Category: New Research

Humans Contaminate DNA Databases

BioTechnology, Genetics, Government Regulations, New Research, Past Articles, Research Funding, Science Policy, Sequencing

Interesting research has been published in the online journal PLoS One, describing a problem with contamination in non-human DNA databases. DNA databases are libraries of genetic information about specific species. When a species has its genome sequenced, its genetic data goes into a database so that other research can be conducted based on that known genetic information.

When a DNA database becomes contaminated it means that there is other information that has corrupted the data stored in the database. In the new PLoS One paper the researchers (from the University of Connecticut) evaluated human contamination of databases that were supposed to contain other species – like the zebrafish. So contamination occurs when human DNA gets incorporated into the database for another species. When researchers go to work with the data about the zebrafish for example, they are actually working with human data without knowing it.

The University of Connecticut researchers looked for human contamination in NCBI genome databases, the University of California Santa Cruz (UCSC) databases, and the Joint Genome Institute databases. They found human DNA where it shouldn’t have been in a total of 492 of 2,749 evaluated databases.

This contamination issue is extremely problematic because research conducted based on contaminated information can not be trusted to be accurate. It can also be very difficult to track down which databases are contaminated unless the resources (time, money, etc) are spent to evaluate databases for clarity – as was done in this new research.

Database contamination is a relatively new issue brought to light be the massive influx of new genetic information made possible by improved genome sequencing technology. A similar issue that has existed for decades is cell line contamination which occurs when cells that are suspended in culture (alive outside of the body) are contaminated with cells that aren’t supposed to be there.

No regulatory body has stepped up and put a stop to cell line contamination in the last thirty years. I just hope that database contamination doesn’t follow suit.

To learn more, read the paper about Database contamination, or read an article I wrote for BioTechniques about cell line contamination. As taxpayers we spend a lot of money to fund scientific research, so it is important to know what problems (like contamination) exist in the research community.

Sequencing Genomes to Save Species

BioTechnology, Conservation, Environment, Genetics, New Research, Sequencing, Zoology

For this post I’m trying something a little different. I mentioned a few weeks ago that I’m using Science Decoded for class, and as a part of that we were assigned to write a post in the form of a list.

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All living organisms are made of DNA, a series of nucleotide bases (Adenine, Guanine, Cytosine, and Thymine) contained in chromosomes. Genome sequencing is an analysis of DNA, conducted by “reading” the different patterns of nucleotides A-G-C-T for differences between species, and abnormalities within a species. Researchers around the world are working to sequence the genomes of a variety of organisms, including those on the endangered species list.

1. Orangutan (Pongo abelii) – In January 2011 the National Institutes of Health (NIH) announced the publication of the orangutan genome sequence. Funded by the NIH, researchers from Washington University School of Medicine in St. Louis, MO and Baylor College of Medicine in Houston, TX sequenced the genome of a female Sumatran orangutan, five additional Sumatran orangutans, and five Bornean orangutans (Pongo pygmaeus.) The research shows that orangutans share 97% of their DNA with humans, but compared to humans and chimpanzees, orangutans have evolved much slower leading to fewer mutations (variations in the code between individuals of a species). (Read more) 

2. Tasmanian Devil (Sarcophilus harrisii) – Fifteen years ago a facial cancer was identified in tasmanian devil populations. The cancer has ravaged the species, resulting in an 80% decline that has forced the species to the brink of extinction. This cancer is transmissible, which means that biting the face of an infected animal passes it between individuals. In September 2010 researcher from the Wellcome Trust Sanger Institute and the genome sequencing company Illumina announced that they sequenced the tasmanian devil genome in an attempt to learn more about the cancer and how to stop it from wiping out the species. (Read more)
3. Giant Panda (Ailuropoda melanoleuca) – Arguably one of the cutest endangered species, the giant panda is a prominent symbol of China, where it lives in a restricted mountain area. According to the Beijing Genomics Institute (BGI) the number of giant pandas left in the wild is estimated between 1600-3000. In December 2009, BGI published the complete sequence of the giant panda genome. With the information obtained by the genetic analysis researchers hope to learn more about the genetic and biological factors that shape this species behavior to assist in disease control and conservation efforts. (Read more)

4. Tibetan Antelope (Pantholops hodgsoni) – Listed by the United Nations as an endangered species since 1979, the Tibetan antelope could hold the key to understanding the pathogenesis of chronic plateau sickness. The species calls China’s Qinghai-Tibet Plateau home, making them ideal for studying the evolution of species that thrive in environments characterized by extreme cold and low oxygen levels. The genome sequence of the Tibetan antelope was announced in December 2009 by researchers from BGI and Qinghai University. (Read more)
5. Coral Reefs (Acropora millepora) – Coral reefs are among the world’s most diverse ecosystems, yet according to the Genome Center at Washington University it has been predicted that in the next 50 years between 40%-60% of the world’s coral reefs will die. In 2005 the NIH funded the sequencing of the coral A. millepora (which is not an endangered species, though coral reefs as a whole are endangered ecosystems) to serve as a “lab rat” for studies of the environmental factors (light, sediment load, or acidity) that can cause coral death. (Read more)
Not quite endangered & not fully sequenced:
6. Polar Bear (Ursus maritimus) – Recently removed from the list of endangered species recognized by the United States, researchers at BGI are still working to sequence the polar bear genome. The polar bear sequence is a part of a three-pronged project to sequence the Tibetan antelope (completed in 2009) and emperor penguin genomes.

7. Emperor Penguin (Aptenodytes fosteri) – One of the most recognizable penguin species, the Emperor Penguin is found in Antarctica. The emperor penguin is currently under consideration for inclusion under the Endangered Species Act, due to the effects of climate change. The genome sequencing project is being conducted by researchers from BGI in conjunction with sequencing the polar bear, and Tibetan antelope genomes. (Read more)
8. Snow Leopard (Uncia uncia) – In October 2009 researchers from Oregon State University, the Western University of Health Sciences, and the Miller Park Zoo (IL) announced plans to sequence the genome of the snow leopard (which is on the Endangered Species list). According to Oregon State, the snow leopard is prone to diseases that do not plague other big cats including pneumonia, enteritis, hip dysplasia, and papillomaviruses. Sequencing the genome could help researchers identify what makes the snow leopard susceptible to these disorders. (Read more)
Genome sequencing technology continues to develop, making it easier and cheaper to sequence the genomes of various organisms. While an endangered species has yet to be saved due to the information obtained by sequencing its genome, what researchers learn will help them gain a better understanding of endangered species, which is a step in the right direction towards improving conservation efforts. 

From Novelist to Lepidopterist

New Research, Public Perceptions, Science History, Science Policy

My first encounter with Vladimir Nabokov was in my high school AP English class. My teacher Mr. Kaplow (author of Me and Orson Welles, which fun fact: is a movie starring High School Musical’s Zac Efron) kept a movie poster of Lolita (based on Nabokov’s most well known novel) hanging on the classroom wall.

I next encountered Nabokov while working through my undergraduate English major. Due to his Russian roots, Nabokov fit nicely into the course materials for my international literature class. I read his memoir Speak, Memory which talks a lot about Nabokov’s interest in lepidoptery, the study of butterflies.

Karner Blue Butterfly. Source: Wikimedia Commons.

I bring up Nabokov and his butterfly hobby because I just read an article on Nabokov’s scientific theories in the New York Times.  Nabokov’s theories were dismissed by lepidopterists during his lifetime,  but genetic analysis has shown that he was exactly right about the origin of a group of butterflies known as the Polyommatus blues. Nabokov theorized that the butterflies had originated in Asia and come to the United States in waves, but in the 1960’s and 1970’s no one took him seriously.

Researchers at Harvard University (where Nabokov was curator of lepidoptera at the Museum of Comparative Zoology) decided to do a genetic analysis on the butterflies to test Nabokov’s 30-year-old theory. The results showed that Nabokov was right all along, Polyommatus blues are genetically linked to butterflies in Asia. Genetic analysis has also been used to validate Nabokov’s hypothesis that Karner Blue Butterflies are a distinct species.

By this point you might be wondering why it matters that this long dead Russian novelist has been vindicated as a legitimate scientist by new technological advances, so I’ll get to my point. Nabokov is an example of how members of the scientific community can be quick to dismiss the work of anyone who isn’t an expert.

If we hold anyone who does scientific research to the same standard of peer review (analysis by other scientists, and the ability to replicate a study or experiment and get the same results as the original researcher) then even people who don’t have their doctorate in a specific science can still contribute new knowledge.

Please note that I’m not advocating that any quack with a theory should be taken seriously by the scientific community. But if promising research or theories are developed by people who might not call science their profession, their value should still be evaluated.

Revising Taxonomy

Conservation, Genetics, New Research, Public Perceptions, Science History

Very few people in the United States give a damn about the Egyptian Jackal. While I have nothing to offer as proof of this, I stand by my hunch that this specific canid isn’t high on the list of most popular animals, because really, who has even heard of it before? (I hadn’t until today…)

Golden Jackal. Source: Wikimedia Commons.

Why then should people care that genomic analysis has revealed that the Egyptian Jackal is actually a wolf, not a jackal at all? Well, because even if you don’t find the power of genomic analysis fascinating (like I do) this revision of current taxonomy (the classification of species based on how they are related to each other) is a great example of how science is a fluid thing that continually changes as new things are discovered. I think that understanding how even accepted scientific information can change is a hurdle that many people have to clear before they can really start to follow science in the news.

For years, the Egyptian Jackal (Canis aureus lupaster) was believed to be a subspecies of the Golden Jackal (both species that call parts of Africa home.) Researchers from the University of Oslo (Norway) noticed physiological differences (ie: differences in the way it looked) between Egyptian Jackals and other Golden Jackals, which led them to pursue a genetic analysis.

Sequencing the Egyptian Jackal’s genome has shown that it is a closer evolutionary relative to wolves found in India and the Himalayas (even to the United States’ Grey Wolf) than to Golden Jackals. Revising the taxonomy could have important impacts on conservation efforts. If Canis aureus lupaster (now renamed the African Wolf — and the only wolf now known to live in Africa) is a distinct species, an evaluation needs to be done to see how many members of this species there are, to determine if it is endangered.

I like this story because its a great example of how scientists are constantly revising accepted information the more they learn. However, I think when you tell people that science is constantly changing it is important to distinguish between making a revision and being flat out wrong. Scientists weren’t just wrong in their taxonomy. The Egyptian Jackal/African Wolf is a canid, so that part of the taxonomy was and still is correct. The genetic analysis enabled research to put the species into an even more specific category.

So when we say that science changes, we mean that it gets more specific and thus more accurate. But that doesn’t mean that the scientists who came before had everything all wrong. Often when scientists revise information their predecessors/colleagues were close, but didn’t have the necessary tools to learn enough to get things exactly right. There is always more that scientists can learn, and as they do, they fine tune, which is the case with the Jackal/Wolf taxonomy.

For more on the Jackal/Wolf revision, the research paper was published in PLoS One.

Shark Vision: It’s a Black and White World

New Research
A great white shark. Source: Wikimedia Commons.

Interesting research out of Australia analyzed the cell types in the eyes of 17 species of sharks, and found the the predators are largely color blind. The find is significant because it could help developers create new fishing industry equipment and water activity gear to reduce shark attacks based on visibility.

The researchers, from the University of Western Australia and the University of Queensland, looked for different types of cone cells in shark eyes. Humans have three different types of cones that enable us to receive and process blue, green, or red light waves. Sharks have only one cone, meaning they do not have the ability to distinguish between colors.