Despite the fact that the foods we eat and the medicines we take can indeed be “natural”, there are still some inherent dangers in some of them.  Similar to prescription medications, some herbal supplements can cause serious side effects such as liver and lung damage, or can interfere with other medications taken at the same time.  What makes herbal supplements perhaps more dangerous is the fact that they are not as highly regulated as prescription drugs. Manufacturers of herbal supplements do not need approval from the FDA in order to be put on the market. This begs the question of whether herbal supplements either have extra ingredients or are missing vital ingredients that affect their efficacy and safety.

This lack of regulation peaked the curiosity of young scientists at Hostos-Lincoln Academy in Bronx, NY. A group of high school students participated in the Urban Barcode Project (www.urbanbarcodeproject.org) and investigated gingko products sold in a variety of pharmacies and tried to identify what species of plants were primarily found in both dried leaf, liquid, and pill forms. The students found an interesting result using DNA barcoding; many of the packaged products contain mostly rice product and very little gingko. Many leaf products contained primarily Atropa belladonna, Thymus vulgaris, Salvia pratensis, and different species from the genus Nicotiana, which may be potentially harmful.

Scientists at the New York Botanical Garden (NYBG) have been working on similar projects.  Damon Little, a bioinformaticist at the NYBG, investigated black cohosh, a menopause herbal supplement that has been known to be inconsistently effective in test trials. He thought these mixed results were due to the varied production of black cohosh pills. Perhaps some of these pills lack the vital ingredient for relieving menopausal symptoms, the actual black cohosh itself.

Little used DNA barcoding to identify the main species found in a variety of black cohosh pills. He discovered that as many as one quarter of the tested pills contained no black cohosh at all, but instead a related species.  This can be a particularly serious problem; not only can a different species decrease the supplement’s effectiveness, but it can be potentially toxic to humans.

Unfortunately, these findings do not prove that the variety of black cohosh pills affect the variety of outcomes for users. The pills that were barcoded were purchased in New York City and online, but they were not the pills used in clinical trials.  The next step would be to see if people who take pills without black cohosh are affected differently compared to those who take pills with black cohosh.   It would be interesting to see if there is such a strong correlation. Perhaps with more convincing evidence, we can push for more regulation of herbal supplement production.

For more information go to:

Urban Barcode Project

Herbal Menopause Supplement Often Contains Other Species, DNA Barcoding Reveals

DNA Barcode Identification of Black Cohosh Herbal Dietary Supplements

Herbal supplements: What to know before you buy

The most expensive bowl of soup I have ever had in my life was a $15 bowl of ramen in the NYC restaurant Ippudo. And this was no ordinary “ramen” you would eat at home as a cash-strapped college student. This was an authentic bowl nuanced with so many rich and hearty flavors of Japanese cuisine.

Little did I know that $15 soup was  considered “cheap” compared to other soups that sell for at least $100 a bowl. One such soup is shark fin soup, which is traditionally served in Chinese cuisine during  special occasions.  One is apt to eat this delicacy, not so much for its taste, but more for the gelatinous texture of its shark fins harvested from the world’s oceans.

The ongoing slashing of shark fins from live sharks (only for the sharks to be tossed back into the water and left to die) is not the only controversial aspect of shark fin collection.  What one eats in that $100 bowl could be shark fin that has come from threatened or endangered sharks.  Scientists from Stony Brook University and the Field Museum in Chicago, with support from the Pew Environment Group,  have used DNA barcoding to identify the species of sharks served in shark fin soups sold in major U.S. cities.  According to their studies, several at-risk shark species have been identified in these soups, including the scalloped hammerhead, which is listed as endangered by the International Union for Conservation of Nature (IUCN).

DNA barcoding is extremely useful in the identification of shark species used in soups because the processing of fins makes it difficult to distinguish species through traditional taxonomic classification. By the time shark fins are in broth, they have been dried, chemically treated and cut into pieces.  After the fins are cooked, there is just enough DNA extracted to generate a DNA barcode, a DNA sequence unique to each individual species.

The continual harvesting of shark fins endangers the livelihood of shark species that are pertinent to the ocean’s ecosystems.  And sharks are particularly prone to over-exploitation as they are slowly reproducing creatures. Sharks must be at least in their teens or twenties to be able to reproduce and they can only a give birth to a few pups in their lifetime.

Despite the scientific facts, consistent laws and regulations need to be enforced in order to prompt effective change. According to the U.S. it is legal to use all the shark species found in these soups because none of these species are on the United States Endangered Species List. Neither are they protected by the Convention on International Trade in Endangered Species (CITES).  And although it is illegal for fishers in the U.S. to cut fins off live sharks and then toss them back into sea, it is legal for the fishers to import fins from countries that may have less restrictions.

So where does that leave us? What can we do to help fix this? Scientists can help by carrying out more studies that expose shark exploitation and more fervently demonstrate the importance of shark species in our ecosystems. Some of us in politics can help generate uniform and more stringent policies that help protect shark species.  For the rest of us, we have a significant opportunity to increase the awareness of this problem by educating our friends and family. The last and certainly not least thing we can do is something quite simple.  We can refuse to eat in restaurants that serve this soup and certainly we can refuse to eat the soup itself.  Plus, with that money, we can each eat at least 6 yummy bowls of ramen.

For more information please go to:

Your Pricey Shark Fin Soup May Also Include Endangered Species

New DNA Study Reveals Fins of Endangered Shark in U.S. Soups

In the Soup, a Dash of Biodiversity

George Amato, the director of the American Museum of Natural History’s Sackler Institute for Comparative Genomics, worked with the CDC by using DNA barcoding to identify imported bushmeat at U.S. international airports that could not be identified by gross examination. Amato and a group of scientists identified bushmeat from non-human primates (including chimpanzees, mangabeys and guenons) and rodents using both DNA barcoding and gross identification. Non-human primate samples were screened for viruses and were found to carry retroviruses (Simian Foamy Virus) and/or herpesviruses (cytomegalovirus and lymphocryptovirus). This study has been the first of its kind to demonstrate the possibility that handling of illegal bushment may help facilitate pathogen spread.

This reminds me of how HIV rapidly spread throughout the world in the late 20th century causing  significant global concern well into our present time. The HIV virus is generally accepted as a descendent of  SIV, the Simian Immunodeficiency Virus that infects non-human primates.  Although it is not completely well understood, many scientists believe that zoonotic transmission of the SIV virus to humans resulted from handling of chimpanzees and mangabeys that have been known to carry SIV. These non-human primates were likely hunted for bushmeat in central and western Africa.

Which now begs the question, can the pathogens we now detect in illegal bushmeat be something that can evolve to something as dangerous and unrelenting as HIV? It is quite possible. Studies like the ones done by this group of scientists need to continue to prevent future disease emergence.

For more information, please go to:

Zoonotic Viruses Associated with Illegally Imported Wildlife Products

Are there ways the computer has out-shined the human mind? Perhaps.  But I think the better question is, can computers ever catch up to our incredible brains? I don’t think so.

I was reminded of this the other day when I read an article from “Nature News” regarding  an online game called, “Phylo”, created by computational biologists at McGill University in Montreal, Canada.   People who played this game were able to more accurately solve problems that computers  have had in matching DNA sequences from different organisms/diseases. And this doesn’t require a person with skills in science.  It only requires someone with visual intelligence, something a computer doesn’t have, at least not in the same way.

In this current genomic era, we are confronted by massive amounts of genomic data that we are trying to make sense of. We are trying to figure out how DNA sequences differ between multiple organisms and between diseased organisms and disease-free organisms. Like putting together a puzzle, people have created computer programs that can take multiple sequences from different sources and align them in a way that accurately compares them, pointing out the differences that indicate evolutionary change.  The problem computers have is in figuring out where to create proper alignments between many different sequences. In other words, where do the matches make the most sense across the board? Computers do a decent job with this enormous task, but are limited in accurately aligning sequences every time, especially with several sequences that may have more differences than similarities.

“Phylo” was created to help address the problems computers have in matching many sequences together. In this game, the goal is to match as many colored blocks from one string of blocks to other strings of blocks. Each string of blocks is a DNA sequence.  Each differently colored block represents a base (A, T, G or C) in our DNA.  This is essentially a game of matching colors between as many as 8 strings of blocks using a set of rules that helps gamers create the best matches.  No scientific experience is required.

The “Phylo” game has been used to help more accurately align sequences of promoter regions that control expression in 521 disease-associated genes in 44 vertebrate species.  The game has drawn over 3000 regular visitors and the gamers have been able to surpass the accuracy of traditional algorithmic Multiple Sequence Alignment (MSA) tools used by the computer in as many as 70% of the sequences.

If you have never had a chance to help out scientists in the comparative genomics field before, now is the time! Plus, it is a lot of fun.

Check out Phylo!

For more information go to:

Kawrykow, A. et al. PLoS ONE 7, e31362 (2012)

Gamers outdo computers at matching up disease genes

When we walk, our shoes pick up various seen and unseen organisms.  Many of us walking through a field or park may be stepping on and carrying seeds from various plants. Seeds blow in the wind and also creep into the crevices of our clothes and bags.  As carriers, we then transport them to new areas, making each of us essentially a seed planter. At first glance this seems like a nice job description.  However, the problem lies in the fact that seeds can find themselves in uncharted territory.

In Antarctica, the landscape has changed dramatically in recent years. As the climate is warming, the Antarctic Peninsula is uncovering more areas that are “ice-free”.  These areas are particularly vulnerable as alien species have flourished here.  This is in large part due to the transfer of seeds from visitors to the continent.  Environment correspondent Richard Black of BBC News wrote in his article, “Alien invaders threaten Antarctic fringes,” that an average of 9.5 seeds are carried by each visitor to this continent.  Many of these seeds, coming from as far as the North hemisphere, can survive and thrive in the warmer areas of the continent, potentially causing a major ecological shift.

Some invasive species, such as the grass species Poa annua, have taken over some of the sub-Antarctic islands such as South Georgia.  It is thought that scientists brought this seed to parts of Antarctica due to the proximity of Poa annua grasslands to the different science research stations.

South Georgia has an even bigger problem. Due to whaling expeditions, rats have infested grasslands and have become the dominant predatory species. Perhaps this island is a microcosm of what is to come in the great White Continent.  Covered with rats.

What is the solution? Well, we can’t completely prevent all unwanted seed from arriving in Antarctica, no matter how hard we try. However, organizations are trying to help reduce the amount of alien seed arriving and surviving on the continent. The International Association of Antarctic Tour Operators (IAATO) has been working diligently to ensure that visitors are “seed-free” and some science organizations have created guidelines for checking of vehicles, bags and clothes for seeds. Perhaps extra surveillance of visitors will ensure that Antarctica never becomes a vast grassland.

For more information:

http://www.bbc.co.uk/news/science-environment-17258799

http://blog.earth-touch.com/nature-news/south-georgias-rats-get-the-death-sentence/

Incidentally, water can taste funny due to substances and/or forms of life found in it.    Too bad Bo wasn’t a scientist.  Perhaps she could have extracted DNA from each glass of water and found out the kinds of organisms that have existed in this water.

Dutch scientists (Thomsen et. al., 2011) have been successful in identifying organisms that have been swimming through as little as a cup of freshwater. These scientists claim that organisms that swam through these waters within two weeks of collection left traces of DNA behind. This is quite a useful tool in determining the ecology of any given freshwater area. Scientists can use this information to identify rare or invasive species and monitor the activity of organisms found in a particular habitat within a period of time.

For more information, please go to:

http://www.scientificamerican.com/podcast/episode.cfm?id=dna-in-a-cup-of-water-reveals-lake-11-12-19#comments

http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2011.05418.x/abstract

Not only is the mislabeling of fish considered a violation of Federal law, but it can also pose a serious public health risk. Simple fish inspections can avert most situations of this nature from materializing, especially if those who inspect the fish are able to identify fish species through taxonomic means. Who is to say that all inspectors are equipped to identify every imported fish species?  And even if there are expert fish taxonomists working for the FDA,  one additional problem is that some imported fish are processed and may not be able to be identified in this way.

In response to this dilemma, the FDA, in collaboration with the “Barcode of Life” initiative, has barcoded 172 commericial fish species to help recognize species that are difficult to identify through more traditional means. This new method of identifying species is also particularly useful for fish samples whose DNA is degraded.  In some cases, fish can be identified from as small a DNA region as 100-200 base-pairs in length.

This has many implications for not only imported foods, but for locally grown foods as well.   State and local regulators can adopt similar measures to barcode fish in detecting food fraud. Restaurants can test the quality of the fish they buy from sellers using this new technology. And customers of restaurants can rest assured that the caviar they are ordering from the menu is not a cheap substitute.

For more information go to:

http://www.huffingtonpost.com/2011/11/27/restaurants-dna-seafood-mislabeling_n_1114937.html

http://www.fda.gov/Food/ScienceResearch/LaboratoryMethods/ucm237391.htm

http://www.ingentaconnect.com/content/iafp/jfp/2009/00000072/00000004/art00018

Recently, researchers at the Smithsonian used the method of DNA barcoding to identify 168 crab species  in a relatively small 20.6 feet square feet area of coral reef.  This is almost as many crab species that have been identified in all the seas of Europe. This then begs the question; can  more than 8.7 million species on Earth be identified through DNA barcoding? It is possible.  Some scientists estimate that as many as 100 million species may be found on Earth.  If this estimate is closer to to actual amount of current species living on Earth, then DNA barcoding will be the most efficient method used to identify species that currently exist on Earth. DNA barcoding is a relatively quick and easy way to identify species and this can lead to future tracking of species within ecosystems. By looking at the DNA of closely related species it is also possible to find species that may similarly create substances that can be used as medicine or used to advance technology.

It is important that we try to identify and catalog as many species as possible.  Coral reefs, like the one described above, are immensely diverse, and yet are some of the most threatened environments in the world due to the human impact of pollution and overharvesting.   We may never truly know the amount of biodiversity that the Earth has and is capable of having if we are using our time destroying it.

To read more go to:

According to a recent study in Molecular Ecology, scientists have shown that DNA fragments found in the soil can not only determine what species occupy a given area, but also how many individuals from each species occupy that area.  The University of Copenhagen team devised a way to roughly estimate the number of individuals of each species found in a particular area  by measuring the quantity of DNA found from each species present. Scientists can now use this information to survey the biodiversity and ecological relationships that exist between different species in an area.

Not only have the scientists recovered DNA from animals currently present in a given location, but they have also recovered DNA from animals that once, but no longer occupy that same location.  Perhaps digging deeper can reveal animals that once occupied an area thousands of years ago.

Now I wonder if I take soil from my backyard, will I find DNA remnants of rabbits, snakes, mice or raccoons? And will I find out which animals have been coming to my yard in droves while I was away?  It should be an interesting experiment.

For more information go to:

http://www.nature.com/news/2011/110923/full/news.2011.556.html?s=news_rss

Andersen, K. et al. Mol. Ecol. http://dx.doi.org/10.1111/j.1365-294X.2011.05261.x (2011).

Welcome to our new DNA barcoding blog.  It truly is an exciting time to be involved in this aspect of genomic science as DNA barcoding has been used to identify new species, help explain the biodiversity of our planet and even detect food fraud.  Just as a universal product code (UPC) identifies an item for sale in a store, a DNA barcode uniquely identifies each species of living thing.  The DNA barcoding technique includes extraction of DNA from an organism of interest, ampliflication of this DNA through PCR (Polymerase Chain Reaction), and sequencing of the DNA at specific locations in the genome.

In 2008, students from the Trinity School in New York City used DNA barcoding to find out that the raw tuna being sold at some sushi restaurants and grocery stores was not actually “tuna”, but instead “tilapia”, which is a cheaper fish.  This type of experiment not only demonstrates the real life applications of DNA barcoding, but just as importantly, shows the accessibility of this type of science to high school students.

This year, students from the New York City area will embark on the first ever Urban Barcode Project (UBP), a high school competition in which students will use DNA barcoding to explore the biodiversity in New York City. If you are a NYC teacher or a scientist interested in leading a team of students, please go to the UBP website for more information.