Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Venomics analysis of Thai Daboia siamensis using integrated omics data

ABSTRACT: Snakebite, classified by World Health Organization (WHO) as a neglected tropical disease, causes more than 100,000 deaths and 400,000 injuries per year. Currently, available antivenoms do not bind with strong specificity to target toxins, which means that severe complications can still occur despite treatment. Moreover, the cost of antivenom is expensive. Knowledge of venom compositions is fundamental for producing a specific antivenom that has high effectiveness, low side effects, and ease of manufacture. With advances in mass spectrometry techniques, venom proteomes can now be analyzed in great depth at high efficiency. However, these techniques require genomic and transcriptomic data for interpreting mass spectrometry data. This study aims to establish and incorporate genomics, transcriptomics, and proteomics data to study venomics of Thai venomous snake, Daboia siamensis. More than a hundred proteins that have not been reported as venom components of this snake such as hyaluronidase-1 and Phospholipase B were discovered. The use of conventional reference databases for mass spectrometry analysis can detect only 46% of proteins identified by integrated omics data. Thus, this multi-omics data is necessary for venomics studies. These findings will be valuable not only for antivenom production but also for the development of novel therapeutics.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

SUBMITTER: Poorichaya Somparn

LAB HEAD: Poorichaya somparn

PROVIDER: PXD030613 | Pride | 2022-07-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Gel_Venom10.mgf	Mgf
	Gel_Venom10.raw	Raw
	Gel_Venom11.mgf	Mgf
	Gel_Venom11.raw	Raw
	Gel_Venom12.mgf	Mgf

Items per page:

1 - 5 of 56

Similar Datasets

Vipera ammodytes ammodytes venom proteomics

Project description:The nose-horned viper, its nominotypical subspecies Vipera ammodytes ammodytes (Vaa) in particular is, medically, the most relevant snake in Europe. The local and systemic clinical manifestations of poisoning by the venom of this snake are the result of the pathophysiological effects inflicted by enzymatic and non-enzymatic venom components acting, most prominently, on blood, cardiovascular and nerve systems. This venom comprises the most complex mixture of pharmacologically active proteins and peptides of all European snakes. To help improve the current antivenom therapy towards higher specificity and efficiency, and to assist drug discovery, we have constructed, by combining transcriptomic and proteomic analyses, the most comprehensive library yet of the Vaa venom proteins and peptides. At the protein level, 57 venom proteins belonging to 16 different protein families have been identified and, with SVSPs, sPLA2s, snaclecs and SVMPs, comprise about 80% of all venom proteins.

2019-05-06 | PXD012752 | Pride

Proteomic Investigations of Two Pakistani Naja Snake Venoms Species Unravel the Venom Complexity, Posttranslational Modifications and Presence of Extracellular Vesicles

Project description:Latest advancement of omics technologies allows in-depth characterization of venom compositions. In the present work we present a proteomic study of two snake venoms of the genus Naja i.e. Naja naja (black cobra) and Naja oxiana (brown cobra), of Pakistani origin. The present study has shown that these snake venoms consist of a highly diversified proteome. Furthermore, the data also revealed variation among closely related species. High throughput mass spectrometric analysis of the venom proteome allowed to identify for the N. naja venom 34 protein families and for the N. oxiana 24 protein families. The comparative evaluation of the two venoms showed that N. naja consists of a more complex venom proteome than N. oxiana venom.

2020-10-29 | PXD018726 | Pride

Tanos2008 - Blood coagulation and Snake Venom

Project description:Mathematical model of the blood coagulation cascade including interaction of snake venom and antivenom.

2018-06-15 | MODEL1806150001 | BioModels

De Novo Transcriptome Sequencing for Tetramorium bicarinatum: The first comprehensive venom gland transcriptome analysis from an ant species.

Project description:In order to provide a global insight on the transcripts expressed in the venom gland of the Brazilian ant species Tetramorium bicarinatum and to unveil the potential of its products, high-throughput expressed sequence tags were generated using Illumina paired-end sequencing technology. A total of 212,371,758 pairs of quality-filtered, 100-base-pair Illumina reads were obtained. The de novo assemblies yielded 36,042 contigs for which 27,873 have at least one predicted ORF among which 59.77% produce significant hits in the available databases. The investigation of the reads mapping toxin class revealed a high diversification with the major part consistent with the classical hymenopteran venom protein signature represented by venom allergen (33.3%) followed by a diverse toxin-expression profile including several distinct isoforms of phospholipase A1 and A2, venom serine protease, hyaluronidase, protease inhibitor and secapin. Moreover, our results revealed for the first time the presence of toxin-like peptides that have been previously identified from unrelated venomous animals such as waprin-like (snakes) and agatoxins (spiders and conus). 300 ant specimens from the species Tetramorium bicarinatum were dissected in order to extract the RNA from their venom gland, The whole ant body was used as a reference,

2015-01-08 | E-GEOD-53988 | biostudies-arrayexpress

Fangs in the ghats: preclinical insights into the medical importance of endemic pit vipers from the Western Ghats

Project description:The socioeconomic burden of snakebite in India is largely attributed to the ‘big four’ snakes, completely neglecting the considerable impact of envenoming by many other snake species. Bites from the so-called ‘neglected many’ are often treated with a polyvalent antivenom that is manufactured against the ‘big four’ snakes - a strategy that has been widely documented to fail. Yet, specific antivenoms are not commercially manufactured against these snakes. While the medical importance of various species of cobras, saw-scaled vipers, and kraits is very well-known, the clinical impact of pit vipers from the rainforests of the Western Ghats, northeastern India, and Andaman and Nicobar islands has remained elusive. Amongst the 90+ species of snakes found in the Western Ghats, the hump-nosed (Hypnale hypnale), Malabar (Craspedocephalus malabaricus) and bamboo (Craspedocephalus gramineus) pit vipers can potentially inflict clinically severe envenoming in humans. To evaluate the severity of toxicity inflicted by these snakes, we characterised their venom composition, biochemical and pharmacological activities, and toxicity- and morbidity-inducing potentials. Our findings highlight the therapeutic inadequacies of the generic Indian and Hypnale-specific Sri Lankan polyvalent antivenoms in neutralising morbidity and mortality resulting from pit viper envenomings and underscore the need for a regional antivenom therapy in India.

2023-07-20 | PXD039139 | Pride

RNA sequencing of venom glands and venom gland organoids

Project description:Both single cell and bulk RNA sequencing was performed on expanding or differentiating snake venom gland organoids (from Aspidelaps Lubricus Cowlesi and Naja Nivea), or tissue (Aspidelaps Lubricus Cowlesi). Bulk RNA sequencing from the snake venom gland, liver and pancreas was performed to construct a de novo transcriptome using Trinity.

2020-02-24 | GSE129581 | GEO

Exploring Top-Down Mass Spectrometric Approaches To Probe Forest Cobra (Naja melanoleuca) Venom Proteoforms

Project description:Three main top-down mass spectrometry methodologies were employed in a proof-of-concept study to characterise selected three finger toxins and phospholipase A2 toxins from the forest cobra (Naja melanoleuca) venom. The novel utility of data-independent acquisition, alternative hybrid ECD-CID fragmentation and the incorporation of cyclic ion mobility separation in a top-down proteomic workflow were explored for snake venom proteins.

2024-09-05 | PXD052561 | Pride

Naja annulifera Snake: New Insights into the Venom Components and Pathogenesis of Envenomation

Project description:Naja annulifera is a dangerous snake that belongs to the Elapidae family. It is found in some of the countries in Sub-Saharan Africa and has caused several accidents in humans and dogs. In this study, we characterized some of the biochemical, toxic and immunogenic properties of N. annulifera venom. We showed that the venom is composed of several proteins, some of which display enzymatic activities, such as phospholipase A2, hyaluronidase, metalloproteinases and serine proteinases. The venom promoted disturbances in the human coagulation system and was cytotoxic to human epidermal cells. Using a mouse model, we showed that the venom promotes local reactions that were reduced with anti-inflammatory drugs. The venom caused systemic inflammation, lung hemorrhage and death. Further, the venom stimulated production of high antibody titers when injected into mice and the antiserum produced was able to inhibit venom-induced death. We therefore conclude that N. annulifera venom contains toxins that play a role in the toxic and inflammatory effects that contribute to the clinical manifestations and death. Moreover, the venom is immunogenic, an important aspect for the production an efficient N. annulifera antivenom.

2019-02-25 | PXD010962 | Pride

Characterisation of the forest cobra (Naja melanoleuca) venom using a multifaceted mass spectrometric-based approach

Project description:Comprehensive understanding of venom compositions and in-depth characterisation of the various proteoforms are necessary to aid the development of targeted antivenom strategies. This work utilises an integrated 'omics' and intact mass spectrometry-based approach to profile the diversity within the venom of the forest cobra.

2024-01-03 | PXD045209 | Pride

Biomarker genes highlight intraspecific and interspecific variations in the responses of Pinus taeda L. and Pinus radiata D. Don to Sirex noctilio F. acid gland secretions

Project description:Sirex noctilio F., a Eurasian horntail woodwasp recently introduced into North America, oviposits in pines and other conifers and in the process spreads a phytopathogenic fungus that serves as a food source for its larvae. During oviposition the woodwasp also deposits a mucus produced in its acid (venom) gland that alters pine defense responses and facilitates infection by the fungus. A 26,496-feature loblolly pine cDNA microarray was used to survey gene expression of pine tissue responding to S. noctilio venom. Six genes were selected for further assessment by qRT-PCR, including one that encoded an apparent PR-4 protein and another that encoded a thaumatin-like protein. Expression of both was strongly induced in response to venom, while expression of an apparent actin gene (ACT1) was stable in response to the venom. The pattern of gene response was similar in Pinus taeda L. and P. radiata D. Don, but the magnitude of response in P. radiata was significantly stronger for each of the induced genes. The magnitude of biomarker gene response to venom also varied according to genotype within these two species. The qRT-PCR assay was used to demonstrate that the primary bioactive component in S. noctilio venom is a polypeptide. Reference design. Two condition experiment, two time points each compared to a common reference. Two biological replicates, two technical replicates, 12 slides total, duplicate/re-scanned images submitted for each slide.

2012-08-09 | E-GEOD-40000 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data