Barcoding CSI: The Hammer

I admit this is a very lurid title but indeed DNA Barcoding already founds its way into criminal forensics. Here the evidence:

(1) Fictional TV shows start using it to track down the bad guys. Yesterday in NCIS they used DNA Barcoding to convict somebody of albacore (Thunnus alalunga) smuggling. Ok, that's probably too far fetched but I have a better one.

Photo of the suspected weapon

(2) Earlier this year our lab helped with an investigation aimed to provide species identification on subsamples taken from a hammer for the OntarioSociety for the Prevention of Cruelty to Animals (OSPCA) and Toronto Police Service. Somebody was suspected to have killed a dog with a hammer. Hair and blood samples could perhaps confirm that the hammer owned by the suspect was the weapon.

Close-up showing a hair that was used to retrieve DNA

The lab was able to retrieve several short length sequences still long enough to be reliably matched to reference sequences of the domestic dog, Canis lupus familiaris. They were also able to retrieve some human DNA from the handle (not surprisingly) which could have been used for a STR profile.

However, that wasn't even necessary as the suspect confessed when confronted with the initial evidence provided by DNA Barcoding. 

Case closed. 

h/t Bradley Zlotnick and Chris Weland 

DNA photos

TEM image with intensity profile of λ-DNA fibers.

With all the hassle about endangered shark species in fin samples and continuous mislabelling of fish products I almost forgot to share what I thought are the pictures of the week.

Researchers from Italy were able to do direct imaging of double stranded λ-DNA in the A conformation, obtained by combining a novel sample preparation method based on a super hydrophobic DNA molecule self-aggregation process with transmission electron microscopy (TEM). A-conformation DNA is thought to be one of three biologically active double helical structures along with the conformations B and Z. It is a right-handed double helix fairly similar to the more common and well-known B form, but with a shorter more compact helical structure. 

A-DNAs superstructures used for image simulations

This is the first time that humans have captured direct photos of DNA. At present, the method only works with superstructures of DNA made up of six molecules wrapped around an seventh acting as a core. That's because the electron energies are high enough to break up a single DNA molecule. However, according to the researchers the problem could likely be solved by using a lower-power electron scope. With this technique, researchers should be able to see how single molecules of DNA interact with other biomolecules.

How cool is that?

Still fishy

I have to admit it is going to be a fishy week on this blog but what can I do. After all one chooses what's close to ones heart ;-)

When it comes to DNA Barcoding in the media the really big stories had to do with fish or more precisely the seafood market. That started with the famous 'Sushigate' where two high school students used the method to show that many items on menus in seafood restaurants were simply mislabeled.

Frozen Tilapia - unfortunately often sold as red snapper

Quite a few broadcasters and newspapers took the idea and conducted their own investigations. Among those the Boston Globe. A year ago they tested seafood from Boston and with our help they found out that about half the time fish bought at restaurants across the region was mislabeled. They concluded:

Massachusetts consumers routinely, and unwittingly, overpay for less desirable, sometimes undesirable, species - or buy seafood that is simply not what it is advertised to be. In many cases, the fish was caught thousands of miles away and frozen, not reeled in by local fishermen, as the menu claimed. It may be perfectly palatable - just not what the customer ordered. But sometimes mislabeled seafood can cause allergic reactions, violate dietary restrictions, or contain chemicals banned in the United States.

Now a year later they went back to the restaurants and retailers to see if things have changed. Aparently they haven't:

Over the past several months, the Globe collected 76 seafood samples from 58 of the restaurants and markets that sold mislabeled fish last year. DNA testing on those samples found 76 percent of them weren’t what was advertised. Some restaurant operators who repeatedly mislabeled fish blamed suppliers. Others said naming inconsistencies were the result of clerical errors. Several made only partial revisions to their menus.

The main problem is that legislation hasn't caught up on the problem. Restaurants and suppliers know they will not face punishment for mislabeling fish. The Food and Drug Administration, which maintains a list of acceptable market names for fish species, has historically focused efforts on food safety, rather than economic fraud such as seafood substitution. However, they have already implemented DNA Barcoding as tool for seafood identification. Only regulation of the nation's seafood trade has to catch up which of course is a long and bureaucratic process. 

Most other nations are not even at this point yet.

Shark fins in BC

Shark finning continues to be a hot topic in Canada.

Just last week a bylaw banning the possession, sale and consumption of shark fins in Toronto had been  struck down by the Ontario Superior Court of Justice because it was supposedly outside the powers of the city.

Graphic by Vancouver Animal Defense League

Yesterday night a news report from Vancouver shows that fins of threatened and endangered shark species are being sold in Vancouver. Dried fins were purchased at local shops earlier this summer, some by an undercover reporter working for CTV and others by the Vancouver Animal Defense League, and sent to me here in Guelph for DNA Barcoding.

I had been in touch with the Vancouver Animal Defense League for a while already as a result of a blog post back in August in which I reported about efforts to ban shark fins from Canadian cites and provinces. What was lacking in all discussions and news releases was a clearer picture of what species are actually sold in Canadian shops. Earlier investigations in US restaurants had given us an idea but the actual extend was unknown. When I received the fins I was pretty sure that some of them were from endangered or at least threatened species according to the IUCN Red List but I was very surprised to find out that 76% of all samples sequenced fell into those categories. This was far worse than I thought and demonstrates how dramatic the situation is. 

If you want to get an impression of the dimension of the problem just go in one of the shops that sell fins as food or health products (if you happen to live close by). Have a look at the shelf's that are jam packed with dried fins and imagine that 3/4 of them are likely from species that are at least threatened. Now think of how many such shops there are.

Yesterday our results officially went public. I know that advocates of a province-wide ban of shark fin products in British Columbia are very positive as our findings will help them to substantiate their claims . 

Still - Very bad news for the sharks.

Number 2 is out!

Just finished working on the second one. The field is very productive and creative.

Have a click if you are interested. All citations in this pdf are hyperlinked. A simple mouse click will bring you to the article page on the publishers website.

Google Impact Award goes to CBOL

Today Google launched their Global Impact Awards to support organizations using technology and innovative approaches to tackle some of the toughest human challenges. From real-time sensors that monitor clean water to DNA barcoding that stops wildlife trafficking, the first round of awards provides $23 million to seven organizations changing the world.

Among them is the Consortium for the Barcode of Life (CBOL) at the Smithsonian Institution that will use its $3 million Impact Awards grant to create and begin implementing DNA Barcoding as an actionable tool for protecting the world’s most endangered wildlife. Working with researchers in six developing countries, CBOL will build a public library of DNA barcodes that law enforcement officials can use to identify confiscated material. The library is supposed to comprise approximately 2,000 endangered species and 8,000 species that are closely related to them or are commonly confused with them. The reference library will be part of GenBank.

Well, first of all, congratulations to CBOL for acquiring this grant. This is a great accomplishment especially in times where funding for biodiversity science is not on top of the list. The greater the news that the money is dedicated to advance the protection of endangered species.

Of course short press releases leave the interested reader with a lot of open questions and I have quite a few but I am sure there will be enough time for a closer look as soon as the project is up and running.

Water fleas in Middle Earth

Daphnia 'pulex'

Daphnia are one of the several small aquatic crustaceans commonly called water fleas because of their erratic swimming style. They live in various aquatic environments ranging from acidic swamps to freshwater lakes.

The identification of Daphnia species is difficult particularly in the so-called Daphnia pulex species complex . Determination of species based on morphological methods is only possible in a small number of species. Most others lack reliable morphological traits as a result of morphological stasis combined with a poor taxonomy. Initially the Daphnia pulex complex was considered to comprise of a few species but in recent years a number of new species have been identified genetically. Furthermore, each of these taxa comprises separate species in North America and Europe, despite carrying the same names.

There seems to be no alternative to a DNA Barcoding approach although there is an additional complicating factor, because similar to several other Daphnia species, North American Daphnia pulex members are able to form viable hybrid populations with Daphnia pulicaria. Any analytics should therefore include an allozyme analysis to confidently determine species status

Researchers from New Zealand have now used DNA Barcoding to identify invasive Daphnia specimens occurring in New Zealand lakes. They were able to document the establishment of non-indigenous North American Daphnia pulex members on the South Island. Cellulose allozyme electrophoresis was used to confirm that individuals were not hybrids with Daphnia pulicaria. 

New Zealand has only one recognized native Daphnia species, the relatively uncommon Daphnia carinata. These first confirmed recordings of members of the Daphnia pulex complex in New Zealand come from South Island lakes that are popular for overseas recreational fishers, indicating a possible means of  introduction in association with fishing and boating equipment.

The question is if this recent invasion will have any perhaps detrimental effect on the local fauna and flora. The authors think that the establishment of non-indigenous Daphnia might have large effects on lake and pond biota by probably reducing the abundances of both phytoplankton and other zooplankton (particularly rotifers). 

Who knows - lets hope that there might be ways to not find this out.