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236 results for “venom”
Data from: Phylogenomic reclassification of the world's most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution
Here we show that the most venomous spiders in the world are phylogenetically misplaced. Australian atracine spiders (family Hexathelidae), including the notorious Sydney funnel-web spider Atrax robustus, produce venom peptides that can kill people. Intriguingly, eastern Australian mouse spiders (family Actinopodidae) are also medically dangerous, possessing venom peptides strikingly similar to Atrax hexatoxins. Based on the standing morphology-based classification, mouse spiders are hypothesized distant relatives of atracines, having diverged over 200 million years ago. Using sequence-capture phylogenomics, we instead show convincingly that atracines are sister to actinopodids, and that hexathelids are non-monophyletic. Three new mygalomorph lineages are elevated to the family level, and a revised circumscription of the family Hexathelidae is presented. Re-writing this phylogenetic story has major implications for how we study venom evolution in these spiders, and potentially genuine consequences for antivenom development and bite treatment research. More generally, our research provides a textbook example of the applied importance of modern phylogenomic research.
Data on global expression of non-coding RNome in mice gastrocnemius muscle exposed to jararhagin, snake venom metalloproteinase
<p>This study describes the data on the global expression profile of small RNA (smRNAs) molecules in mice gastrocnemius muscle exposed to jararhagin, snake venom metalloproteinase. The data include smRNAs and microRNAs in mice gastrocnemius muscle challenged with Jararhagin (Jar; n=4) in the right paw or phosphate-buffered saline (PBS; control; n=4) in the left paw. smRNA-Seq libraries were generated after 24hs of exposure to PBS or jararhagin. </p>
Host aphid immunosuppression by Aphidius ervi venom
<p>Dataset referred to the manuscript: </p> <p><span><span><span><strong>Host aphid immunosuppression by </strong></span></span></span><span><span><span><em><strong>Aphidius</strong></em></span></span></span><span><span><span><strong> </strong></span></span></span><span><span><span><em><strong>ervi</strong></em></span></span></span><span><span><span><strong> venom</strong></span></span></span></p> <p><span><span><strong>Elia Russo</strong></span></span><span><sup><span><strong>1§</strong></span></sup></span><span><span><strong>, Andrea Becchimanzi</strong></span></span><span><sup><span><strong>1,2§</strong></span></sup></span><span><span><strong>, Giulia Magoga</strong></span></span><span><sup><span><strong>1</strong></span></sup></span><span><span><strong>, Matteo Montagna</strong></span></span><span><sup><span><strong>1,2</strong></span></sup></span><span><span><strong>, Ilaria Di Lelio</strong></span></span><span><sup><span><strong>1,2</strong></span></sup></span><span><span><strong>* & Francesco Pennacchio</strong></span></span><span><sup><span><strong>1,2</strong></span></sup></span><span><span><strong>*</strong></span></span></p> <p> </p> <p><sup><span>1</span></sup><span>University of Naples ‘Federico II’ - Department of Agricultural Sciences, Naples, Italy, and </span><sup><span>2</span></sup><span>BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples ‘Federico II’, Naples, Italy</span></p> <p> </p> <p><span><span><strong>bstract </strong></span></span></p> <p><span><span>The host immunosuppression by parasitic wasps is an important component of the host regulation strategy. The venom injected at the oviposition is one of the key-factors involved in this host alteration and, in some parasitoids, its immunosuppressive role is complemented by wasp’s symbionts. Most studies in this research area are related to hosts belonging to Lepidoptera and Diptera, for which a strong immune response is observed, whereas little is known for hemimetabolous host species, characterized by apparently much weaker defense barriers. To fill this research gap, here we focus on the host–parasitoid system </span></span><span><span><em>Acyrthosiphon pisum</em></span></span><span><span> </span></span><span>(Harris) </span><span><span>(Hemiptera: Aphididae) – </span></span><span><span><em>Aphidius ervi</em></span></span><span><span> Haliday (Hymenoptera: Braconidae). We functionally characterized </span></span><span><span>a serine</span></span><span><span> protease homolog (</span></span><span><span><em>Ae</em></span></span><span><span>SPH) protein </span></span><span><span>in vivo, </span></span><span><span>identified in the venom of the aphid endoparasitoid </span></span><span><span><em>A. ervi</em></span></span><span><span>, generating </span></span><span><span><em>Ae</em></span></span><span><span>SPH-depleted female wasps by RNA interference and evaluating their capacity to successfully parasitize the host. Parasitism success rate was negatively affected by </span></span><span><span><em>Ae</em></span></span><span><span>SPH knockdown and associated with an increased phenoloxidase (PO) cascade activation in aphids, scored by measuring PO enzymatic activity and the expression of</span></span><span><span><em> phenoloxidase activating factor 2</em></span></span><span><span>, a</span></span><span><span> proPO-activating gene upregulated in response to </span></span><span><span><em>A. ervi</em></span></span><span><span> parasitism. Our results indicate that </span></span><span><span><em>Ae</em></span></span><span><span>SPH contributes to parasitism success by inhibiting the melanization response of the host, which is therefore an important component of the defense barriers involved in the parasitoid egg suppression. The undergoing studies on other virulence factors in </span></span><span><span><em>A. ervi</em></span></span><span><span> venom will allow to further characterize the immunosuppression strategy and its possible broader role in the host regulation through its action on aphid symbiont development. </span></span></p>
DATASET - Mass Spectrometry - Snake venom proteomics of seven taxa of the genera Vipera, Montivipera, Macrovipera and Daboia across Türkiye
<p><strong>Publication: Damm <em>et al.</em> 2024 - <a title="DOI URL" href="https://doi.org/10.1021/acs.jproteome.4c00171">https://doi.org/10.1021/acs.jproteome.4c00171</a></strong></p> <p> </p> <p><strong>This DATASET collection includes the mass spectrometry files for proteomics venom investigation of seven taxa of the genera <em>Vipera</em>, <em>Montivipera</em>, <em>Macrovipera</em> and <em>Daboia </em>across Türkiye.</strong></p> <p><strong>Species list:</strong></p> <ol> <li>Vipera berus barani</li> <li>Vipera darevskii</li> <li>Montivipera bulgardaghica bulgardaghica </li> <li>Montivipera bulgardaghica albizona</li> <li>Montivipera xanthina</li> <li>Macrovipera lebetinus obtusa</li> <li>Daboia palaestinae</li> </ol> <p><strong>Folders 01-07 - BOTTOM-UP PROTEOMICS</strong>: The venom pools were investigated by the bottom-up "snake venomics" (labled as SVX) approach and in short: separated by RP-HPLC, followed by SDS-PAGE separation and the single bands were in-gel processed by DTT, IAC and finally o/n tryptic digested. Samples submitted to HPLC-MS/MS. Early peptidic fractions of the first HPLC run were directly submitted to HPLC-MS/MS analytic w/o further gel procession. Folders 01 to 07 include the MS and MS/MS spectra of the snake species 1-7, respectively. Files are included as RAW and MZML format.</p> <p>Used instrument: LTQ Orbitrap XL mass spectrometer (Thermo, Bremen, Germany) with an Agilent 1260 HPLC system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Grace Vydac 218MS C18 (2.1 × 150 mm; 5 μm particle size) column.</p> <p>Modifications: UNIMOD:4 - \"Iodoacetamide derivative.\"</p> <p>Used protein database: Uniprot_8570_serpentes_reviewed_canonical_2640_entries_cRAP_210408.fasta</p> <p><strong>Folders 10-11 - TOP-DOWN PROTEOMICS</strong>: The venom pools were investigated by the non-reduced and TCEP reduced top-down (labled as TD) approach and in short: untreated or TCEP reduced samples submitted to HPLC-MS/MS. Folders 10 and 11 include the MS and MS/MS spectra of the snake species 1-7 as labled. Files are included as RAW and MZML format.</p> <p>Used instrument: Q Exactive HF mass spectrometer (Thermo, Bremen, Germany) with a Vanquish ultra-high performance liquid chromatography (UHPLC) system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Supelco Discovery BIO wide C18 (2.0 × 150 mm; 3 μm particle size; 300 Å pore size).</p> <p>Modifications: none (either red. or non-red. disulfide bridges)</p> <p>Used protein database for TopPIC analysis: Uniprot_8570_serpentes_reviewed_ISOandCAN_2749_entries_NOcRAP_231011.fasta</p> <p> </p>
Aphidius ervi venom regulates Buchnera contribution to host nutritional suitability
<p>Dataset referred to the manuscript "Aphidius ervi venom regulates Buchnera contribution to host nutritional suitability" by </p> <p><a href="../search?q=metadata.creators.person_or_org.name%3A%22Russo,+Elia%22"><span>Russo, Elia</span><sup>1 </sup></a><a href="../search?q=metadata.creators.person_or_org.name%3A%22Di+Lelio,+Ilaria%22"><span>Di Lelio, Ilaria</span><sup>2 </sup></a><a href="../search?q=metadata.creators.person_or_org.name%3A%22Shi,+Min%22"><span>Shi, Min</span><sup>3 </sup></a><a href="../search?q=metadata.creators.person_or_org.name%3A%22Becchimanzi,+Andrea%22"><span>Becchimanzi, Andrea</span><sup>2 </sup></a><a href="../search?q=metadata.creators.person_or_org.name%3A%22Pennacchio,+Francesco%22"><span>Pennacchio, Francesco</span><sup>2</sup></a></p> <p><sup>Abstract: The association between the pea aphid, Acyrthosiphon pisum (Harris) (Homoptera: Aphididae), and the endophagous parasitoid wasp Aphidius ervi Haliday (Hymenoptera: Braconidae) offers a unique model system for studying the molecular mechanisms underlying the complex interactions between the parasitoid, its host and the associated primary symbiont. Here, we investigate in vivo the functional role of the most abundant component of A. ervi venom, Ae-γ-glutamyl transpeptidase (Ae-γ-GT), which is known to induce host castration. Microinjections of double-stranded RNA into A. ervi pupae stably knocked down Ae-γ-GT1 and Ae-γ-GT2 paralogue genes in newly emerged females. These females were used to score the phenotypic changes both in parasitized hosts and in the parasitoid's progeny, as affected by a venom blend lacking Ae-γ-GT. Ae-γ-GT gene silencing enhanced growth both of host and parasitoid, supported by a higher load of the primary bacterial symbiont Buchnera aphidicola. Emerging adults showed a reduced survival and fecundity, suggesting a trade-off with body size. This demonstrates in vivo the primary role of Ae-γ-GT in host ovary degeneration and suggests that this protein counterbalances the proliferation of Buchnera likely triggered by other venom components. Our study provides a new approach to unravelling the complexity of aphid parasitoid venom in vivo, and sheds light on a novel role for Ae-γ-GT in host regulation.</sup></p> <p> </p>
Phylogenetically diverse diets favor more complex venoms in North American pitvipers
<p>The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are traits composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates considerably over evolutionary timescales, with apparent increases and decreases in complexity, yet the evolutionary causes of this variation is unclear. Here, we tested alternative hypotheses for the link between venom complexity and ecological sources of selection related to diet in the largest clade of front-fanged venomous snakes in North America: the rattlesnakes, copperheads, cantils, and cottonmouths <em>Crotalus, Sistrurus </em>and <em>Agkistrodon</em>. We generated independent transcriptomic and proteomic measures of venom complexity and then estimated prey diversity using the past century's extensive natural history studies on these snakes. We then conducted comparative tests relating different measures of predator venom complexity and prey community diversity using the first, genome-scale, dated phylogenies for this clade of snakes. Strikingly, phylogenetic diversity of prey was more strongly correlated to venom diversity than was species diversity, implicating prey species divergence, rather than the number of lineages alone, in the evolution of venom complexity. This positive relationship was observed within three of the four largest toxin gene families in viper venom. Given documented examples of taxonomic specificity of venoms spanning several levels of divergence, we suggest that the phylogenetic diversity of prey measures functionally-relevant divergence in the molecular targets of venom, a claim supported by diversity in the coagulation cascade targets of snake venom serine proteases. Our results support the general concept that the evolved diversity of species in an ecological community is more important than their overall number in determining evolutionary patterns in predator trait complexity.</p>
Data accompanying "Identification of capsid-like proteins in venomous and parasitic animals"
<p>This data accompanies the pub "Identification of capsid-like proteins in venomous and parasitic animals". The DOI for this pub is <a href="https://doi.org/10.57844/arcadia-14b2-6f27" target="_blank" rel="noopener noreferrer">https://doi.org/10.57844/arcadia-14b2-6f27</a></p> <p> </p> <p><strong>Files and folders included: </strong></p> <p> </p> <p><strong>1.</strong> Manually annotated results of searching VOG HMMs against venom transcriptomes: Annotated_capsid_no_cutoffs_summary_with_seqs_05092024.xlsx</p> <p><strong>2.</strong> Manually annotated results of running preHGT on the genomes of venomous species: Annotated_hgt_results_venom_050924.xlsx</p> <p><strong>3. </strong>The genomes we input into preHGT: preHGT_input_genomes.csv</p> <p><strong>4.</strong> Genbank files of the genomic neighborhood of putatively horizontally transferred viral genes in the tick genome. There are seven GenBank files, one for each contig. Named with protein name.</p> <p><strong>5.</strong> BLAST results from searching putatively endogenized viral proteins against tick salivary transcriptomes: TSA_blast_results.csv</p> <p><strong>6.</strong> Results from searching the putatively endogenized viral capsid proteins against AlphaFold/UniProt50 version 4, AlphaFold/Swiss-Prot version 4, and AlphaFold/Proteome version 4 using the Foldseek webserver: Foldseek_capsid_followup_05092024.xlsx</p> <p><strong>7.</strong> Newick files of the three trees displayed in Figure 3 and Figure 5 . </p>
ProteinCartograhpy data accompanying "Identification of capsid-like proteins in venomous and parasitic animals"
<p>This is the data for the <a href="https://github.com/Arcadia-Science/ProteinCartography/releases/tag/v0.4.2">ProteinCartography</a> analysis in the pub "<a href="https://doi.org/10.57844/arcadia-14b2-6f27">Identification of capsid-like proteins in venomous and parastic animals.</a>" Note that ProteinCartography (v0.4.2) was run in "Cluster" mode or "From-folder" mode using the parameters set in the <code>config_ff.yml</code> and the <em>Ornithodoros turicata </em>proteins. Notebooks used to fetch data and prepare custom plots can be found in the capsids GitHub <a href="https://github.com/Arcadia-Science/capsids">repository</a>.</p> <p> </p> <p><strong>Files in this data repository include: </strong></p> <p><code>output.zip</code> is a folder containing all of the output files for the <em>Ornithodoros</em> ProteinCartography run, including the maps, aggregated features files, and the all-v-all similarity matrix.</p> <p><code>structures.zip</code> is a folder containing all the structures used in the ProteinCartography analysis. Structures beginning with "VOG" are viral capsid proteins folded using <a href="https://doi.org/10.1126/science.ade2574">ESMFold</a>.</p> <p><code>ornithodoros_aggregated_features.tsv</code> is a file containing all the metadata gathered for each protein in the analysis from either <a href="https://www.uniprot.org">UniProt</a> or the <a href="https://vogdb.org">VOG database</a>.</p> <p><code>ornithodoros_aggregated_features_pca_umap.html</code> is the final map of the capsid proteins with the <em>Ornithodoros</em> proteins with metadata overlays.</p> <p><code>ornithodoros_aggregated_features_pca_umap.tsv</code> is a file containing all of the metadata gathered for each protein in the analysis, as well as the coordinates for the map.</p> <p><code>ornithodoros_leiden_similarity.html</code> is a heatmap showing the average between-cluster and within-cluster similarity between every cluster in the analysis.</p> <p><code>tick_or_virus_umap.html</code> is a version of the final map that specifically highlights which proteins are from capsids and which proteins are from <em>Ornithodoros</em>. </p> <p><code>uniprot_features1.tsv</code> is a file containing all of the UniProt metadata fetched for the <em>Ornithodoros</em> proteins, as well as the viral capsid VOG identifiers. This file is used as an input for the ProteinCartography analysis.</p> <p><code>ornithodoros.txt</code> us a file containing all of the <em>Ornithodoros</em> proteins fetched from the <a href="https://doi.org/10.1038/s41586-021-03819-2">AlphaFold</a> <a href="https://doi.org/10.1093/nar/gkab1061">database.</a></p> <p><code>config_ff.yml</code> is the configuration file for the ProteinCartography run. </p>
Video of Juveniles of the Bluespotted Trevally, Caranx bucculentus (Teleostei: Carangidae), schooling with venomous catfishes (Plotosidae): a new case of mimicry
<p>Video of Juveniles of the Bluespotted Trevally, Caranx bucculentus (Teleostei: Carangidae), schooling with venomous catfishes (Plotosidae): a new case of mimicry: part of the publication:</p> <p>Smith-Vaniz, W.F., DeLoach, A. & DeLoach, N. (2018) Juveniles of the Bluespotted Trevally, Caranx bucculentus (Teleostei: Carangidae), schooling with venomous catfishes (Plotosidae): a new case of mimicry. Journal of the Ocean Science Foundation, 30, 82–84.<br> </p>
DATASET - Mass Spectrometry - Snake venom proteomics of Deinagkistrodon acutus
<p><strong>This DATASET collection includes the mass spectrometry files for shotgun proteomics venom investigation the sharp-nosed viper (<em>Deinagkistrodon acutus</em>) from China.</strong></p> <p><strong>Species list:</strong></p> <ol> <li>Deinagkistrodon acutus</li> </ol> <p><strong>Folders 01-02 - BOTTOM-UP SHOTGUN PROTEOMICS</strong>: The venom pool was investigated by the bottom-up shotgun (labled as SG) approach and in short: in-solution processed by DTT, IAC and finally o/n tryptic digested. Samples submitted to HPLC-MS/MS. Folders includes the MS and MS/MS spectra of Deinagkistrodon acutus. Files are included as RAW and MZML format in folder 01 and 02, respectively.</p> <p>Used instrument:</p> <p>Advion TriVersa NanoMate (Advion BioSciences) into an Orbitrap Eclipse Tribrid MS instrument (Thermo Fisher Scientific) with an UltiMate 3000RSLCnano system (Thermo Fisher Scientific) using 50 cm μPAC C18 column (Pharma Fluidics).</p> <p>Modifications: UNIMOD:4 - \"Iodoacetamide derivative.\"</p>
Data from: Local prey community composition and genetic distance predict venom divergence among populations of the northern Pacific rattlesnake (Crotalus oreganus)
Identifying the environmental correlates of divergence in functional traits between populations can provide insights into the evolutionary mechanisms that generate local adaptation. Here, we assess patterns of population differentiation in expressed venom proteins in Northern Pacific rattlesnakes (Crotalus oreganus) from 13 locations across California. We evaluate the relative importance of major biotic (prey species community composition), abiotic (temperature, precipitation, and elevation) and genetic factors (genetic distance based on RADseq loci) as correlates of population divergence in venom phenotypes. We found that over half of the variation in venom composition is associated with among-population differentiation for genetic and environmental variables, and that this variation occurred along axes defining previously observed functional trade-offs between venom proteins that have neurotoxic, myotoxic and hemorrhagic effects. Surprisingly, genetic differentiation among populations was the best predictor of venom divergence, accounting for 46% of overall variation, whereas differences in prey community composition and abiotic factors explained smaller amounts of variation (23% and 19%, respectively). The association between genetic differentiation and venom composition could be due to an isolation by distance effect or, more likely it may reflect an isolation-by-environment effect where selection against recent migrants is strong, producing a correlation between neutral genetic differentiation and venom differentiation. Our findings suggest that even coarse estimates of prey community composition can be useful in understanding the selection pressures acting on patterns of venom protein expression. Additionally, our results suggest that factors other than adaptation to spatial variation in prey need to be considered when explaining population divergence in venom.
FIGURE 8 in New materials of Estesia mongoliensis (Squamata: Anguimorpha) and the evolution of venom grooves in lizards
FIGURE 8. Postcrania of Estesia mongoliensis (IGM 3/760). Scale bar = 10 mm.
FIGURE 2 in New materials of Estesia mongoliensis (Squamata: Anguimorpha) and the evolution of venom grooves in lizards
FIGURE 2. Lateral view of IGM 3/196. Scale bar = 10 mm.
Figure 2 in The evolution of venom-delivery systems in snakes
Figure 2. Relationships among colubroid snakes proposed by Cadle (1988).
Figure 3 in The evolution of venom-delivery systems in snakes
Figure 3. Relationships among colubroid snakes proposed by Kraus & Brown (1998).
Figure 1 in The evolution of venom-delivery systems in snakes
Figure 1. Phylogenetic relationships among living snakes (Pough et al., 2001).
Snakes on a plain: Complex biotic and abiotic factors determine venom variation in North America's widest-ranging rattlesnake
<p><strong>Background</strong>. Snake venoms are trophic adaptations that represent an ideal model to examine the evolutionary factors that shape polymorphic traits under strong natural selection. Venom compositional variation is substantial within and among venomous snake species. However, the forces shaping this phenotypic complexity, as well as the potential integrated roles of biotic and abiotic factors, have received little attention. Here, we investigate geographic variation in venom composition in a wide-ranging rattlesnake (<em>Crotalus viridis viridis</em>) and contextualize this variation by investigating dietary, phylogenetic, and environmental variables that covary with venom.</p> <p><strong>Results</strong>. Using shotgun proteomics, venom biochemical profiling, and lethality assays, we identify 2 distinct divergent phenotypes that characterize major axes of venom variation in this species: a myotoxin-rich phenotype and a snake venom metalloprotease (SVMP)-rich phenotype. We find that dietary availability and temperature-related abiotic factors are correlated with geographic trends in venom composition.</p> <p><strong>Conclusions</strong>. Our findings highlight the potential for snake venoms to vary extensively within species, for this variation to be driven by biotic and abiotic factors, and for the importance of integrating biotic and abiotic variation for understanding complex trait evolution. Links between venom variation and variation in biotic and abiotic factors indicate that venom variation likely results from substantial geographic variation in selection regimes that determine the efficacy of venom phenotypes across populations and snake species. Our results highlight the <a>implicit </a>influence of abiotic factors on biotic factors that ultimately shape venom phenotype, providing evidence for a central role of local selection as a key driver of venom variation.</p>
Venom: Toxin Accessory Domain Search
<p>This contains the different fasta files used and generated for the search of accessory domains fused with toxin proteins in a variety of venoms and tick saliva. </p> <p>2023-06-15-updated-venom-tick-proteins.fasta : fasta file of our custom "venom proteins from transcriptomes” data set, that was generated from the transcriptomes of venom glands of 124 species and from the salivary glands of 21 tick species</p> <p>uniprot-toxin-clustering_rep_seq.fasta: fasta file of all the representative sequences of the UniProt manually curated database of proteins and toxins from various venoms (from the animal toxin annotation project ) obtained after clustering.</p> <p>2023-06-20-outliers-accessory-hits.fasta: fasta file of the accessory sequences identified on the toxin outliers observed in venoms and saliva.</p> <p>updated-accessory-toxin-clustering_rep_seq.fasta: fasta file of the representative sequences of the toxin outliers accessory sequences obtained after clustering.</p> <p> </p>
The Effect of Antihypertensive Drugs on Severity of Anaphylaxis and Side-effects During Venom Immunotherapy
ClinicalTrials.gov study NCT04269629. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Snakes on a plain: Complex biotic and abiotic factors determine venom variation in North America's widest-ranging rattlesnake
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