This web page was produced as an assignment for an undergraduate course at Davidson College.
What was the research project?
The research project described focused on trying to identify the definitive set of toxins that are responsible for the severe effects of Chironex fleckeri or box jellyfish stings. This was done using both Illumina genome sequencing of the transcriptome from the tentacles and analysis of the proteome, done mainly using tandem mass spectrometry. This was essential as there was, prior to this study, not database containing the genome or transcriptome of C. fleckeri, so a combination of both proteomic and transcriptomic analysis was essential for the then proteomic analysis of the venom of C. fleckeri to determine exactly which sequences were those of toxins (Ashford, 2015).
Were they testing a hypothesis or doing discovery science?
This project was an example of discovery science as the researchers were trying to discover the proteins involved. Because they were not testing whether or not specific genes contributed to the toxic sting effects, this does not qualify as a hypothesis being tested. However, their analysis did confirm the presence of a number of previously characterized toxin proteins and a handful of uncharacterized proteins from the same family.
What genomic technology was used in the project?
The researchers in this group utilized a number of genomic technologies for this project. Firstly, they used Illumina sequencing to sequence the transcriptome isolated from the tentacles of the C. fleckeri that they were studying. This was done through a de novo assembly of the sequence, as there was no previously sequenced data to compare their sequence to (Ashford, 2015).They also used mass spectrometry to compare isolated toxins to sequences in order to isolate which sequences were representative of the proteins that they were looking for. The researchers also utilized the UniProt animal toxin database and BLAST technology to help identify which sequences had strong links to previously sequenced, closely related toxins (Brinkman et al., 2015).
What was the take home message?
This project allowed for the investigators to discover the proteins responsible for the human response to being stung by a C. fleckeri as well as allowing them a jumping board for future research. These future studies will focus on the proteins within humans that interact with these toxins to inhibit their effects as well as a comparison with other types of Jellyfish venoms, to see similarities and differences.
What is your evaluation of the project?This project provides and interesting insight into the mechanisms behind the potent C. fleckeri venom. While this project successfully identifies some significant families of toxins that exist in the venom, the lack of previously sequenced data makes it harder for the reader to have faith in the accuracy of the data. The paper itself comments on the fact that a lot of the transcripts had poor read support, indicating an incomplete assembly occurred (Brinkman et al., 2015). Furthermore, the process of mass spectometry destroys the sample that is being examined. The comparison using BLAST was a helpful alternative to the lack of an entirely sequenced transcriptome, but the paper itself mentioned that around 40 percent of the transcripts did not match the top 8- percent of hits, suggesting a necessity for further characterization of the transcriptome (Brinkman et al., 2015). Finally, while the paper addresses some of the divergences seen in their data, they fail to fully explore alternative possibilities for their results.
Figure 1. This is a photograph of a Box Jellyfish and was taken for the Great Barrier Reef Marine Park Authority in Australia and obtained online
1. Ashford M. 2015. Box Jellyfish Transcriptome, Venom Proteome Reveal Sting Mechanics, Could Inform New Treatments [Internet]. GenomeWeb; [cited 2016 Jan 28]. Available from https://www.genomeweb.com/proteomics-protein-research/box-jellyfish-transcriptome-venom-proteome-reveal-sting-mechanics-could
2. Brinkman DL, Jia X, Potriquet J, Kumar D, Dash D, Kvaskoff D, Mulvenna J. 2015. Transcriptome and venom proteome of the box jellyfish Chironex fleckeri. BMC Genomics. [Internet]. [cited 2016 Jan 28]. 16 (407). Available from: http://www.ncbi.nlm.nih.gov/pubmed/26014501
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