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236 results for “venom”
Dataset from "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2‑like Peptides"
<p>Dataset from "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2‑like Peptides", containing the most relevant all-atom output trajectories and input files ran with GROMACS 2021:</p> <p>1) <strong>pure_membrane_systems.7z</strong> - pure bilayer systems (AA1, AA2, AA5), including equilibration, calcium insertion, and umbrella sampling simulations;</p> <p>2) <strong>single_peptide_systems.7z</strong> - single peptide-containing systems (AA3, AA4, AA6), including equilibration, calcium insertion, and umbrella sampling simulations;</p> <p>3) <strong>multiple_peptide_systems.7z</strong> - multiple peptide-containing systems (AA7, AA8), including equilibration, calcium insertion, and umbrella sampling simulations.</p> <p>We have included the input files (.mdp), system topology (.top and .itp), initial and final structure files (.gro), the index file (.ndx), and the portable binary run input files (.tpr). We have also included the output trajectories of systems AA3, AA4, AA6-8 in .xtc format, and spaced every 500 ps.</p> <p>System composition is given in Table Z1. More details can be found in the related publication.</p> <p><strong>Table Z1. Simulated systems' details, including name, composition (in number of lipid and peptide molecules), number of atoms composing the systems, simulation (sim.) time, and total umbrella sampling (US) time.</strong> </p> <table> <tbody> <tr> <td><strong>System</strong></td> <td><strong>POPC/POPS/Peptide</strong></td> <td><strong>no. atoms (a)</strong></td> <td><strong>sim. time (µs)</strong></td> <td><strong>US time (µs)</strong></td> </tr> <tr> <td><strong>AA1</strong></td> <td>128/0/0</td> <td>40,226</td> <td>0.3</td> <td>10.8</td> </tr> <tr> <td><strong>AA2</strong></td> <td>0/128/0</td> <td>39,458</td> <td>0.3</td> <td>10.8</td> </tr> <tr> <td><strong>AA3</strong></td> <td>128/0/1</td> <td>40,504</td> <td>0.5</td> <td>32.3</td> </tr> <tr> <td><strong>AA4</strong></td> <td>0/128/1</td> <td>39,724</td> <td>0.5</td> <td>32.3</td> </tr> <tr> <td><strong>AA5</strong></td> <td>96/32/0</td> <td>40,034</td> <td>1.0</td> <td>-</td> </tr> <tr> <td><strong>AA6</strong></td> <td>96/32/1</td> <td>40,300</td> <td>1.0</td> <td>-</td> </tr> <tr> <td><strong>AA7</strong></td> <td>96/32/5</td> <td>41,364</td> <td>1.0</td> <td>10.8</td> </tr> <tr> <td><strong>AA8</strong></td> <td>96/32/13</td> <td>55,128</td> <td>2.0</td> <td>10.8</td> </tr> </tbody> </table> <p>(a) for the US simulations, the total number of atoms was reduced in 1 because two sodium ions were substituted by a single calcium ion.</p>
DATASET - Mass Spectrometry - Snake venom proteomics of three subspecies of the North African mountain viper (Vipera monticola, Saint-Girons 1954) from Morocco
<p><strong>This DATASET collection includes the mass spectrometry files for proteomics venom investigation of three subspecies of the North African mountain viper (<em>Vipera monticola</em>, Saint-Girons 1954) from Morocco.</strong></p> <p><strong>Species list:</strong></p> <ol> <li>Vipera monticola monticola</li> <li>Vipera monticola atlantica</li> <li>Vipera monticola saintgironsi</li> </ol> <p><strong>Folders 01-03 - 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 03 include the MS and MS/MS spectra of the snake species 1-3, 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_CandIso_2747_entries_230398.fasta</p>
Fig. 4 in Expressed sequence tags in venomous tissue of Scorpaena plumieri (Scorpaeniformes: Scorpaenidae)
Fig. 4. Sequence alignment of putative lectin from Scorpaena plumieri. Alignment of a lectin-like EST in silico translated sequence from S. plumieri (ClustalW2 EBI) with fish-egg lectin from Oplegnathus fasciatus (BAL618145), Dicentrarchus labrax (CBK52298), Maylandia zebra (XP_004574029), and Oreochromis niloticus (XP003443389). The recombinant clone was isolated with antibody fraction derived from S. plumieri venom. * identifies and identical residue;: identifies a conserved residue. Underlined residues represent invariable sites, underlined IRLS = N-acetylation site.
Fig. 3 in Expressed sequence tags in venomous tissue of Scorpaena plumieri (Scorpaeniformes: Scorpaenidae)
Fig. 3. The classification of EST from Scorpaena plumieri based on their putative fractions. Three-hundred fifty-six EST edited sequences were initially analyzed with Blast and Swiss protein databanks. The consensus sequence was attributed a function based on the strongest match.
Fig. 2 in Expressed sequence tags in venomous tissue of Scorpaena plumieri (Scorpaeniformes: Scorpaenidae)
Fig. 2. Agarose gel electrophoresis of DNA isolated from clones. White colonies containing insert were grown and the plasmidial DNA isolated and digested with EcoRI enzyme. An aliquot from each clone (1-27) was electrophoresed on 1% Agarose gel and stained with ethidium bromide.
Fig. 1 in Expressed sequence tags in venomous tissue of Scorpaena plumieri (Scorpaeniformes: Scorpaenidae)
Fig. 1. Agarose- formaldehyde electrophoresis of RNA from Scorpaena plumieri. A) 1) 2 µg of E. coli tRNA; 2) 2 µg de rRNA de Rattus norvegicus; 3) and 4) 2 µg total RNA from S. plumieri spine gland. B) 1) 2 µg de total RNA from S. plumieri; 2) the same sample incubated 2 h a 37ºC before electrophoresis.
DATASET - Mass Spectrometry - Snake venom proteomics of island and mainland V. ammodytes populations from North Macedonia
<p><strong><span>This DATASET collection includes the mass spectrometry files for proteomics venom investigation of island and mainland <em>V. ammodytes</em> populations from North Macedonia.</span></strong></p> <p><strong><span>Sample list:</span></strong></p> <ol> <li><span>Island - adult - male</span></li> <li><span>Island - adult - female</span></li> <li><span>Island - juvenile</span></li> <li><span>Island - subadult</span></li> <li><span>Mainland - adult</span></li> <li><span>Mainland - subadult</span></li> <li><span>Mainland - juvenile</span></li> </ol> <p><strong><span>Folders 01-07 - BOTTOM-UP PROTEOMICS</span></strong><span>: The venom pools were investigated by the bottom-up "snake venomics" (labelled 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 <em>V. ammodytes</em> sample pools from different populations. Files are included as RAW and MZML format.</span></p> <p><span>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 </span><span>μ</span><span>m particle size) column.</span></p> <p><span>Modifications: UNIMOD:4 - \"Iodoacetamide derivative.\"</span></p> <p><span>Used protein database: Uniprot_8750_serpentes_CanNIso_2674_entries_220210_cRAP_220210.fasta</span></p>
Fig. 2 in Whole body solvent soak gives representative venom alkaloid profile from Solenopsis invicta (Hymenoptera: Formicidae) workers
Fig. 2. Gas chromatograms of hexane extracts obtained from Solenopsis invicta workers by different extraction methods. Capillary milking, gland dissection, and body without gland represent chromatograms from the sequential extraction of the same individual ants; whole body represents the chromatogram from whole body solvent-soaking extracts of 20 intact workers.
Fig. 1 in Whole body solvent soak gives representative venom alkaloid profile from Solenopsis invicta (Hymenoptera: Formicidae) workers
Fig. 1. Total ion chromatogram of whole body solvent-soaking extract of 20 intact Solenopsis invicta workers in hexane.
Tentacle transcriptomes of the speckled anemone (Actiniaria: Actiniidae: Oulactis sp.): venom-related components and their domain structure
<p>This data set pertains to the transcriptome and proteomic analysis conducted on the tentacles of the speckled anemone (<em>Oulactis</em> sp. - yet to be formally described) from Australia. The aim of the study was to mine for novel peptide and proteins related to the venom in the tentacles of the speckled anemone. These sequences could then be used in structure, function and evolution studies in the search for sequences with potential therapeutic use.</p> <p>The data set includes the quant.sf for each individual (1, 2 and 3) and the Trinotate annotation reports for each individual and their assembly annotation.</p>
Proteo-transcriptomic characterization of the venom from the endoparasitoid wasp Pimpla turionellae with aspects on its biology and evolution
<p>Within mega-diverse Hymenoptera non-aculeate parasitic wasps represent 75 % of all hymenopteran species. Their ovipositor dual-functionally injects venom and employs eggs into (endoparasitoids) or onto (ectoparasitoids) diverse host species. Few endoparasitoid wasps such as <em>Pimpla turionellae</em> paralyze the host and suppress its immune responses, such as encapsulation and melanization, to guarantee their offspring’s survival. In our proteo-transcriptomic analysis we shed new light on the venom biology of the endoparasitoid <em>Pimpla turionealle</em>.</p> <p>All additional data is made available here, such as the transcriptome assembly file, CDS prediction and all proteome data files including the raw data. All alignments to train HMMsearch and JACKHMMERsearch are stored here as well and the alignments of identified venom proteins (known and novel).</p> <p>The readme file gives further explanation/information.</p>
Figure 4 in Age-dependent variations in the venom proteins of Vipera kaznakovi Nikolsky, 1909 and Vipera ammodytes (Linnaeus, 1758) (Ophidia: Viperidae)
Figure 4. Gel photograph showing the electrophoretic separation of the venom protein sample obtained from the 55-cm-long Vipera kaznakovi specimen, together with its densitometric tracing curve. For further explanation, see caption of Figure 2.
Figure 1 in Age-dependent variations in the venom proteins of Vipera kaznakovi Nikolsky, 1909 and Vipera ammodytes (Linnaeus, 1758) (Ophidia: Viperidae)
Figure 1. Polyacrylamide gel electrophoresis of venoms of V. kaznakovi of different lengths. A. 16.5 cm, B. 30 cm, C. 55 cm (S: Start, junction between the stacking and separation gels).
Figure 3 in Age-dependent variations in the venom proteins of Vipera kaznakovi Nikolsky, 1909 and Vipera ammodytes (Linnaeus, 1758) (Ophidia: Viperidae)
Figure 3. Gel photograph showing the electrophoretic separation of the venom protein sample obtained from the 30-cm-long Vipera kaznakovi specimen, together with its densitometric tracing curve. For further explanation, see caption of Figure 2.
Figure 8 in Age-dependent variations in the venom proteins of Vipera kaznakovi Nikolsky, 1909 and Vipera ammodytes (Linnaeus, 1758) (Ophidia: Viperidae)
Figure 8. Gel photograph showing the electrophoretic separation of the venom protein sample obtained from the 51.5-cm-long Vipera ammodytes specimen, together with its densitometric tracing curve. For further explanation, see caption of Figure 2.
Figure 5 in Age-dependent variations in the venom proteins of Vipera kaznakovi Nikolsky, 1909 and Vipera ammodytes (Linnaeus, 1758) (Ophidia: Viperidae)
Figure 5. Polyacrylamide gel electrophoresis of venoms of V. ammodytes of different lengths. A. 28.5 cm, B. 36.7 cm, C. 51.5 cm (S: Start, junction between the stacking and separation gels).
Fig. 4 in Proteomic analysis of the venom of the social wasp Apoica pallens (Hymenoptera: Vespidae)
Fig. 4. Identified proteins of social wasp Apoica pallens venom and their functions according to the literature.
Fig. 2 in Proteomic analysis of the venom of the social wasp Apoica pallens (Hymenoptera: Vespidae)
Fig. 2. Two-dimensional reference gel (14%) of the venom of the social wasp Apoica pallens, showing the proteins identified by MALDI-TOF/TOF analysis.
Fig. 3 in Proteomic analysis of the venom of the social wasp Apoica pallens (Hymenoptera: Vespidae)
Fig. 3. Classification of proteins according to the representativity in number of proteins identified in the Apoica pallens venom.
Fig. 1 in Proteomic analysis of the venom of the social wasp Apoica pallens (Hymenoptera: Vespidae)
Fig. 1. Two-dimensional gel (14%) in triplicate (three extracts from a colony), with the three gels (A, B, and C) of the Apoica pallens wasp venom.
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