in agar (C). Each dot represent data from individual CoNS clone. The most potent antimicrobial CoNS isolate was selected and identified as S. capitis E12 (red), whilst S. hominus A9 (blue) did not exhibit activity against C. acnes C2. (D) Table showing the inhibitory activity of S. capitis E12 and S. hominus A9, against several skin commensal and pathogen strains, including several strains of C. acnes isolated from healthy and acne skin, as measured by size of zone inhibition by antimicrobial agar assay (+ small, ++ medium, +++ large). (E) Growth of C. acnes C2 after 24 h incubation in media alone or increasing concentrations of sterile supernatant of S. capitis E12 or S. hominus A9. (F) Survival of several species of staphylococci and C. acnes after 24 h post-treatment with increasing concentrations of sterile S. capitis E12 supernatant, as measured by the number of surviving CFU plated onto the appropriate selective agar.

Article Snippet: This amphipathic structure is common amongst many well characterized antimicrobial peptides ( Tossi et al. 2000 ) ( ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 3. caption a7 Whole genome sequencing of S. capitis E12 reveals sequence and predicted properties of the PSMβ peptides. (A ) Schematic highlighting the S. capitis E12 genetic cluster containing six gene-encoding PSMβ peptides (PSMβ1-6). (B) Multiple sequence alignment (ClustalW) of all six PSMβ peptides, including the predicted charge for each peptide. (C) Absence of antimicrobial activity against C. acnes C2 during live coculture or sterile supernatant exposure with ATCC S. capitis strains 35661 and 27840 that lack PSMβ genes.

Techniques: Functional Assay, High Throughput Screening Assay, Selection, Activity Assay, Incubation, Isolation, Inhibition

Journal: The Journal of investigative dermatology

Article Title: Identification of a human skin commensal bacterium that selectively kills Cutibacterium acnes

doi: 10.1016/j.jid.2019.12.026

Figure Lengend Snippet: HPLC purification and identification of S. capitis E12 antimicrobial peptides. (A,B) 60% ammonium sulphate-precipitated supernatant of S. capitis E12 was loaded onto a HLB column and the antimicrobial factor eluted by 80% acetonitrile. The HLB 80% eluant was loaded onto a C8 cartridge (indicated by arrow) and the antimicrobial factor was eluted by 50% acetonitrile. Fractions were measured for activity against C. acnes C2 by agar assay (A) and liquid culture (B). Error bars depict mean ± SEM. *P < 0.05; **P < 0.01 t tests comparing values against media control. (C) Silver stain of the total protein content of S. capitis E12 treated or untreated supernatant and the SPE flow-through and eluted fractions. (D) HPLC purification of S. capitis supernatant identified several peptide peaks, of which a single fraction (21) was identified as having anti-C. acnes C2 activity (E) by liquid culture assay. (F) Fraction 21 was pooled from five separate HPLC runs and purified by second step HPLC resulting in two fractions (15 and 16) with anti-C. acnes C2 activity (G) by liquid culture assay. (H) Results of the top 8 peptide hits from MS detection of HPLC purified active fractions (15 and 16) and control non-active fractions (13,14, 17 and 18) revealing peptides corresponding to ‘antibacterial protein’ and later identified as PSMβ peptides by BLAST analyses.

Article Snippet: This amphipathic structure is common amongst many well characterized antimicrobial peptides ( Tossi et al. 2000 ) ( ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 3. caption a7 Whole genome sequencing of S. capitis E12 reveals sequence and predicted properties of the PSMβ peptides. (A ) Schematic highlighting the S. capitis E12 genetic cluster containing six gene-encoding PSMβ peptides (PSMβ1-6). (B) Multiple sequence alignment (ClustalW) of all six PSMβ peptides, including the predicted charge for each peptide. (C) Absence of antimicrobial activity against C. acnes C2 during live coculture or sterile supernatant exposure with ATCC S. capitis strains 35661 and 27840 that lack PSMβ genes.

Techniques: Purification, Activity Assay, Silver Staining

Journal: Journal of theoretical biology

Article Title: Comparison of genomic data via statistical distribution

doi: 10.1016/j.jtbi.2016.07.032

Figure Lengend Snippet: Bacteria genome used in the clustering method

Article Snippet: It should be denoted that we tried couple multiple alignment MAFFT, CLUSTAL and MUSCLE on these data but after one week none of them succeeded to get alignment of them although the proposed method provide result in less that hour in Mac 2.3 GHz Intel Core i7 with 16 GB, it can be done in few moments see conclusion section for the discussion. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 9 caption a7 Dendrogram for the Bacteria family using DFR. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 Dendrogram for the Bacteria family using DKLd table ft1 table-wrap mode="anchored" t5 caption a7 group Genome GenBank Length Label Bacteria-Aquificae Aquifex aeolicus NC 000918.1 1551335 A1 Hydrogenobacter thermophilus TK-6 NC 013799.1 1743135 A2 Hydrogenobaculum sp. 3684 NC 015557.1 1552775 A3 Hydrogenobaculum sp. Y04AAS1 NC 011126.1 1559514 A4 Persephonella marina EX-H1 NC 012440.1 1930284 A5 Sulfurihydrogenibium sp. YO3AOP1 NC 010730.1 1838442 A6 Sulfurihydrogenibium azorense Az-Fu1 NC 012438.1 1640877 A7 Bacteria-Bacteroidetes Bacteroides thetaiotaomicron VPI-5482 NC 004663.1 6260361 B1 Cytophaga hutchinsonii ATCC 33406 NC 008255.1 4433218 B2 Flavobacterium johnsoniae UW101 NC 009441.1 6096872 B3 Gramella forsetii KT0803 NC 008571.1 3798465 B4 Porphyromonas gingivalis W83 NC 002950.2 2343476 B5 Salinibacter ruber DSM 13855 NC 007677.1 3551823 B6 Bacteria-Cyanobacteria Anabaena variabilis ATCC 29413 NC 007413.1 6365727 C1 Nostoc sp. PCC 7120 NC 003272.1 6413771 C2 Gloeobacter violaceus PCC 7421 NC 005125.1 4659019 C3 Prochlorococcus marinus CCMP1375 NC 005042.1 1751080 C4 Synechococcus elongatus PCC 7942 NC 007604.1 2695903 C5 Synechococcus sp. WH 8102 NC 005070.1 2434428 C6 Thermosynechococcus elongatus NC 004113.1 2593857 C7 Trichodesmium erythraeum IMS101 NC 008312.1 7750108 C8 Open in a separate window Sulfurihydrogenibium yellowstonense SS-5, Hydrogenivirga sp. 128-5-R1-1 and Crocosphaera watsonii WH 8501 are not added because the complete genome is not available or has not identified Bacteria genome used in the clustering method

Techniques:

Journal: Journal of theoretical biology

Article Title: Comparison of genomic data via statistical distribution

doi: 10.1016/j.jtbi.2016.07.032

Figure Lengend Snippet: Bacteria genome used in the clustering method

Article Snippet: It should be denoted that we tried couple multiple alignment MAFFT, CLUSTAL and MUSCLE on these data but after one week none of them succeeded to get alignment of them although the proposed method provide result in less that hour in Mac 2.3 GHz Intel Core i7 with 16 GB, it can be done in few moments see conclusion section for the discussion. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 9 caption a7 Dendrogram for the Bacteria family using DFR. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 Dendrogram for the Bacteria family using DKLd table ft1 table-wrap mode="anchored" t5 caption a7 group Genome GenBank Length Label Bacteria-Aquificae Aquifex aeolicus NC 000918.1 1551335 A1 Hydrogenobacter thermophilus TK-6 NC 013799.1 1743135 A2 Hydrogenobaculum sp. 3684 NC 015557.1 1552775 A3 Hydrogenobaculum sp. Y04AAS1 NC 011126.1 1559514 A4 Persephonella marina EX-H1 NC 012440.1 1930284 A5 Sulfurihydrogenibium sp. YO3AOP1 NC 010730.1 1838442 A6 Sulfurihydrogenibium azorense Az-Fu1 NC 012438.1 1640877 A7 Bacteria-Bacteroidetes Bacteroides thetaiotaomicron VPI-5482 NC 004663.1 6260361 B1 Cytophaga hutchinsonii ATCC 33406 NC 008255.1 4433218 B2 Flavobacterium johnsoniae UW101 NC 009441.1 6096872 B3 Gramella forsetii KT0803 NC 008571.1 3798465 B4 Porphyromonas gingivalis W83 NC 002950.2 2343476 B5 Salinibacter ruber DSM 13855 NC 007677.1 3551823 B6 Bacteria-Cyanobacteria Anabaena variabilis ATCC 29413 NC 007413.1 6365727 C1 Nostoc sp. PCC 7120 NC 003272.1 6413771 C2 Gloeobacter violaceus PCC 7421 NC 005125.1 4659019 C3 Prochlorococcus marinus CCMP1375 NC 005042.1 1751080 C4 Synechococcus elongatus PCC 7942 NC 007604.1 2695903 C5 Synechococcus sp. WH 8102 NC 005070.1 2434428 C6 Thermosynechococcus elongatus NC 004113.1 2593857 C7 Trichodesmium erythraeum IMS101 NC 008312.1 7750108 C8 Open in a separate window Sulfurihydrogenibium yellowstonense SS-5, Hydrogenivirga sp. 128-5-R1-1 and Crocosphaera watsonii WH 8501 are not added because the complete genome is not available or has not identified Bacteria genome used in the clustering method

Techniques:

Journal: Journal of theoretical biology

Article Title: Comparison of genomic data via statistical distribution

doi: 10.1016/j.jtbi.2016.07.032

Figure Lengend Snippet: Bacteria genome used in the clustering method

Article Snippet: It should be denoted that we tried couple multiple alignment MAFFT, CLUSTAL and MUSCLE on these data but after one week none of them succeeded to get alignment of them although the proposed method provide result in less that hour in Mac 2.3 GHz Intel Core i7 with 16 GB, it can be done in few moments see conclusion section for the discussion. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 9 caption a7 Dendrogram for the Bacteria family using DFR. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 Dendrogram for the Bacteria family using DKLd table ft1 table-wrap mode="anchored" t5 caption a7 group Genome GenBank Length Label Bacteria-Aquificae Aquifex aeolicus NC 000918.1 1551335 A1 Hydrogenobacter thermophilus TK-6 NC 013799.1 1743135 A2 Hydrogenobaculum sp. 3684 NC 015557.1 1552775 A3 Hydrogenobaculum sp. Y04AAS1 NC 011126.1 1559514 A4 Persephonella marina EX-H1 NC 012440.1 1930284 A5 Sulfurihydrogenibium sp. YO3AOP1 NC 010730.1 1838442 A6 Sulfurihydrogenibium azorense Az-Fu1 NC 012438.1 1640877 A7 Bacteria-Bacteroidetes Bacteroides thetaiotaomicron VPI-5482 NC 004663.1 6260361 B1 Cytophaga hutchinsonii ATCC 33406 NC 008255.1 4433218 B2 Flavobacterium johnsoniae UW101 NC 009441.1 6096872 B3 Gramella forsetii KT0803 NC 008571.1 3798465 B4 Porphyromonas gingivalis W83 NC 002950.2 2343476 B5 Salinibacter ruber DSM 13855 NC 007677.1 3551823 B6 Bacteria-Cyanobacteria Anabaena variabilis ATCC 29413 NC 007413.1 6365727 C1 Nostoc sp. PCC 7120 NC 003272.1 6413771 C2 Gloeobacter violaceus PCC 7421 NC 005125.1 4659019 C3 Prochlorococcus marinus CCMP1375 NC 005042.1 1751080 C4 Synechococcus elongatus PCC 7942 NC 007604.1 2695903 C5 Synechococcus sp. WH 8102 NC 005070.1 2434428 C6 Thermosynechococcus elongatus NC 004113.1 2593857 C7 Trichodesmium erythraeum IMS101 NC 008312.1 7750108 C8 Open in a separate window Sulfurihydrogenibium yellowstonense SS-5, Hydrogenivirga sp. 128-5-R1-1 and Crocosphaera watsonii WH 8501 are not added because the complete genome is not available or has not identified Bacteria genome used in the clustering method

Techniques: