Friday, August 24, 2012

B ID


"Concerning the generation of animals akin to them, as hornets and wasps, the facts in all cases are similar to a certain extent, but are devoid of the extraordinary features which characterize bees; this we should expect, for they have nothing divine about them as the bees have."
~ Aristotle 384 BC – 322 BC

I like this quote - it might not be overly friendly to wasps and hornets but describes human's fascination with bees. Of course we don't know if Aristotle meant the honey bee in particular or if he had more insight into the diversity of these little guys that are so important to us. 20 000 - 30 000 species of bees are out there and the western honey bee (Apis mellifera) is only one of them. Bees are the most important pollinator on the planet and at the same time they may be among the most extinction-prone organisms. Therefore, the study of bees and their ecosystems seems paramount but taxonomic knowledge for many groups is incomplete. Furthermore, individual species can't be identified in a timely fashion. Proper morphological taxonomy takes time especially when the characters you have to look for are minute and require a specialists eye. Community studies that could deliver data for biodiversity studies and ecosystem assessments need more rapid systems.


A case for DNA Barcoding?

Absolutely. Bee scientists have already acknowledged the value of DNA Barcoding:

"In the case of bees, the ability to identify all life stages and to associate individuals of different sex represents an important extension of existing identification capabilities. The assembly of a barcode library for the bees of the world will not only provide insights into the origins and extent of bee diversity, but it will create a new tool for both routine and challenging identifications." (Sheffield et al. 2009).

A global campaign to barcode all bees has been established in 2010 but similar to many such efforts funding is sparse or simply non-existent. This is especially surprising given the importance of bees. The following quote from Laurence Packer, one of the worlds leading melittologists illustrates this very nicely:

"If all birds dropped dead tomorrow, only chicken farmers and academic ornithologists would be inconvenienced. If all bees died out, there would be worldwide food shortages and perhaps one-quarter of the human population would starve."

As you can see he is much better with words than I, a fact also well documented in his wonderful book "Keeping the bees". The quote I stole from his website though.


High resolution imaging

But DNA Barcoding isn't the only new thing that can help with bee taxonomy. Cory Sheffield, Curator of Invertebrate Zoology at the Royal Saskatchewan Museum is using high resolution imaging to help with identifying the species he is interested in. The power of such high resolution images becomes obvious when you look at a small online key to the subfamily Andreninae developed at York University, Toronto in Laurence Packer's lab. The resolution and the quality of the images are stunning. I remember my taxonomic training during the years as undergrad. I wish we would have had such keys. Instead one had to go through endless pages filled with cryptic paragraphs describing features we never knew existed. Unless you are a taxonomic expert this vocabulary is quickly forgotten and it is immensely helpful to have good pictures at hand. After all most of us are best at visual learning and perhaps more importantly  images of such superb quality give many people a greater appreciation of these little critters and their beauty. Furthermore, new keys for farmers will make it easier to identify the bees that pollinate their crops.
Euherbstia excellens from the Andreninae key at York University

Thursday, August 23, 2012

A very unpleasant souvenir


DNA Barcoding in Medicine

Imagine you are back from a wonderful vacation in the Tibetan mountains and aside from all the great memories you bring back a nasty and painful surprise. 

This happened to a German tourist who seem to have a mysterious disease. The Tibet traveler complained about severe pain and swellings across the upper part of the body. After several months of suffering a physician was able to extract a small white maggot from one of the swellings. As the physician suspected an infection with fly larvae she submitted the sample to the State Collection in Munich.

The resident fly specialist Dieter Doczkal was able to identify the maggot as larva of the yak warble fly (Hypoderma sinense) using DNA Barcoding.

Hypoderma sinense (source ZSM Press Release)
Larvae belonging to the genus Hypoderma (Diptera, Oestridae) cause myiasis in wild and domestic ruminants that is characterized by migrations within deep tissues. Especially in Asia this is a significant problem for livestock breeding. The adult fly will lay eggs on the foreleg of an animal, these will then be ingested by licking.  Once swallowed the eggs will pass on through the esophagus muscles and the spinal cord before re-emerging just beneath the skin.  When they re-emerge, the larvae cause swellings or warbles under the skin, causing quite some pain to the infected animal. 
Warble fly larvae under the skin of a caribou

These parasites can also infest humans with similar consequences: The infestation in hosts often causes serious tissue destruction by the larval migrations in the body. Fortunately humans are incidental hosts meaning that such infestations are rare and accidental.Actually this case is only the second ever reported for this particular fly species. The first was also a tourist traveling in India.

Identifying adult flies is a difficult business already but even for experts it is often impossible when it comes to larvae. This is what makes this case so exciting as Doczkal was able to match a COI sequence retrieved from the maggot to some Hypoderma sinense records on BOLD (www.boldsystems.org) a database that hosts the majority of DNA Barcode data .

This is a good example how a library of DNA Barcodes for pathogens, parasites and creatures that transmit disease-causing organisms can help to distinguish them, as well as allowing eggs and juveniles to be identified accurately, something that is currently extremely difficult. The library is still far from complete and requires a lot of efforts from researchers and public health experts but already the method has been proven very useful.

By the way - the patient felt much better after the larva was removed.





A new Blog on DNA Barcoding


What is DNA Barcoding?
DNA Barcoding is a technique that uses a short DNA sequence from a standardized and agreed-upon position in the genome as a molecular diagnostic for species-level identification. DNA barcode sequences are very short relative to the entire genome and they can be obtained reasonably quickly and cheaply.
It was proposed in 2003 by Paul Hebert a researcher at the University of Guelph in Ontario, Canada. In the last nine years it developed from a hotly debated idea into a widely recognized and used tool in research and applied science.

Why a blog?
Well, this is not the first blog on DNA Barcoding. A few colleagues have been writing about new developments and discoveries over the last couple of years. The most prominent one by Mark Stoeckle from the Rockefeller University in New York went on hiatus. At least that's what I assume as the last post is from January 2012. Too bad, as it was always very interesting and entertaining to follow Mark's thoughts.
However, DNA Barcoding has now matured and deserves all attention it can possibly get. Another blog won't hurt!

Why me?
Why not? I am involved in DNA Barcoding research since 2005 and I am working for over 6 years at the very place it has been developed. Being at the cutting edge of DNA Barcoding science for some time comes with some advantages and I am certainly in a good position to find the most newsworthy information for interested readers. I will also try to find a good balance between scientific and non-scientific contributions as I hope that my audience will not consist of DNA Barcoding scientists alone although I would be more than happy to welcome all those friends here.

Gene Watch - Council for Responsible Genetics 2012