> Chemicals & Drugs > Amino Acid > Neuropeptides

Neuropeptides

Neuropepides are a class of small peptide molecules produced and released by neurons in the nervous system.
They play crucial roles in neurological processes, including neurotransmission, neuromodulation, and neurohormonal regulation.
Neuropeptides are involved in a wide range of physiological functions, such as pain perception, stress response, appetite, and mood.
They are also implicated in the pathogenesis of various neurological and psychiatric disorders.
Reserach on neuropeptides is critical for understanding the complexities of the nervous system and developing potential therapeutic interventions.
This MeSH term provides a comprehensive overview of the scientific concpets and applications related to this important class of neurochemicals.

Most cited protocols related to «Neuropeptides»

Bayesian Analysis of Intranasal Oxytocin's Impact on Spirituality

Cited 37 times

A dataset from van Cappellen and colleagues [28 (link)] will be used to compare and contrast NHST and Bayesian hypothesis testing using JASP (version 0.8.5.1). A core feature of JASP is the ability to save the entire analysis pipeline as a .jasp file, which includes the data, analysis input options, and output. Thus, interested readers can follow each step of the described analyses by examining the associated .jasp file (https://osf.io/emz4r/).
The primary interest of the study from van Cappellen and colleagues [28 (link)] was whether a single intranasal administration of the neuropeptide oxytocin could impact self-reported spirituality. The role of the oxytocin system in human interconnection has been the subject of considerable research interest in psychiatry [29 (link)], however, it is not known if the oxytocin system is also involved in spiritual interconnection. In this study, participants were randomized to receive a single administration of either intranasal oxytocin or placebo, after which they responded to measures assessing spirituality. One of the outcomes used to index spirituality was a single item measure that asked, “Right now, would you say that spirituality is important for you?”. After receiving the nasal spray, participants responded on a scale from 0 (Not at all) to 7 (Completely). The study dataset was collected from manuscript’s Open Science Framework webpage (https://osf.io/rk2x7/) For pedagogic purposes, several variables not used in the current demonstration were removed from the original dataset and we perform additional analyses that were not reported in the original manuscript.

Quintana D.S, & Williams D.R. (2018). Bayesian alternatives for common null-hypothesis significance tests in psychiatry: a non-technical guide using JASP. BMC Psychiatry, 18, 178.

Full text: Click here

Publication 2018

Administration, Intranasal Homo sapiens Nasal Sprays Neuropeptides Oxytocin Placebos Spiritual Therapies

Glycoproteomics Searching with MSFragger

Cited 24 times

Deisotoping has been incorporated as an option in MSFragger starting with version 2.3. All searches described here were performed in a beta version of MSFragger (2.4-RC6-glyco) that included glycoproteomics search capabilities to enable searches of glyco data, but all beta capabilities have since been incorporated into the released version of MSFragger (starting with v3.0)^{28 (link)}. Full parameters for all MSFragger searches and Philosopher validation and filtering can be found in the supporting information. Parameter files are named to match the labels provided in figures and tables. Briefly, searches were performed as follows. The reviewed Human proteome from UniProt (downloaded 8/22/2019, 20464 sequences) was used with reversed decoys appended in Philosopher^{29 (link)} for all searches except the mouse N-glycopeptide data of Riley et al. and mouse neuropeptide data of Anapindi et al.. For searching data from Anapindi et al., the reviewed mouse (Mus musculus) proteome from Uniprot (downloaded 9/24/2019, 17019 sequences) was used with decoys appended in Philosopher. For Riley et al., the glycoprotein-focused database with 3,574 sequences used by Riley et al. was used with reversed decoys appended in Philosopher. For all searches except the peptidomics (nonspecific) search of neuropeptide data, trypsin digestion with 1 or 2 missed cleavages was allowed with resulting peptide lengths of 7 to 50 amino acids. Variable modifications of Met oxidation (up to 2 per peptide), protein N-terminal acetylation and peptide N-terminal pyroglutamate formation (Gln, Cys) were allowed with no more than 3 total modifications per peptide. For closed searches, the precursor mass tolerance was 20 ppm and the fragment mass tolerance was 10 ppm (Orbitrap) or 20 ppm (TOF) with mass calibration enabled (without parameter optimization) and isotope off-by-X errors of 0/1/2 allowed. Spectra were square root transformed and had precursor peaks removed prior to analysis. For open searches, precursor mass tolerance was −150 to 500 Da, with the same fragment tolerances as closed searches, calibration enabled, no isotope errors, and localization of delta masses enabled³⁰. Each search was performed with and without deisotoping, with all other parameters identical.
For nonspecific searches of endogenous neuropeptides, no enzyme was specified and variable modifications of oxidation (Met), deamidation (peptide C-terminus), acetylation (protein N-terminus, Lys), pyroglutamate formation (N-terminal Gln), and water loss (N-terminal Glu) were allowed, with a maximum of 1 each and 3 total modifications per peptide. Peptide lengths of 7 to 70 amino acids were allowed with masses of 500 to 12,000 Da. Three matched ions were required for modeling and five matched ions were required for reporting to pepXML output file. Precursor and fragment mass tolerances were 20 and 25 ppm, no calibration was performed, and isotope errors of 0/1/2 were allowed. Since the number of candidate peptides exceeded the maximum possible within MSFragger (~ 2 billion), it was run using the split database method available within FragPipe.
For N-glycopeptide searches in the data of Riley et al., raw files were split into separate mzML files by activation type (HCD or AI-ETD). Up to 3 missed cleavages were allowed and a list of 182 glycan masses (identical to those used in Riley et al.) were set as N-glycan mass offsets. For HCD spectra, b, y, Y, b~, and y~ ions were considered (~ refers to the addition of one HexNAc, 203.0794 Da), without localization of delta masses. AI-ETD spectra considered b, y, c, z, and Y ions, used delta mass localization, and removed precursor and M + e⁻ peaks. Default Y and oxonium ion lists were used.
FDR filtering was performed with the Philosopher^{29 (link)} pipeline, including PeptideProphet^{31 (link)} modeling of peptide probabilities, ProteinProphet^{32 (link)} protein inference, and Philosopher’s internal FDR filter. In PeptideProphet, closed searches used the accmass, ppm, nonparam, expectscore and decoyprobs options, while open searches used nonparam, expectscore, and decoyprobs options along with the extended mass model^{1 (link)} (masswidth 1000) and clevel −2. All searches used ProteinProphet with default options except maxppmdiff increased to 20,000,000. All searches were filtered to 1% PSM and protein level FDR using the razor peptides method with a sequential filtering step to remove any PSMs from proteins that did not pass FDR.

Teo G.C., Polasky D.A., Yu F, & Nesvizhskii A.I. (2020). A fast deisotoping algorithm and its implementation in the MSFragger search engine. Journal of proteome research, 20(1), 498-505.

Publication 2020

Acetylation Amino Acids Cytokinesis Digestion Enzymes Glycopeptides Glycoproteins Homo sapiens hydronium ion Immune Tolerance Isotopes link protein Mice, House Neuropeptides nucleoprotein, Measles virus Peptide Biosynthesis Peptides Plant Roots polypeptide C Polysaccharides Proteins Proteome PRSS1 protein, human Pyroglutamate SH2B protein, human Strains

Neuropeptide Precursor Identification in Asterias

Cited 15 times

To search for transcripts encoding putative neuropeptide or peptide hormone precursor proteins in A. rubens, the sequences of neuropeptide or peptide hormone precursors previously identified in the sea urchin S. purpuratus [5 (link),6 (link),11 (link),16 (link),17 (link),37 (link),38 (link)], the sea cucumber A. japonicus [10 (link)] and the starfish species Asterina pectinifera [39 (link)] were submitted individually as queries in tBLASTn searches of the contig database with the BLAST parameter e-value set to 1000. Contigs identified as encoding putative precursors were analysed after translation of their full-length DNA sequence into protein sequence using the ExPASy Translate tool (http://web.expasy.org/translate/). Proteins were assessed as potential precursors of secreted bioactive peptides by investigating: (i) the presence of a putative N-terminal signal peptide sequence, using the SignalP v. 3.0 online server [40 (link)], (ii) the presence of putative monobasic or dibasic cleavage sites N-terminal and C-terminal to the putative bioactive peptide(s), with reference to known consensus cleavage motifs [41 (link)–43 (link)], and (iii) the presence, in some cases, of a C-terminal glycine residue that is a potential substrate for amidation.

Semmens D.C., Mirabeau O., Moghul I., Pancholi M.R., Wurm Y, & Elphick M.R. (2016). Transcriptomic identification of starfish neuropeptide precursors yields new insights into neuropeptide evolution. Open Biology, 6(2), 150224.

Full text: Click here

Publication 2016

Amino Acid Sequence Asterina pectinifera Cytokinesis DNA Sequence Glycine Neuropeptides Peptide Hormone Peptides polypeptide C Protein Precursors Proteins Ruthenium Ben Sea Cucumbers Sea Urchin Signal Peptides Starfish

Immunostaining of Larval Marine Invertebrates

Cited 12 times

For immunostainings, larvae were fixed in 4% formaldehyde in PTW (PBS + 0.1% Tween-20) for 2 h and stored in 100% methanol at −20°C until use. After stepwise rehydration to PTW, samples were permeabilized with proteinase-K treatment (100 μg/ml in PTW, for 1 to 3 min). To stop proteinase-K activity, larvae were rinsed with glycine buffer (5 μg/ml in PTW) and post-fixed in 4% formaldehyde in PTW for 20 min followed by two 5 minwashes in PTW and two 5 minwashes in THT (0.1 M TRIS–HCl pH 8.5 + 0.1% Tween-20). Larvae and antibodies were blocked in 5% sheep serum in THT for 1 h. Primary antibodies were used at a final concentration of 1 μg/ml for rabbit neuropeptide antibodies and 0.5 μg/ml for mouse anti-acetylated tubulin antibody (Sigma, Saint Louis, USA) and incubated overnight at 6°C. Weakly bound primary antibodies were removed by two 10 min washes in 1 M NaCl in THT, followed by five 30 min washes in THT. Larvae were incubated overnight at 6°C in the dark in 1 μg/ml anti-rabbit Alexa Fluor® 647 antibody (Invitrogen, Carlsbad, CA, USA) and in 0.5 μg/ml anti-mouse FITC antibody (Jackson Immuno Research, West Grove, PA, USA) and then washed six times for 30 min with THT-buffer, and mounted in 87% glycerol including 2.5 mg/ml of the anti-photobleaching reagent 1,4-diazabicyclo[2.2.2]octane (Sigma, St. Louis, MO, USA). Pecten larvae were additionally treated with 4% paraformaldehyde in PBS with 50 μM EDTA pH 8.0 for 1 h to decalcify their shells before the immunostaining procedure (performed as described previously). For cnidarian larvae, we also used a mouse anti-tyrosylated tubulin antibody (Sigma, Saint Louis, USA) at 1 μg/ml. For immunostaining with multiple rabbit primary antibodies in the same sample, antibodies were directly labelled with a fluorophore using the Zenon® Tricolour Rabbit IgG Labelling Kit (Invitrogen, Carlsbad, CA, USA) and used in combination with mouse anti-acetylated tubulin antibody.
For blocking experiments, we pre-incubated the antibodies in 5 mM of the respective full-length Platynereis peptides (YYGFNNDLamide, AHRFVamide, AKYFLamide, VFRYamide, RGWamide) for 2 h before immunostainings.

Conzelmann M, & Jékely G. (2012). Antibodies against conserved amidated neuropeptide epitopes enrich the comparative neurobiology toolbox. EvoDevo, 3, 23.

Full text: Click here

Publication 2012

Alexa Fluor 647 Antibodies Antibodies, Anti-Idiotypic Buffers Cnidaria Edetic Acid Endopeptidase K Fluorescein-5-isothiocyanate Formaldehyde Glycerin Glycine Larva Methanol Mice, House Neuropeptides octane paraform Pecten Peptides Rabbits Rehydration Serum Sheep Sodium Chloride Tromethamine Tubulin Tween 20

Bioinformatic Identification of Prohormone Genes in Planarian Genome

Cited 11 times

Two distinct bioinformatic approaches were used to identify prohormone genes in the S. mediterranea genome. First, similarity searches were performed with collections of peptides or prohormones from invertebrate species such as Drosophila melanogaster, Aplysia californica, Apis mellifera[32] (link), Caenorhabditis elegans[73] (link), and various Platyhelminthes [39] (link) with stand-alone BLAST (BLOSSUM62 or PAM30 matrices and Expect values ≥10). Peptides and prohormones were obtained from genome databases (i.e. Wormbase, http://www.wormbase.org), from NCBI, or from an online catalog of bioactive peptides (http://www.peptides.be, [103] (link)). Additionally, sequence tags generated by de novo MS sequencing of unassigned peptides were also used as queries for genomic BLAST searches (BLOSSUM62 or PAM30 matrices and Expect values ≥10). As an alternative to similarity searching we analyzed translated S. mediterranea EST [98] (link),[104] (link) and 454 (Roche, Mannheim, Germany) sequence data (Y. Wang and P.A. Newmark, unpublished) for sequences that possessed characteristics of prohormone genes including multiple dibasic cleavage sites and a signal sequence (www.cbs.dtu.dk/services/SignalP). Translations of nucleotide sequences were performed with longorf.pl, a script that translates the longest open reading frame in a nucleotide sequence (www.bioperl.org/wiki/Bioperl_scripts). Putative prohormone genes identified using these two approaches were used as queries to search the S. mediterranea genome to determine if additional related prohormones existed in the genome. The full-length coding sequences of prohormone genes were predicted using a variety of gene and splice-site prediction tools, including NetGene2 (http://www.cbs.dtu.dk/services/NetGene2), FSPLICE (http://www.softberry.com), GENSCAN (http://genes.mit.edu/GENESCAN.html), and GeneQuest (v8.0.2, DNASTAR, Madison, WI). Where full-length sequences could not be predicted in silico, 5′ and 3′ Rapid Amplification of cDNA Ends (RACE) (FirstChoice RLM-Race Kit, Ambion, Austin, TX) analyses were performed following the manufacturer's protocol. The predictions of all genes reported here were independently verified by cDNA analysis (see below). Once verified, genes were considered to be genuine prohormone genes if they (1) possessed a signal sequence, (2) possessed basic cleavage sites that flanked predicted or MS-confirmed peptides, and (3) were less than 200 amino acids in length. Sequences were excluded if they shared similarity with genes previously annotated to be other than neuropeptide prohormones. All genes were named according to the S. mediterranea genome nomenclature guidelines [105] (link).

Collins JJ I.I.I., Hou X., Romanova E.V., Lambrus B.G., Miller C.M., Saberi A., Sweedler J.V, & Newmark P.A. (2010). Genome-Wide Analyses Reveal a Role for Peptide Hormones in Planarian Germline Development. PLoS Biology, 8(10), e1000509.

Full text: Click here

Publication 2010

Amino Acids Apis Aplysia austin Base Sequence Caenorhabditis elegans Cytokinesis DNA, Complementary Drosophila melanogaster Exons Flatworms Genes Genes, vif Genome Invertebrates Mediterranea Neuropeptides Peptides Signal Peptides

Most recents protocols related to «Neuropeptides»

Exploring Histone Modification's Role in Insect Flight

As flight activity is closely related to wing development, and long-distance migration is an important and widespread flight activity, we acquired a list of previously documented genes involved in wing development of B. dorsalis and migration-associated genes from recent papers (Supplementary Table S2), and compared them to peak-annotated genes identified above to investigate the possible functional relevance of histone modification to flight activity (Jones et al., 2015 (link); Guo et al., 2018 (link); Doyle et al., 2022 (link)). Specifically, Guo et al. (2018) (link) profiled transcriptomes of B. dorsalis, and identified a group of key genes with functions relevant to wing development, which showed highest expression level in the pupal stage and poised state in other stages, through comparative transcriptome analyses. Jones et al. (2015) (link) used comparative transcriptomics of flight phenotypes to determine a suite of expressed candidate genes associated with flight activity in the cotton bollworm, Helicoverpa armigera, including odorant binding proteins, flight muscle structure, fatty acid synthesis, etc. Doyle et al. (2022) (link) undertook a genome-wide transcriptomic comparison of actively migrating marmalade hoverfly, Episyrphus balteatus and found the features of the migrant phenotype have arisen by the integration and modification of pathways such as insulin signalling for diapause and longevity, JAK/SAT for immunity, and those leading to octopamine production and fuelling to boost flight capabilities. Specifically, upregulated genes associated with migration include genes related to metabolic processes, sensory functions, octopamine synthesis, neuropeptide hormones, muscle function, and immunity genes, and the downregulated genes include genes involved in insulin and TGF-β signalling, hormonal regulation, and multiple ankyrin repeats single KH domain (mask). We then compared the proportion of peak-annotated genes in each gene category to the proportion of peak-annotated genes in the reference genome using G test.

Zhao Y., Hu J., Wu J, & Li Z. (2023). ChIP-seq profiling of H3K4me3 and H3K27me3 in an invasive insect, Bactrocera dorsalis. Frontiers in Genetics, 14, 1108104.

Full text: Click here

Publication 2023

Anabolism Ankyrins Diapause Fatty Acids Gene Expression Profiling Genes Genes, vif Genome Gossypium Histones Hormones Insulin Metabolism Migrants Muscle Tissue Neuropeptides Octopamine odorant-binding protein Phenotype Pupa Response, Immune Transforming Growth Factor beta

Comprehensive Neural Interaction Database

Cited 1 time

NeuronChatDB is curated from existing databases (including KEGG^{53 (link)} and IUPHAR/BPS Guide to PHARMACOLOGY^{54 (link)}) and literature (e.g., neuropeptide interactions are from the reference^{16 (link)}), and contains neural-specific intercellular molecular interactions for both mouse and human. There are 373 entries in total. Each entry of NeuronChatDB represents an interaction pair, including one ligand and a cognate target as well as genes related to them. The ligands include small-molecule neurotransmitters, neuropeptides, gap junction proteins, gasotransmitters and synaptic adhesion molecules: small-molecule neurotransmitters include glutamate (Glu), GABA, glycine (Gly), acetylcholine (ACh), serotonin (5-HT), dopamine (DA), epinephrine (Epi) and norepinephrine (NE); gasotransmitters include carbon monoxide (CO) and Nitric oxide (NO); synaptic adhesion molecules refer to neurexins (regarded as the ligand) and neuroligins (regarded as the target). The targets are typically but not limited to receptors. For example, the target proteins for neurotransmitters can also be uptake transporters or deactivating enzymes; the target proteins for gap junction proteins are other compatible gap junction proteins. For non-peptide neurotransmitters, corresponding synthesizing enzymes and/or vesicular transporters are included in the entry; for heteromeric receptors that contain multiple different subunits, corresponding subunits are split into different entries with the same ligand. To be compatible with the inference model of NeuronChat, for the non-peptide neurotransmitters, related genes including vesicular transporters and synthesizing enzymes responsible for different catalyzing steps are annotated into separate groups.

Zhao W., Johnston K.G., Ren H., Xu X, & Nie Q. (2023). Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. Nature Communications, 14, 1128.

Full text: Click here

Publication 2023

Acetylcholine Cell Adhesion Molecules Connexins Dopamine Enzymes Epinephrine gamma Aminobutyric Acid Gasotransmitters Genes Glutamate Glycine Homo sapiens Ligands Membrane Transport Proteins Monoxide, Carbon Nervous Mice Neuropeptides Neurotransmitters Norepinephrine Oxide, Nitric Peptides Proteins Protein Subunits Protein Targeting, Cellular

Peptide Antibody Production and Purification

Peptides corresponding to the C-terminal region of the A. rubens asterotocin precursor (ArASTP; KERLLDALLRQP; Fig. 1a), corazonin-type precursor (ArCRZP; KLLDNVRLPQTERK; Fig. 1b) and luqin-type precursor (ArLQP; KGKVPATA; Fig. 1c) were custom synthesized by Peptide Protein Research Ltd (Fareham, UK). Naturally occurring lysine residues at the N-terminus of ArASTP and ArCRZP peptide antigens and an introduced lysine at the N-terminus of the ArLQP peptide antigen, replacing a naturally occurring cysteine residue (Fig. 1c), facilitated glutaraldehyde-mediated coupling to porcine thyroglobulin (Sigma-Aldrich, Gillingham, UK) as a carrier protein, using 5% glutaraldehyde (Sigma-Aldrich, Gillingham, UK) in phosphate buffer (0.1 M; pH 7.2). Then, antigen peptide-thyroglobulin conjugates were used for the immunisation of one rabbit per antigen peptide (70-day protocol; Charles River Biologics, Romans, France). Conjugates were emulsified in Freund’s complete adjuvant for primary immunisations (~100 nmol antigen peptide) and in Freund’s incomplete adjuvant for three booster immunisations (~50 nmol antigen peptide). The presence of antibodies to the antigen peptides in post-immunisation serum samples was assessed using an enzyme-linked immunosorbent assay (ELISA; see below), in comparison with pre-immune serum.Fig. 1

Amino acid sequences of a vasopressin/oxytocin-type (asterotocin) precursor (ArASTP), b corazonin-type precursor (ArCRZP) and c luqin-type precursor (ArLQP) in Asterias rubens. Predicted signal peptides are shown in blue, neuropeptides are shown in red but with C-terminal glycine residues that are substrates for amidation shown in orange, dibasic cleavage sites are shown in green and the neurophysin domain of ArASTP is shown in pink. The cysteine residues in ArASTP that form a disulphide bridge in the mature neuropeptide are underlined. The sequences of the C-terminal peptides that were used as antigens for antibody production are shown in bold yellow. Note, however, that the underlined cysteine residue in ArLQP was replaced with a lysine residue at the N-terminus of the antigen peptide to provide reactive sites for glutaraldehyde-mediated coupling to a carrier protein (thyroglobulin). GenBank Accession numbers: a ALJ99953.1 (Semmens et al. 2016 (link); Odekunle et al. 2019 (link)); b ALJ99955.1 (Semmens et al. 2016 (link); Tian et al. 2017 (link), 2016 (link)); c ALJ99961.1 (Semmens et al. 2016 (link); Yañez-Guerra et al. 2018 (link))

Antibodies to the antigen peptides were purified from the final bleed antiserum by affinity purification using the AminoLink Plus Immobilization Kit (Thermo Fisher Scientific, Waltham, MA), with bound antibodies eluted using glycine elution buffer (6.3 ml of 100 mM glycine [VWR Chemicals, Leicestershire, UK] and 0.7 ml of Tris [1 M, pH = 7.0]) and trimethylamine (TEA) elution buffer (6.3 ml of TEA [Sigma-Aldrich, Gillingham, UK] and 0.7 ml of Tris [1 M, pH = 7.0]). Eluates were dialysed and sodium azide (0.1%) was added for long-term storage of the affinity-purified antibodies at 4 °C. ArASTP, ArCRZP and ArLQP antibodies eluted with TEA were diluted in 5% normal goat serum (NGS; Sigma-Aldrich, Gillingham, UK)/PBST (phosphate-buffered saline containing 0.1% Tween-20) at 1:20, 1:15 and 1:15, respectively, and then used for immunohistochemistry (see below). The rabbit antisera to ArASTP, ArCRZP and ArLQP have been assigned the RRID numbers RRID:AB_2922389, RRID:AB_2922390 and RRID:AB_2922391, respectively.

Tinoco A.B., Egertová M, & Elphick M.R. (2023). Immunohistochemical localisation of vasopressin/oxytocin-type, corazonin-type and luqin-type neuropeptide expression in the starfish Asterias rubens using antibodies to the C-terminal region of precursor proteins. Cell and Tissue Research, 391(3), 441-456.

Full text: Click here

Publication 2023

Acids Antibodies Antibody Affinity Antibody Formation Antigens Asterias AVP protein, human Biological Factors Carrier Proteins Chromatography, Affinity corazonin protein, insect Cysteine Cytokinesis Disulfides Enzyme-Linked Immunosorbent Assay Freund's Adjuvant Glutaral Glycine Goat Immobilization Immune Sera Immunization Immunohistochemistry LUQIN Lysine Neuropeptides Neurophysins Oxytocin Peptides Phosphates Pigs polypeptide C Proteins Rabbits Rivers Ruthenium Ben Saline Solution Secondary Immunization Serum Signal Peptides Sodium Azide Thyroglobulin trimethylamine Tromethamine Tween 20 Vaccines, Peptide

Phylogenetic Analysis of Neuropeptide Precursors

FASTA files of aligned peptide precursor sequences were converted into PHYLIP and NEXUS formats using AliView 1.18-beta7 (Larsson, 2014 (link)). After defining the N-terminus of each neuropeptide precursor as starting partition, best-fit partitioning schemes and substitution models for subsequent phylogenetic analyses were predicted with ModelFinder (Chernomor, von Haeseler & Minh, 2016 (link); Kalyaanamoorthy et al., 2017 (link); Minh et al., 2021 (link)) implemented in IQ-TREE release 2.1.4b (Minh et al., 2020 (link)). Models and concatenated alignments for all analyses of both data sets are listed in Data S1 and S2. All phylogenetic analyses have been rooted using the Cleroidea Melyris sp. Bayesian inference (BI) analyses were run with MrBayes, with four runs, using eight chains and a sample frequency of 1,000 until convergence was achieved (PSFR value between 1.00–1.02) with a 10,000,000 generations (Ronquist et al., 2012 (link)). Maximum likelihood (ML) analyses were carried out using IQ-TREE 2.1.4b. ML analyses of both data sets were ran with the nearest-neighbour interchange search to consider all possible nearest-neighbour interchanges (-allnni) and branch support was evaluated with 1,000 ultra-fast bootstrap (UFBoot) (Hoang et al., 2017 ) and the Shimodaira–Hasegawa-like approximate likelihood ratio test (SH-aLRT) (Guindon et al., 2010 (link)). Trees were visualized using FigTree 1.4.2 (http://tree.bio.ed.ac.uk/) and designed in Inkscape 1.0 (https://inkscape.org/).

Ragionieri L., Zúñiga-Reinoso Á., Bläser M, & Predel R. (2023). Phylogenomics of darkling beetles (Coleoptera: Tenebrionidae) from the Atacama Desert. PeerJ, 11, e14848.

Full text: Click here

Publication 2023

Neuropeptides Nexus Peptides Trees

Comparative Analysis of Insect Neuropeptide Precursors

Available amino acid sequences of neuropeptide precursors of Tr. castaneum and Te. molitor (Li et al., 2008 (link); Veenstra, 2019 (link); Marciniak, Pacholska-Bogalska & Ragionieri, 2022 (link)) were used as initial queries to search for orthologous sequences in the transcriptome assemblies. The assembled transcripts were analysed with the tblastn algorithms provided by NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi) or BioEdit version 7.0.5.3 (Hall, 1999 ). In case of missing data, precursor sequences of closely related taxa were used as alternative query sequences. Candidate nucleotide precursor gene sequences were translated into amino acid sequences using the ExPASy Translate tool (Artimo et al., 2012 (link); http://web.expasy.org/translate/) with the standard genetic code. Orthologous neuropeptide precursor sequences were aligned using the MAFFT-L-INS-i algorithm (Katoh & Standley, 2013 (link)) (dvtditr (amino acid) Version 7.299b alg=A, model=BLOSUM62, 1.53, −0.00, −0.00, noshift, amax =0.0); terminal sequences which were only found in few species were manually trimmed. The results were then manually checked for misaligned sequences using, e.g., N-termini of signal peptides and conserved amino-acid residues (cleavage signals, Cys as target for disulfide bridges) as anchor points. Individual amino acid alignments of each group of orthologous neuropeptide precursors were concatenated with catsequences 1.3 (https://zenodo.org/record/4409153#.YmJYT35Byot). The average evolutionary divergence for each neuropeptide precursor was calculated as in Bläser & Predel (2020) (link). Briefly, overall mean distances (± standard error after 500 bootstrap generations) were computed with MEGA X (Kumar et al., 2018 (link)) implementing the Poisson correction model (Zuckerkandl & Pauling, 1965 ). Amino acid compositions and parsimony informative sites of the combined alignment were calculated using MEGA X.

Ragionieri L., Zúñiga-Reinoso Á., Bläser M, & Predel R. (2023). Phylogenomics of darkling beetles (Coleoptera: Tenebrionidae) from the Atacama Desert. PeerJ, 11, e14848.

Full text: Click here

Publication 2023

Amino Acids Amino Acid Sequence Base Sequence Biological Evolution Cytokinesis Disulfides Genes Genetic Code Neuropeptides Signal Peptides Transcriptome

Top products related to «Neuropeptides»

Syntocinon spray by Novartis

Sourced in Switzerland

Syntocinon Spray is a pharmaceutical product manufactured by Novartis. It contains the active ingredient oxytocin, which is a naturally occurring hormone. The primary function of Syntocinon Spray is to provide a metered dose delivery system for the administration of oxytocin.

High capacity cdna reverse transcription kit by Thermo Fisher Scientific

Sourced in United States, Germany, United Kingdom, Japan, Lithuania, France, Italy, China, Spain, Canada, Switzerland, Poland, Australia, Belgium, Denmark, Sweden, Hungary, Austria, Ireland, Netherlands, Brazil, Macao, Israel, Singapore, Egypt, Morocco, Palestine, State of, Slovakia

The High-Capacity cDNA Reverse Transcription Kit is a laboratory tool used to convert RNA into complementary DNA (cDNA) molecules. It provides a reliable and efficient method for performing reverse transcription, a fundamental step in various molecular biology applications.

Imagequest by Thermo Fisher Scientific

Sourced in Germany

ImageQuest is a software platform designed for image acquisition, analysis, and management in scientific research laboratories. It provides a comprehensive solution for capturing, processing, and organizing digital images from various imaging techniques.

Ez link sulfo nhs lc biotinylation kit by Thermo Fisher Scientific

Sourced in United States, China

The EZ-Link Sulfo-NHS-LC-Biotinylation kit is a reagent kit designed for the covalent labeling of proteins with biotin. The kit includes the Sulfo-NHS-LC-Biotin reagent, which reacts with primary amine groups on proteins to form a stable amide bond, allowing the attachment of biotin to the target protein.

Trizol reagent by Thermo Fisher Scientific

Sourced in United States, China, Japan, Germany, United Kingdom, Canada, France, Italy, Australia, Spain, Switzerland, Netherlands, Belgium, Lithuania, Denmark, Singapore, New Zealand, India, Brazil, Argentina, Sweden, Norway, Austria, Poland, Finland, Israel, Hong Kong, Cameroon, Sao Tome and Principe, Macao, Taiwan, Province of China, Thailand

TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.

Colchicine by Merck Group

Sourced in United States, Germany, France, Canada, India, Japan, United Kingdom, Italy, Spain, Macao

Colchicine is a chemical compound used in various laboratory and research applications. It is a naturally occurring alkaloid derived from the autumn crocus plant. Colchicine is primarily used as a research tool to study cell division and microtubule dynamics.

Xcalibur by Thermo Fisher Scientific

Sourced in United States, Germany, France, Canada, Italy, United Kingdom, Slovenia, Switzerland

Xcalibur is a powerful data acquisition and analysis software for Thermo Fisher Scientific mass spectrometry systems. It enables users to control instrument operation, acquire data, and perform data analysis.

Akta purifier system by GE Healthcare

Sourced in United States, Sweden, United Kingdom, China

The AKTA Purifier system is a versatile and automated chromatography platform designed for protein purification. It provides precise control and monitoring of key parameters, enabling efficient separation and purification of biomolecules. The system is equipped with advanced software for method development and data analysis.

Horseradish peroxidase hrp by BBI Solutions

Sourced in United States

Horseradish peroxidase (HRP) is an enzyme that catalyzes the oxidation of various substrates in the presence of hydrogen peroxide. It is commonly used as a detection and labeling agent in various biochemical and immunological applications.

More about "Neuropeptides"

Neuropeptides are a diverse class of small, bioactive peptide molecules produced and released by neurons in the central and peripheral nervous systems.
These neurochemicals play crucial roles in a wide range of neurological processes, including neurotransmission, neuromodulation, and neurohormonal regulation.
Neuropeptides are involved in a variety of physiological functions, such as pain perception, stress response, appetite, mood, and more.
They are also implicated in the pathogenesis of various neurological and psychiatric disorders, making them a key focus of research in the field of neuroscience.
Syntocinon Spray, a synthetic version of the neuropeptide oxytocin, is used to treat certain medical conditions related to neuropeptide imbalances.
The High-Capacity cDNA Reverse Transcription Kit is a valuable tool for studying neuropeptide gene expression, while the ImageQuest software can be used to analyze and quantify neuropeptide-related imaging data.
The EZ-Link Sulfo-NHS-LC-Biotinylation kit enables the labeling and detection of neuropeptides, and the TRIzol reagent is commonly used for neuropeptide RNA extraction and purification.
Colchicine, a plant-derived compound, is known to affect neuropeptide transport and distribution within cells.
The Xcalibur software is often used for the analysis of neuropeptide mass spectrometry data, and the AKTA Purifier system is a valuable tool for the purification and separation of neuropeptides.
Horseradish peroxidase (HRP) is a commonly used enzyme for the detection and quantification of neuropeptides in various experimental and clinical applications.
Ongoing research on neuropeptides is critical for enhancing our understanding of the complexities of the nervous system and developing potential therapeutic interventions for neurological and psychiatric disorders.
The insights gained from studying these important neurochemicals can lead to advancements in the diagnosis, treatment, and management of a wide range of neurological conditions.