What Did Deep DNA Sequencing of Traditional Chinese Medicines (TCMs) Really Reveal?

A recent study published in PLOS genetics[1] on a genetic audit of Traditional Chinese Medicines (TCMs) was widely covered in the news. The headlines are a bit confusing as they said different things. Some headlines say “Dangers of Chinese Medicine Brought to Light by DNA Studies“, others that Bear and Antelope DNA are Found in Traditional Chinese Medicine, and still others more neutrally: Breaking down traditional Chinese medicine.

What have Bunce and his group really done and what is the newsworthiness of this article?

Photos from 4 TCM samples used in this study doi/10.1371/journal.pgen.1002657.g001

The researchers from the the Murdoch University, Australia,  have applied Second Generation, high-throughput sequencing to identify the plant and animal composition of 28 TCM samples (see Fig.). These TCM samples had been seized by Australian Customs and Border Protection Service at airports and seaports across Australia, because they contravened Australia’s international wildlife trade laws (Part 13A EPBC Act 1999).

Using primers specific for the plastid trnL gene (plants) and the mitochondrial 16S ribosomal RNA (animals), DNA of sufficient quality was obtained from 15 of the 28 (54%) TCM samples. The resultant 49,000 amplicons (amplified sequences) were analyzed by high-throughput sequencing and compared to reference databases.

Due to better GenBank coverage, the analysis of vertebrate DNA was simpler and less ambiguous than the analysis of the plant origins.

Four TCM samples – Saiga Antelope Horn powder, Bear Bile powder, powder in box with bear outline and Chu Pak Hou Tsao San powder were found to contain DNA from known CITES- (Convention on International Trade in Endangered Species) listed species. This is no real surprise, as the packages were labeled as such.

On the other hand some TCM samples, like the “100% pure” Saiga Antilope powder, were “diluted” with  DNA from bovids (i.e. goats and sheep), deer and/or toads. In 78% of the samples, animal DNA was identified that had not been clearly labeled as such on the packaging.

In total 68 different plant families were detected in the medicines. Some of the TCMs contained plants of potentially toxic genera like Ephedra and Asarum. Ephedra contains the sympathomimetic ephedrine, which has led to many, sometimes fatal, intoxications, also in Western countries. It should be noted however, that pharmacological activity cannot be demonstrated by DNA-analysis. Similarly, certain species of Asarum (wild ginger) contain the nephrotoxic and carcinogenic aristolochic acid, but it would require further testing to establish the presence of aristolochia acid in the samples positive for Asarum. Plant DNA assigned to other potentially toxic, allergic (nuts, soy) and/or subject to CITES regulation were also recovered. Again, other gene regions would need to be targeted, to reveal the exact species involved.

Most newspapers emphasized that the study has brought to light “the dangers of TCM”

For this reason The Telegraph interviewed an expert in the field, Edzard Ernst, Professor of Complementary Medicine at the University of Exeter. Ernst:

“The risks of Chinese herbal medicine are numerous: firstly, the herbs themselves can be toxic; secondly, they might interact with prescription drugs; thirdly, they are often contaminated with heavy metals; fourthly, they are frequently adulterated with prescription drugs; fifthly, the practitioners are often not well trained, make unsubstantiated claims and give irresponsible, dangerous advice to their patients.”

Ernst is right about the risks. However, these adverse effects of TCM have long been known. Fifteen years ago I happened to have written a bibliography about “adverse effects of herbal medicines*” (in Dutch, a good book on this topic is [2]). I did exclude interactions with prescription drugs, contamination with heavy metals and adulteration with prescription drugs, because the events (publications in PubMed and EMBASE) were to numerous(!). Toxic Chinese herbs mostly caused acute toxicity by aconitine, anticholinergic (datura, atropa) and podophyllotoxin intoxications. In Belgium 80 young women got nephropathy (kidney problems) after attending a “slimming” clinic because of mixup of Stephania (chinese: fangji) with Aristolochia fanghi (which contains the toxic aristolochic acid). Some of the women later developed urinary tract cancer.

In other words, toxic side effects of herbs including chinese herbs are long known. And the same is true for the presence of (traces of) endangered species in TCM.

In a media release the complementary health council (CHC) of Australia emphasized that the 15 TCM products featured in this study were rogue products seized by Customs as they were found to contain prohibited and undeclared ingredients. The CHC emphasizes the proficiency of rigorous regulatory regime around complementary medicines, i.e. all ingredients used in listed products must be on the permitted list of ingredients. However, Australian regulations do not apply to products purchased online from overseas.

Thus if the findings are not new and (perhaps) not applicable to most legal TCM, then what is the value of this paper?

The new aspect is the high throughput DNA sequencing approach, which allows determination of a larger number of animal and plant taxa than would have been possible through morphological and/or biochemical means. Various TCM-samples are suitable: powders, tablets, capsules, flakes and herbal teas.

There are also some limitations:

1. DNA of sufficient quality could only be obtained from appr. half of the samples.
2. Plants sequences could often not be resolved beyond the family level. Therefore it could often not be established whether an endangered of toxic species was really present (or an innocent family member).
3. Only DNA sequences can be determined, not pharmacological activity.
4. The method is at best semi-quantitative.
5. Only plant and animal ingredients are determined, not contaminating heavy metals or prescription drugs.

In the future, species assignment (2) can be improved with the development of better reference databases involving multiple genes and (3) can be solved by combining genetic (sequencing) and metabolomic (for compound detection) approaches. According to the authors this may be a cost-effective way to audit TCM products.

Non-technical approaches may be equally important: like convincing consumers not to use medicines containing animal traces (not to speak of  endangered species), not to order  TCM online and to avoid the use of complex, uncontrolled TCM-mixes.

Furthermore, there should be more info on what works and what doesn’t.

*including but not limited to TCM

References

1. Coghlan ML, Haile J, Houston J, Murray DC, White NE, Moolhuijzen P, Bellgard MI, & Bunce M (2012). Deep Sequencing of Plant and Animal DNA Contained within Traditional Chinese Medicines Reveals Legality Issues and Health Safety Concerns. PLoS genetics, 8 (4) PMID: 22511890 (Free Full Text)
2. Adverse Effects of Herbal Drugs 2 P. A. G. M. De Smet K. Keller R. Hansel R. F. Chandler, Paperback. Springer 1993-01-15. ISBN 0387558004 / 0-387-55800-4 EAN 9780387558004
3. DNA may weed out toxic Chinese medicine (abc.net.au)
4. Bedreigde beren in potje Lucas Brouwers, NRC Wetenschap 14 april 2012, bl 3 [Dutch]
5. Dangers in herbal medicine (continued) – DNA sequencing to hunt illegal ingredients (somethingaboutscience.wordpress.com)
6. Breaking down traditional Chinese medicine. (green.blogs.nytimes.com)
7. Dangers of Chinese Medicine Brought to Light by DNA Studies (news.sciencemag.org)
8. Chinese herbal medicines contained toxic mix (cbc.ca)
9. Screen uncovers hidden ingredients of Chinese medicine (Nature News)
10. Media release: CHC emphasises proficiency of rigorous regulatory regime around complementary medicines (http://www.chc.org.au/)

Silly Sunday #50: Molecular Designs & Synthetic DNA

As a teenager I found it hard to picture the 3D structure of DNA, proteins and other molecules. Remember we didn’t have a computer then, no videos, nor 3D-pictures or 3D models.

I tried to fill the gap, by making DNA-molecules of (used) matches and colored clay, based on descriptions in dry (and dull 2D) textbooks, but you can imagine that these creative 3D clay figures beard little resemblance to the real molecular structures.

But luckily things have changed over the last 40 years. Not only do we have computers and videos, there are also ready-made molecular models, specially designed for education.

O, how I wished, my chemistry teachers would have had those DNA-(starters)-kits.

Hattip: Joanne Manaster‏ @sciencegoddess on Twitter: 

Curious? Here is the Products Catalog of http://3dmoleculardesigns.com/news2.php

Of course, such “synthesis” (copying) of existing molecules -though very useful for educational purposes- is overshadowed by the recent “CREATION of molecules other than DNA and RNA [xeno-nucleic acids (XNAs)], that can be used to store and propagate information and have the capacity for Darwinian evolution.

But that is quite a different story.

Related articles

• Friday Foolery #49: The Shortest Abstract Ever! [2] (laikaspoetnik.wordpress.com)
• Synthetic DNA substitute gets its own enzymes, undergoes evolution (arstechnica.com)
• DNA Alternative Created By Scientists (freeinternetpress.com)
• Evolution seen in ‘synthetic DNA’ (talesfromthelou.wordpress.com)

Friday Foolery [3] Showing the invisible

I always found it difficult to think abstract. It was not until physics class at college, that I started to understand physics formulas,  because our professor gave practical examples from real life, i.e. he made me understand why the sky was blue. Mathematics was all right as long as we stayed in two dimensions, but stereometry was already one dimension too much. Molecules, chemical bonds and atomic structure were also vague especially when wave-particle duality came into play. It was even hard to imagine what DNA really looks like. At one stage I even tried to make a DNA structure at home from matches and colored clay. But the model was so fragile, that it crashed before the first minor groove was finished.

Nowadays, students are so lucky: a computer, the internet, beautiful graphs, videos, 3D-animations.

Below a mixture of recent  and some old animations and 3D representations, that highlight our understanding of numbers and dimensions, the infinite small and the infinite large.

First 3D image of an individual molecule and its bonds!

A real breakthrough was the visualization of the atomic backbone of an individual molecule (pentacene) and its atomic bonds. As reported in the August 28 issue of Science magazine, IBM Research Zurich scientists (in collaboration with Peter Liljeroth of Utrecht University), accomplished this by using an atomic force microsope (ATM) operated in an ultrahigh vacuum and at very low temperatures ( 268oC or 451oF). According to the researchers this is reminiscent of X-rays that pass through soft tissue to enable clear images of bones.

Below you see:

• the chemical structure of pentacene with 22 carbon atoms (Wikipedia).
• the force map image of pentacene (IBM).
• a video-interview with the researchers explaining their research (IBM-Labs).

Hattip: @jensmccabe (twitter) and Greg Laden (twitter and blog)
More info: www.physorg.com and gizmodo.com

The Galaxy mapped

Now quite the opposite infinity: the universe: “what 100,000 nearby large (i.e., Milky Way sized and larger) galaxies, look like reduced each reduced to a point” (translation by @dreamingspires) or “will give you an idea how totally insignificant we are” (@scanman). These tweople referred to Etann Siegel’s blog “It starts with a bang”.

One of the original researchers (Dominique Proust) has also posted a short description of the study and an image on the internet which shows the clustering pattern of about 100,000 nearby galaxies, revealed by the 6dF Galaxy Survey (see here) : “Each galaxy is shown as a dot. The galaxy we live in is at the centre of the pattern” (an enlargement of the image is here).

The astronomers came from all over the world (Australia, the UK, USA, South Africa, France and Japan). Their survey “will reveal not only where the galaxies are but also where they’re heading, how fast, and why. “It’s like taking a snapshot of wildebeest on the African plain. We can tell which waterholes they’re heading to, and how fast they’re travelling,” said D. Heath Jones of the Anglo-Australian Observatory (AAO), lead scientist for the Six-Degree Field Galaxy Survey (6dFGS)”

Dimensions

1, 2, 3 ….no here are 10 dimensions explained

but the 4th dimensions will do for me

Powers of 10

A classical video: the powers of ten. It dates from 1977. I have seen it during college and it made a lasting impression.
Powers of Ten explores the relative size of things from the microscopic to the cosmic. The 1977 film travels from an aerial view of a man in a Chicago park to the outer limits of the universe directly above him and back down into the microscopic world contained in the man’s hand.

There is even a website “powers of ten”. At the right you can click on a power of ten. Like 10 ¹³ and 10 -¹³

13

Measuring in meters, this power of ten is equal to 10 billion kilometers. We see the outer planets as they circulate counterclockwise, all in nearly the same plane.

Measuring in seconds, this power of ten equals

• Space 10 billion kilometers
• 317, 097 years.
• Unmanned Space Probes
• Johannes Keppler
• Space First Images Of Jupiter through Time

-13

Measuring in meters, this power of ten is equal to .1 picometer or 100 fermis. We see the kernel of a carbon atom, bound by six neutrons and six protons. This nucleus is dubbed carbon-12.

Measuring in seconds, this power of ten equals 100 femtoseconds.

• 100 fermis
• 100 femtoseconds
• Lasers
• Niels Bohr

Also the Wikipedia explains large numbers and astronomically large numbers. The Dutch Wikipedia gives more examples from daily life:

Do you still need some help in mathematics? Here is a tip from a Dutch educator @trendmatcher: your free online 24/7 math help, meant to help high school students with their homework. (There is also non-free material)

More frivolous:

Modern steps through time (via @scanman and @drves) : kalman.blogs.nytimes.com

And a  Twitter visualization tool that shows about 11,000 “good morning” tweets over a 24 hour period, between August 20th and 21st. All tweets are color-coded: green blocks are early tweets, orange ones are around 9am, and red tweets are later in the morning. Black blocks are ‘out of time’ tweets which said “good morning” (or a non-english equivalent) at a strange time in the day. Seen at the blog of @zbdigitaal (Edwin)
The original post and the video can be found here

Vodpod videos no longer available.

more about “ZB DIGITAAL: Goede Morgen! 24 uur twe…“, posted with vodpod

REFERENCES:

Leo Gross, Fabian Mohn, Nikolaj Moll, Peter Liljeroth, and Gerhard Meyer. “The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy.” Science, 28 August 2009: Vol. 325. no. 5944, pp. 1110 – 1114. DOI: 10.1126/science.1176210.

The 6dF Galaxy Survey: Final Data Release (DR3) and Southern Large Scale Structures
Jones D Heath., Read Mike A., Saunders Will., Colless Matthew., Jarrett Tom., Parker Quentin., Fairall Anthony., Mauch Thomas., Sadler Elaine., Watson Fred., Burton Donna., Campbell Lachlan., Cass Paul., Croom Scott., Dawe John., Fiegert Kristin., Frankcombe Leela., Hartley Malcolm., Huchra John., James Dionne., Kirby Emma., Lahav Ofer., Lucey John., Mamon Gary., Moore Lesa., Peterson Bruce., Prior Sayuri., Proust Dominique., Russell Ken., Safouris Vicky., Wakamatsu Ken-ichi., Westra Eduard., Williams Mary: 2009,
submitted to Monthly Notices of the Royal Astronomical Society