Journal: Frontiers in Endocrinology

Article Title: Evaluating conserved domains and motifs of decapod gonadotropin-releasing hormone G protein-coupled receptor superfamily

doi: 10.3389/fendo.2024.1348465

Figure Lengend Snippet: Cluster analysis of (A) the class A GPCR-encoding transcripts, and (B) the Gonadotropin-Releasing Hormone (GnRH) superfamily of receptor-encoding transcripts with predicted ligands. The images were generated using the CLANS2 algorithm with E-values less than 1e-50.

Article Snippet: Firstly, all available class A decapod GPCR ORFs were downloaded from the Interpro database using the search terms ‘Rhodopsin-like’ and ‘7TM’.

Techniques: Generated

Journal: Frontiers in Endocrinology

Article Title: Evaluating conserved domains and motifs of decapod gonadotropin-releasing hormone G protein-coupled receptor superfamily

doi: 10.3389/fendo.2024.1348465

Figure Lengend Snippet: Heatmaps depicting the diversity of the amino acid sequences of GPCR-encoding transcript DRY motif loci of A) the eleven decapod species reported in this study (n=1289), and B) of a dataset of human GPCRs that was reported by others (n=270) ( 8 ).

Article Snippet: Firstly, all available class A decapod GPCR ORFs were downloaded from the Interpro database using the search terms ‘Rhodopsin-like’ and ‘7TM’.

Techniques:

Journal: Frontiers in Endocrinology

Article Title: Evaluating conserved domains and motifs of decapod gonadotropin-releasing hormone G protein-coupled receptor superfamily

doi: 10.3389/fendo.2024.1348465

Figure Lengend Snippet: Snake plots of the functionally annotated receptors of (A) Corazonin (Cm_CrzR), (C) Red Pigment Concentrating Hormone (Cm_RPCHR) and (E) Crustacean Cardioactive Peptide (Sp_CCAPR), compared with GPCR-encoding transcripts (B) Gl_GPCR_A7 (D) Po_GPCR_A146 and (F) Cm_GPCR_A117 of this dataset. The exploded views depict the conserved function-related DRY, CWxP and NPxxY motifs. Noting the similarity of the GPCR topological domains that are represented including the N-terminus (H 2 N), C-terminus (COOH), three intracellular loops, three extracellular loops, canonical seven transmembrane domains, N-glycosylation sites (depicted by green) and conserved motifs. Yellow, green and pink ovals mean next to the receptor names correspond to the DRY motifs listed in Table 3 .

Article Snippet: Firstly, all available class A decapod GPCR ORFs were downloaded from the Interpro database using the search terms ‘Rhodopsin-like’ and ‘7TM’.

Techniques: Glycoproteomics

Journal: Frontiers in Endocrinology

Article Title: Evaluating conserved domains and motifs of decapod gonadotropin-releasing hormone G protein-coupled receptor superfamily

doi: 10.3389/fendo.2024.1348465

Figure Lengend Snippet: Conserved GPCR motifs (that is, DRYxxx, CWxP and NPxxY) observed in transcripts of the GnRHR-like receptors of this dataset and in protein sequences published on NCBI.

Article Snippet: Firstly, all available class A decapod GPCR ORFs were downloaded from the Interpro database using the search terms ‘Rhodopsin-like’ and ‘7TM’.

Techniques:

Journal: Hearing research

Article Title: Deletion of Shank1 has minimal effects on the molecular composition and function of glutamatergic afferent postsynapses in the mouse inner ear

doi: 10.1016/j.heares.2015.01.008

Figure Lengend Snippet: Organs of Corti from 4 week old mice were immunostained with either a mouse monoclonal IgG1 antibody against CTBP2 (green, A) or rabbit polyclonal antibody against Shank1 (green, E) and a mouse monoclonal IgG2A antibody against PSD95 (red, B,F). Observations of individual samples revealed that almost every presynaptic CTBP2-positive ribbon was juxtaposed to a PSD95-positive PSD and vice versa (C) and that almost every PSD95-positive PSD also expressed Shank1 immunoreactivity and vice versa (G). Images are presented as Z-projections of a stack of confocal micrographs from the 32 kHz region. Mean values (± SEM) of CTBP2-positive presynaptic ribbons (D) or Shank1-positive PSDs (H) and PSD95-positive PSDs across samples are compared at two tonotopic regions (8 and 32 kHz). Statistically significant differences are indicated with an asterisk.

Article Snippet: Alexa Fluor secondary antibodies (Life Technologies) included: goat anti-mouse IgG1 488; goat anti-mouse IgG2b 488 and 647; goat anti-mouse IgG2a 594 and 647; goat anti-rabbit IgG 488 and 568; donkey anti-goat 488; donkey anti-rabbit 594; and donkey anti-mouse 647. table ft1 table-wrap mode="anchored" t5 caption a7 Target Protein(s) Antibody Isotype Epitope/ Immunogen Accession Number Vendor Catalogue Number CTBP2 Mouse IgG1 aa 361–445 (mouse CtBP2) Not provided BD Biosciences 612044 PSD95 Mouse IgG2a Fusion protein aa 77- 299 (human PSD-95) {"type":"entrez-protein","attrs":{"text":"P78352","term_id":"71658825","term_text":"P78352"}} P78352 Neuromab 75–028 Shank1 Rabbit IgG SGPIYPGLF DIRSS (Shank1a C- teminus) Not provided Neuromics RA19016 Shank1 Mouse IgG1 Fusion protein amino acids 469- 691 (rat Shank1) {"type":"entrez-protein","attrs":{"text":"Q9WV48","term_id":"22001985","term_text":"Q9WV48"}} Q9WV48 Neuromab Shank2 Mouse IgG1 Fusion protein aa 84- 309 (rat Shank2) {"type":"entrez-protein","attrs":{"text":"Q9QX74","term_id":"22001984","term_text":"Q9QX74"}} Q9QX74 Neuromab 75–088 Shank3 Mouse IgG2b Synthetic peptide aa 840–857 PEKLPGSLR KGIPRTKSV (rat Shank3) QNJLU4 Neuromab 75–109 panShank Goat IgG C-terminus (human Shank1) {"type":"entrez-protein","attrs":{"text":"Q9Y566","term_id":"229462779","term_text":"Q9Y566"}} Q9Y566 Santa Cruz Biotechnology sc-23543 GluA2/3 Rabbit IgG EGYNVYGI ESVKI (rat GluR2 C- terminus) NP 000817 Millipore AB1506 GKAP Mouse IgG2b Fusion protein aa 772–992 (rat GKAP1) {"type":"entrez-protein","attrs":{"text":"P97836","term_id":"17374679","term_text":"P97836"}} P97836 Neuromab 75–156 TuJ Mouse IgG1 ESESQGPK (human human class III β-tubulin NM 00686.2 Millipore MAB1637 Open in a separate window Primary antibodies for immunofluorescence

Techniques:

Journal: Hearing research

Article Title: Deletion of Shank1 has minimal effects on the molecular composition and function of glutamatergic afferent postsynapses in the mouse inner ear

doi: 10.1016/j.heares.2015.01.008

Figure Lengend Snippet: Organs of Corti from 4 week old Shank1+/+ (A–D) and Shank1−/− (E–H) littermate mice were immunostained with a mouse monoclonal IgG1 antibody against CTBP2 (blue, A and E), a rabbit polyclonal antibody against Shank1 (red, B and F) and a goat polyclonal antibody that recognizes all three Shank isoforms (panShank, green, C and G). Colocalized Shank1 and panShank immunoreactivity was observed juxtaposed to CTBP2-positive presynaptic ribbons in Shank1+/+ mice (D). Although CTBP2-positive presynaptic ribbons were observed, neither Shank1 nor panShank immunoreactivity was observed in Shank1−/− mice (H). Images are presented as Z-projections of a stack of confocal micrographs from the 16 kHz region. Shank1–3 transcript expression was investigated in the cochleae of Shank1+/+ mice (and presented normalized to control gene expression in Shank1+/+ mice, I). Shank2–3 transcript expression was investigated in Shank1−/− mice (and presented relative to Shank2 and Shank3 expression in Shank1+/+ mice, J). Two-fold or more greater changes in expression are indicated with asterisks.

Article Snippet: Alexa Fluor secondary antibodies (Life Technologies) included: goat anti-mouse IgG1 488; goat anti-mouse IgG2b 488 and 647; goat anti-mouse IgG2a 594 and 647; goat anti-rabbit IgG 488 and 568; donkey anti-goat 488; donkey anti-rabbit 594; and donkey anti-mouse 647. table ft1 table-wrap mode="anchored" t5 caption a7 Target Protein(s) Antibody Isotype Epitope/ Immunogen Accession Number Vendor Catalogue Number CTBP2 Mouse IgG1 aa 361–445 (mouse CtBP2) Not provided BD Biosciences 612044 PSD95 Mouse IgG2a Fusion protein aa 77- 299 (human PSD-95) {"type":"entrez-protein","attrs":{"text":"P78352","term_id":"71658825","term_text":"P78352"}} P78352 Neuromab 75–028 Shank1 Rabbit IgG SGPIYPGLF DIRSS (Shank1a C- teminus) Not provided Neuromics RA19016 Shank1 Mouse IgG1 Fusion protein amino acids 469- 691 (rat Shank1) {"type":"entrez-protein","attrs":{"text":"Q9WV48","term_id":"22001985","term_text":"Q9WV48"}} Q9WV48 Neuromab Shank2 Mouse IgG1 Fusion protein aa 84- 309 (rat Shank2) {"type":"entrez-protein","attrs":{"text":"Q9QX74","term_id":"22001984","term_text":"Q9QX74"}} Q9QX74 Neuromab 75–088 Shank3 Mouse IgG2b Synthetic peptide aa 840–857 PEKLPGSLR KGIPRTKSV (rat Shank3) QNJLU4 Neuromab 75–109 panShank Goat IgG C-terminus (human Shank1) {"type":"entrez-protein","attrs":{"text":"Q9Y566","term_id":"229462779","term_text":"Q9Y566"}} Q9Y566 Santa Cruz Biotechnology sc-23543 GluA2/3 Rabbit IgG EGYNVYGI ESVKI (rat GluR2 C- terminus) NP 000817 Millipore AB1506 GKAP Mouse IgG2b Fusion protein aa 772–992 (rat GKAP1) {"type":"entrez-protein","attrs":{"text":"P97836","term_id":"17374679","term_text":"P97836"}} P97836 Neuromab 75–156 TuJ Mouse IgG1 ESESQGPK (human human class III β-tubulin NM 00686.2 Millipore MAB1637 Open in a separate window Primary antibodies for immunofluorescence

Techniques: Expressing, Control, Gene Expression

Journal: Hearing research

Article Title: Deletion of Shank1 has minimal effects on the molecular composition and function of glutamatergic afferent postsynapses in the mouse inner ear

doi: 10.1016/j.heares.2015.01.008

Figure Lengend Snippet: The vestibular sensory epithelia of the utricular maculae was isolated from 4 week old Shank1+/+ (A–D) and Shank1−/− (E–H) mice and immunostained with a rabbit polyclonal antibody against Shank1 (red, A and E), a mouse monoclonal IgG2A antibody against PSD95 (green, B and F), and a mouse monoclonal antibody against tubulin J (TuJ, blue, C and G). Shank1 immunoreactivity was colocalized to PSD95-positive PSDs observed in TuJ-positive calyx and bouton afferent terminals in Shank1+/+ mice (D). In contrast, no Shank1 immunoreactivity was observed in PSD95-positive PSDs in Shank1−/− mice (H). Images are presented as a single optical section from the striolar region. Vestibular evoked potentials (VsEPs) showed comparable thresholds (I), P1-N1 amplitude (I/O) slopes (J) and P1 latency I/O slopes (K) between genotypes.

Article Snippet: Alexa Fluor secondary antibodies (Life Technologies) included: goat anti-mouse IgG1 488; goat anti-mouse IgG2b 488 and 647; goat anti-mouse IgG2a 594 and 647; goat anti-rabbit IgG 488 and 568; donkey anti-goat 488; donkey anti-rabbit 594; and donkey anti-mouse 647. table ft1 table-wrap mode="anchored" t5 caption a7 Target Protein(s) Antibody Isotype Epitope/ Immunogen Accession Number Vendor Catalogue Number CTBP2 Mouse IgG1 aa 361–445 (mouse CtBP2) Not provided BD Biosciences 612044 PSD95 Mouse IgG2a Fusion protein aa 77- 299 (human PSD-95) {"type":"entrez-protein","attrs":{"text":"P78352","term_id":"71658825","term_text":"P78352"}} P78352 Neuromab 75–028 Shank1 Rabbit IgG SGPIYPGLF DIRSS (Shank1a C- teminus) Not provided Neuromics RA19016 Shank1 Mouse IgG1 Fusion protein amino acids 469- 691 (rat Shank1) {"type":"entrez-protein","attrs":{"text":"Q9WV48","term_id":"22001985","term_text":"Q9WV48"}} Q9WV48 Neuromab Shank2 Mouse IgG1 Fusion protein aa 84- 309 (rat Shank2) {"type":"entrez-protein","attrs":{"text":"Q9QX74","term_id":"22001984","term_text":"Q9QX74"}} Q9QX74 Neuromab 75–088 Shank3 Mouse IgG2b Synthetic peptide aa 840–857 PEKLPGSLR KGIPRTKSV (rat Shank3) QNJLU4 Neuromab 75–109 panShank Goat IgG C-terminus (human Shank1) {"type":"entrez-protein","attrs":{"text":"Q9Y566","term_id":"229462779","term_text":"Q9Y566"}} Q9Y566 Santa Cruz Biotechnology sc-23543 GluA2/3 Rabbit IgG EGYNVYGI ESVKI (rat GluR2 C- terminus) NP 000817 Millipore AB1506 GKAP Mouse IgG2b Fusion protein aa 772–992 (rat GKAP1) {"type":"entrez-protein","attrs":{"text":"P97836","term_id":"17374679","term_text":"P97836"}} P97836 Neuromab 75–156 TuJ Mouse IgG1 ESESQGPK (human human class III β-tubulin NM 00686.2 Millipore MAB1637 Open in a separate window Primary antibodies for immunofluorescence

Techniques: Isolation

Journal: Hearing research

Article Title: Deletion of Shank1 has minimal effects on the molecular composition and function of glutamatergic afferent postsynapses in the mouse inner ear

doi: 10.1016/j.heares.2015.01.008

Figure Lengend Snippet: Primary antibodies for immunofluorescence

Article Snippet: Alexa Fluor secondary antibodies (Life Technologies) included: goat anti-mouse IgG1 488; goat anti-mouse IgG2b 488 and 647; goat anti-mouse IgG2a 594 and 647; goat anti-rabbit IgG 488 and 568; donkey anti-goat 488; donkey anti-rabbit 594; and donkey anti-mouse 647. table ft1 table-wrap mode="anchored" t5 caption a7 Target Protein(s) Antibody Isotype Epitope/ Immunogen Accession Number Vendor Catalogue Number CTBP2 Mouse IgG1 aa 361–445 (mouse CtBP2) Not provided BD Biosciences 612044 PSD95 Mouse IgG2a Fusion protein aa 77- 299 (human PSD-95) {"type":"entrez-protein","attrs":{"text":"P78352","term_id":"71658825","term_text":"P78352"}} P78352 Neuromab 75–028 Shank1 Rabbit IgG SGPIYPGLF DIRSS (Shank1a C- teminus) Not provided Neuromics RA19016 Shank1 Mouse IgG1 Fusion protein amino acids 469- 691 (rat Shank1) {"type":"entrez-protein","attrs":{"text":"Q9WV48","term_id":"22001985","term_text":"Q9WV48"}} Q9WV48 Neuromab Shank2 Mouse IgG1 Fusion protein aa 84- 309 (rat Shank2) {"type":"entrez-protein","attrs":{"text":"Q9QX74","term_id":"22001984","term_text":"Q9QX74"}} Q9QX74 Neuromab 75–088 Shank3 Mouse IgG2b Synthetic peptide aa 840–857 PEKLPGSLR KGIPRTKSV (rat Shank3) QNJLU4 Neuromab 75–109 panShank Goat IgG C-terminus (human Shank1) {"type":"entrez-protein","attrs":{"text":"Q9Y566","term_id":"229462779","term_text":"Q9Y566"}} Q9Y566 Santa Cruz Biotechnology sc-23543 GluA2/3 Rabbit IgG EGYNVYGI ESVKI (rat GluR2 C- terminus) NP 000817 Millipore AB1506 GKAP Mouse IgG2b Fusion protein aa 772–992 (rat GKAP1) {"type":"entrez-protein","attrs":{"text":"P97836","term_id":"17374679","term_text":"P97836"}} P97836 Neuromab 75–156 TuJ Mouse IgG1 ESESQGPK (human human class III β-tubulin NM 00686.2 Millipore MAB1637 Open in a separate window Primary antibodies for immunofluorescence

Techniques:

Journal: Hearing research

Article Title: Deletion of Shank1 has minimal effects on the molecular composition and function of glutamatergic afferent postsynapses in the mouse inner ear

doi: 10.1016/j.heares.2015.01.008

Figure Lengend Snippet: Organs of Corti from 4 week old Shank1+/+ (A-D,I,K) and Shank1−/− (E-H,J,L) littermate mice were immunostained with a mouse monoclonal IgG1 antibody against CTBP2 (green, A and E), a rabbit polyclonal antibody against GluA2/3 (red, B and F,I-L), and a mouse monoclonal IgG2B antibody against GKAP (blue, C and G,I-L). Colocalized GluA2/3 and GKAP immunoreactivity was observed juxtaposed to CTBP2-positive presynaptic ribbons in both Shank1+/+ (D) and Shank1−/− mice (H). Images are presented as Z-projections through a stack of confocal micrographs from the 32 kHz region (AH) or as 3D reconstructions comparing the 8 and 32 kHz region (I–L) from Shank1+/+ and Shank1−/− mice. Mean values (± SEM) of GluA2/3-positive and GKAP-positive immunopuncta per hair cell (M) and mean values (± SEM) of GluA2/3-positive and GKAP-positive immunopuncta volumes (N) for each genotype are compared at two tonotopic regions (8 and 32 kHz). Statistically significant differences are indicated with an asterisk.

Article Snippet: Alexa Fluor secondary antibodies (Life Technologies) included: goat anti-mouse IgG1 488; goat anti-mouse IgG2b 488 and 647; goat anti-mouse IgG2a 594 and 647; goat anti-rabbit IgG 488 and 568; donkey anti-goat 488; donkey anti-rabbit 594; and donkey anti-mouse 647. table ft1 table-wrap mode="anchored" t5 caption a7 Target Protein(s) Antibody Isotype Epitope/ Immunogen Accession Number Vendor Catalogue Number CTBP2 Mouse IgG1 aa 361–445 (mouse CtBP2) Not provided BD Biosciences 612044 PSD95 Mouse IgG2a Fusion protein aa 77- 299 (human PSD-95) {"type":"entrez-protein","attrs":{"text":"P78352","term_id":"71658825","term_text":"P78352"}} P78352 Neuromab 75–028 Shank1 Rabbit IgG SGPIYPGLF DIRSS (Shank1a C- teminus) Not provided Neuromics RA19016 Shank1 Mouse IgG1 Fusion protein amino acids 469- 691 (rat Shank1) {"type":"entrez-protein","attrs":{"text":"Q9WV48","term_id":"22001985","term_text":"Q9WV48"}} Q9WV48 Neuromab Shank2 Mouse IgG1 Fusion protein aa 84- 309 (rat Shank2) {"type":"entrez-protein","attrs":{"text":"Q9QX74","term_id":"22001984","term_text":"Q9QX74"}} Q9QX74 Neuromab 75–088 Shank3 Mouse IgG2b Synthetic peptide aa 840–857 PEKLPGSLR KGIPRTKSV (rat Shank3) QNJLU4 Neuromab 75–109 panShank Goat IgG C-terminus (human Shank1) {"type":"entrez-protein","attrs":{"text":"Q9Y566","term_id":"229462779","term_text":"Q9Y566"}} Q9Y566 Santa Cruz Biotechnology sc-23543 GluA2/3 Rabbit IgG EGYNVYGI ESVKI (rat GluR2 C- terminus) NP 000817 Millipore AB1506 GKAP Mouse IgG2b Fusion protein aa 772–992 (rat GKAP1) {"type":"entrez-protein","attrs":{"text":"P97836","term_id":"17374679","term_text":"P97836"}} P97836 Neuromab 75–156 TuJ Mouse IgG1 ESESQGPK (human human class III β-tubulin NM 00686.2 Millipore MAB1637 Open in a separate window Primary antibodies for immunofluorescence

Techniques: