Category: Genetics

Humans Contaminate DNA Databases

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

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.

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. 

Revising Taxonomy

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.

To Test, Or Not To Test: A Regulatory Question

My internship with BioTechniques dumped me headfirst into the world of genome sequencing. One of the hottest (and by that I mean most talked about, funded, and hyped up) biotechnology fields, genome sequencing has a lot of power. The media loves genome sequencing because it attracts a lot of public interest, so its no wonder the technology is a headline maker.

For those who are unfamiliar with the term, genome sequencing is a process by which a machine takes a sample of your DNA (from saliva or blood) and “reads” it by identifying the nucleotide bases (Adenine, Guanine, Cytosine, or Thymine) that make up your personal DNA sequence. By comparing this sequence to the human draft sequence (a previously “read” and studied human DNA strand) researchers can tell if anything in your DNA sequence is out of place, indicating a chance for genetic disease.

I tried looking into personal genome sequencing companies for an article for my J800 class last semester. While I did come up with an article eventually, I decided not to pitch it on the grounds that none of the personal genome sequencing companies would make a representative available to talk to me, therefore my article was slightly off kilter. Apparently, no one wants to bother with helping a student, and if you don’t have a definite place to publish you just aren’t important enough for the corporate world to give a damn.

But, I still find personal genomics incredibly interesting, which is why the New York Times article Heavy Doses of DNA Data, With Few Side Effects caught my eye. The article takes a look at research from the Scripps Translational Science Institute that shows that people who pay money to have their genome analyzed often did nothing with the data, and even when the results indicated a higher risk for disease people didn’t feel any extra anxiety.

The results are interesting because they go against what you would think the common reaction to obtaining your genetic data would be. There has been controversy about public access to genetic information on the grounds that people won’t understand it and will thus act rashly or misunderstand their results. The new research shows that most people either didn’t do anything with the information they obtained, or consulted a medical professional before acting.

The new research doesn’t close the door on the issues surrounding personal genomics by any means. The idea that the technology and service should be regulated, and by who, and how strictly are all still prominent concerns. However, the study could serve to help policy makers decide how to regulate the industry.

The Plant That Took Over America

Sphagnum subnitens. Source: Wikimedia Commons.

It grows, it spreads, it takes over North America… its peat moss. Now I know that peat moss isn’t exactly the most exciting of topics, but the article Single peat moss plant ‘conquered America’ stood out to me for a few reasons.

I have written a lot about genome sequencing and genetics, and this research sequenced the genome of the peat moss Sphagnum subnitens, and found that all the samples they collected were genetically identical. This means that there is a common ancestor for the peat moss that spread prolifically throughout North America. 
The research was conducted by teams from Ramapo College in New Jersey (another reason why this article caught my attention,) Binghamton University in New York, and Duke University in North Carolina.  The different types of peat moss vary in color and are found in distinct locations, which makes the 100% genetic match all the more amazing. 
The moss species reproduces sexually, but a single plant can make both the necessary sperm and eggs so its offspring are genetically identical, without being asexually reproduced clones.