Finding platypus venom
Platypuses[1] are one of Australia’s oddest creatures.
They’re furry, mainly nocturnal aquatic creatures that swim with their eyes shut paddling with their webbed front feet and steering (or braking) with their rear feet. Their homes are burrows in the river banks. While not endangered, water pollution is an issue for their survival.[2]

Platypuses are monotremes, best known as mammals that lay eggs.[3] Their duck bill-like snout is famous world-wide. Important for our story, males squirt venom from a venom gland through a spur on their hind legs.
Toxins and venoms have useful medical applications. They are molecules that have powerful biological effects in small amounts.
As an hypothetical example,[4] consider one way evolution might result in a (snake) venom molecule that induces heart attacks in victims. An ancestral form of the animal had a gene that coded for a very short protein, a peptide, used to control it’s own heart. Imagine now the gene coding for that peptide duplicating, to create a second copy. If the second copy is active in the venom gland, the peptide can act on the animal’s attacker or victim. Over time, the gene may adapt so that the second copy is only active in the venom gland. It’s now free to evolve to become more potent without affecting the animal it’s from. A new venom-encoding gene has evolved. Careful use of it might be valuable for controlling the heart in medical applications.

Thus, we can imagine (some) venoms as modified regulatory molecules that have become particularly potent in their effect.
There is a limited supply of platypus venom, and only a few venom peptides have been fully identified so far.[5]
Rather than battle this head-on using a more traditional approach of collecting venom samples and identifying what in them are toxic, an Australian group lead by Wesley Warren collected the genes that are expressed in the venom gland and worked from them.
Since these venomous peptides are coded in genes, they reasoned they could collect all the active genes from the venom gland tissue of an in-season male platypus, then compare the genes being expressed there with those known to code for venomous peptides in other species they might identify more of the remaining platypus venomous peptides.

Genes code for RNA molecules, mRNAs, that are translated into proteins. DNA is usually found as two strands, each complementing the other. Given a single strand of linear RNA, such as mRNA, researchers can enzymatically make a complementary DNA strand.
(The enzyme used, RNA reverse transcriptase, is the same used by RNA viruses to make a DNA copy of their RNA genome to insert into their host species.)
These complementary DNAs, cDNAs, can be inserted in small independent genomes (plasmid genomes) to be added to bacteria that are grown to create larger amounts of the cDNA that are sequenced.
The sequenced cDNAs, usually short compared to the full-length genes, are compared to the genome of the animal they came from to identify the genes the cDNAs are from.
You can see how this work builds on the recently sequenced platypus genome, by using it to identify the genes the shorter cDNAs come from, and how the genome sequence of an odd animal like the platypus might help work towards medical uses.
Comparing[6] the genes the cDNAs indicate are expressed in platypus venom glands to databases of known toxin proteins (the Tox-Prot database), they found 83 new candidate venom genes, which will now be studied more closely.[7]

Aside from that platypuses are interesting little animals, and that venom is interesting too, my interest is that this work in part depends on my field, bioinformatics, at many different points. (Too many to bore you with here.) One challenge for the bioinformatics is that there are no genomes for species closely related to platypus.[6]
Their results show that very divergent species – platypus, reptiles fish, even insects – share some venom proteins, suggesting that particular proteins are repeatedly uncovered in evolution as being toxic.
Because their work relies on comparing with known toxin proteins, it will miss ones that are unique to platypus.
Footnotes
Factoid: While some sources claim young platypi are called puggles, this is disputed elsewhere, claiming their is no established name for their young.
1. Below is a short list of resources describing platypuses:
- http://australian-animals.net/plat.htm
- http://www.australianfauna.com/platypus.php
- http://rainforest-australia.com/Platypus_page_2.htm
- http://www.expasy.org/spotlight/back_issues/sptlt029.shtml
2. Recent local news from Melbourne reports the return of a platypus to city areas of a river.
3. Based on an article at Evolution Bites.
4. While best known for laying eggs, the term monotreme is because these creatures have their urinary, defecatory, and reproductive systems all opening into a single duct. (Mono = one; treme = hole.) They do lactate, but have no nipples, oozing milk via glands close to the surface of patches of the skin. They also feature electro-location (via receptors on the snout in the case of platypuses) and lack a corpus callosum, the nervous tissue that connects the two hemispheres of the brain in placental mammals.
5. 19 fractions have been identified, but only three peptides fully sequenced according to Whittington et al.
6. Being a nit-picky computational biologist, I wonder if more sophisticated (and sensitive) approaches for the comparisons might yield more findings. But then, I’m sitting on the sidelines, fidgeting.
7. As this is an initial screen of the venom genes, they go on to present each found, what kind of gene it is and how it might act. I’ve left this out. Way too much for a blog article.
(Updated to add tags. And again to add Research Blogging ‘Editor’s Selection’ badge.)
Whittington, C., Papenfuss, A., Locke, D., Mardis, E., Wilson, R., Abubucker, S., Mitreva, M., Wong, E., Hsu, A., Kuchel, P., Belov, K., & Warren, W. (2010). Novel venom gene discovery in the platypus Genome Biology, 11 (9) DOI: 10.1186/gb-2010-11-9-r95
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-OtÃn C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, & Wilson RK (2008). Genome analysis of the platypus reveals unique signatures of evolution. Nature, 453 (7192), 175-83 PMID: 18464734
Other articles on Code for life:
Choosing an algorithm – benchmarking bioinformatics
Autism – looking for parent-of-origin effects
GoPubMed – PubMed browsing using ontologies
22 Responses to “Finding platypus venom”
[…] This post was mentioned on Twitter by Sciblogs NZ, Grant Jacobs. Grant Jacobs said: Finding platypus venom (blog article) http://bit.ly/dpm13d […]
[…] Finding platypus venom […]
[…] Ho hum, what shall we do in the lab? Why not figure out how to synthesize platypus venom! […]
Arr, I used to have a puggle, one of those from The Lost Forest. Do ye remember them? I never knew they were a potential name for young platapuses / platapi.
Ahoy there, Capt’n 🙂
Fine of ye to drop anchor here. Haul yerself up m’ ladder. (Hint: the surname’s Jacobs.)
Can’t even remember The Lost Forest. ’orrible li’l man, I am. P’haps it’s a’ Aussie thing?
Platypi. Arr, ya jabbed me w’ that. Thought I’d gotten rid of all references to platypi. Missed t’ one hiding out in the Footnotes. Sigh. (It’s a wrong usage, as it adds a Latin suffix to a Greek root… or so the grammar skunks someplace told me.)
(PS: for readers not familiar with Captain Skellett’s pirate talk: check out ’er blog. ’den you’ll why I’m writin’ like this. I can’t do this style well, eh?)
For a really, um, unusual view on platypuses, try this from Answers in Genesis:
http://www.answersingenesis.org/creation/v8/i3/platypus.asp
Oh, thanks, Grant, now I’ll have to rinse my brain out 🙂
Srsly, though: In other words, there is no evidence that platypuses have evolved, but there is abundant evidence they have degenerated – this reflects the common misconception that evolution is always ‘striving’ towards perfection, whereas in reality natural selection results in the adaptation of a population to its current environment. SIgh. I suspect we don’t teach that concept particularly well in schools, BTW.
As for the idea of platypuses walking across landbridges to get to Australia during an ice age – sorry, guys, but even at the peak of the last glaciation (which was actually too long ago to fit within the YEC mindset of that dreadful website) there was no land bridge between Asia & Australia. Flores Strait is a deep-water strait & would still have been there.
Erk! Grant, can you close off the tag?
Hi Alison,
I still haven’t found a picture that competes fairly with that snake. That’s a hard act to top! 🙂
Grant, can you close off the tag? Done.
(which was actually too long ago to fit within the YEC mindset of that dreadful website)
You’d be horrified to learn that the author of that article is a geologist who lives in and earned his Ph.D. from where Cap’n Skellett hails. (She can avoid this by saying she never sets foot on shore…)
He claims on his biography page that “by the commencement of university studies, Andrew already had a clear Scriptural perspective on the literalness of Creation and Noah’s Flood, and an unmistakable call from the Lord for a life-long involvement in creationist ministry.â€
It makes you wonder how he managed to keep his thesis in line enough to earn the thing. It also reminds me of you recently mentioning in passing (in your teaching evolution post) of AiG being, in part, based in Australia and having an impact here. I’m guessing he’d be one of those kicking up a fuss (?).
He quite possibly is…. Hey, we’re not talking that guy who studied with Gould, are we? He must have some interesting stuff going on in his head!
I’ve no idea, but this is his biography page on AiG:
http://www.answersingenesis.org/Home/Area/bios/a_snelling.asp
[…] Platypuses; thoroughly strange creatures which look like an animated bean-bag with a duck-like beak on one end and a beaver tail on the other (both structures are not actually homologous with those of bird or rodent). The males also have a poisonous spur, as described at Code For Life. [link] […]
[…] Finding Platypus Venom […]
[…] Australian platypuses. In fact, the comments about platypuses produced a link to a Grant Jacobs post on the subject on his terrific blog, Code for […]
[…] Platypus venom […]
[…] Finding platypus venom […]
Scientific American has a post out discussing concerns that temperature needs (and hence possibly) climate change may affect the platypus:
http://www.scientificamerican.com/blog/post.cfm?id=platypus-threatened-by-climate-chan-2011-06-23
[…] Finding platypus venom […]
You had me at “platypus venom”. Awesome.
Thanks: praise is always welcome 🙂
Saw this joke on twitter:
@adzebill (Mike Dickison; retweeted by @pjacock)
Because the platypus both lays eggs and produces milk, it is one of the few animals that can make its own custard.
[…] Australian platypuses. In fact, the comments about platypuses produced a link to a Grant Jacobs post on the subject on his terrific blog, Code for […]