Category: Zoology

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. 

Animals On The Black Market

Environment, Past Articles, Zoology

I’ve been thinking a lot about how humans use animals due to the readings I was assigned for my zoology class for next week. I like to think that my position on the use of animals is somewhat middle of the road. I believe in animal research, in work animals (like a sheep dog), and I do eat meat. BUT, I am a firm believer in protecting animal welfare and conducting all animal related activities in a humane way.

Chimpanzee (Pan troglodytes).
Source: Wikimedia Commons

I bring up animal welfare, because I saw an article in the BBC today about a huge raid on suspected illegal animal traders conducted by Gabon’s ministries of water, forestry, and defense. The government agencies weren’t able to save any live animals, but they found enough evidence (heads, hands, skins, etc) to charge the five suspects with poaching.

According to the World Wildlife Federation, the raid resulted in the largest haul of dismembered animals in Central Africa in the last decade. Included in the seizure were parts (I know, awful) of a gorilla, at least 15 chimpanzees (probably several more if the parts came from different animals), 12 leopards, a lion, five elephants, and several snakes.

I feel like animal poaching is the type of issue that can be easy for people to ignore because we associate it with being a far away problem, it can be easy for us to forget about. I realize that there are some cultures that hunt and eat these animals – but selling them for exorbitant prices on the black market, when killing them is illegal in the first place is a problem.

About a year ago I wrote an article for BioTechniques about a new method to track animal poaching using genetic analysis of poached animals. Genetics Cracks Down On Animal Trafficking focuses on animals poached in Nigeria and Cameroon, but it is still an interesting way to crack down on illegal animal trafficking.

First Day Of School

Grad School, Zoology

Yesterday was the first day of classes for the spring semester. As much as I struggled to come back to Wisconsin this semester I know that it will be a busy and productive few months. My first class was my science elective, the Biology and Psychology of Human and Animal Relationships.

A border collie like Willie. Source: Wikimedia Commons

I was a little concerned signing up for a zoology course, considering the majority of my science background is in environmental science (with a little biology on the side.) But, I think this class will be incredibly interesting, and judging by the readings the material won’t be anything that I can’t handle.

My professor Patricia McConnell brought her dog Willie to class for the first day. He served as an example of the emotions that some humans feel toward animals, and started a discussion about why we feel more connected to animals like dogs than we do to say a chicken. Willie is a border collie and a trained sheep herding dog, so he was well behaved enough to be allowed to wander the huge lecture hall walking up and down the rows to be petted.

It is just the beginning of the semester, but already I’ve got the ball rolling on several projects. I’m still doing background for my first Primate Center assignment, but I’ve got my first interview for that scheduled for next week. I’ve got a freelance project that I’m working on that is more health/medical writing so that is also something that is taking up my time. Being so busy is helping with my homesickness.