Category: Sequencing

BioTech’s New Hot Shot

There was an interesting article in the New York Times today (yes, I was magically granted access to their website again, not sure why but I’m glad) by Andrew Pollack. Taking DNA Sequencing to the Masses takes an in-depth look at the work of Jonathan M. Rothberg.

Dr. Rothberg is the founder of the genome sequencing company Ion Torrent. The article looks at Ion Torrent’s role in providing cheap (under $50,000) sequencing technology with the launch of their Personal Genome Machine. The technology isn’t intended for the general public, but will make obtaining a sequencing system more feasible for smaller universities and clinics that can’t afford larger machines.

The article draws a parallel between Rothberg and Apple founder Steve Jobs on several occasions. Pollack paints Rothberg as a bit of a rebellious nerd, who certainly has high hopes for his company and the technology they are developing.

Pollack ends the article with Rothberg saying that he believes that genome sequencing will become as useful for medical applications as imaging (like X-rays, CAT Scans, etc.) I like this article because statements like that aren’t blown out of proportion. I think that for an article that is focused on what can be achieved in the future the ideas all stay grounded in what is really feasible, which can sometimes be difficult in a science technology article.

Elephant Species

Source: Wikimedia Commons.
Photographer: Johnny Liunggren.

Researchers have put an end to debate about whether the African Elephant is one species, or two. New findings published in the journal Public Library of Science Biology show that the African Elephants that dwell in the savannah are a distinct species from those that dwell in the forests.

Loxodonta africana, the savannah dwellers, are much larger and in some cases twice as heavy as Loxodonta cyclotis, the forest dwellers. The debate about whether the elephants were separate species has been going on for at least a decade. The research shows that the two species diverged from their common ancestor around the same time that humans and chimpanzees evolved. How long ago the species split was a surprise for the researchers.

What Happened to Amelia Earhart?

Source: Wikimedia Commons.

Bones found on an island in the South Pacific are being tested against surviving members of Amelia Earhart’s family to see if the remains could belong to the famous aviator. Earhart disappeared in 1937 during an attempt to become the first woman to fly around the world. Her mysterious disappearance has been the topic of books, movies, and enough speculation to make her a household name – even today.

Along with other artifacts found on the island including makeup and glass bottles, a DNA confirmation that the bones belong to Earhart would finally put to rest the mystery of what happened to her. If the bones are Earhart it would be valid to conclude that her plane crashed, and that she survived as a castaway for some time before dying on the island.

If DNA can give an ending to the story of Amelia Earhart, it will definitely be a win for genetics, and scientific research in general. The question that would be left (at least for me) is what happened to her plane (or her navigator for that matter)?

Titanic Rusticles Home to New Species

An example of rusticles. Source: Wikimedia Commons.

I pretty much picked this story to highlight as today’s science find because I like the word rusticles, also the history of the Titanic. A rusticle is an icicle-like formation made by rust that forms on iron. Researchers have discovered a new type of bacteria in the rusticles that were formed by the wreckage of the Titanic.

New species of bacteria found in Titanic ‘rusticles’ explains that the Halomonas titanicae bacterium actually feeds off the rust formations. The bacteria are of interest because they could help researchers understand how bacteria participate in the breakdown of metal, which could have an impact on the safety of offshore oil drilling rigs and pipelines. After the BP Gulf Oil spill that was in the headlines all Summer, I’m sure we all want safer drilling mechanisms.
The story is also notable because the researchers sequenced the bacteria’s genome to establish that it is in fact a new species. Genome sequencing is a relatively new tool for establishing taxonomy.

1000 Genomes Project

For as long as I can remember my parents have been telling me that I’m special (in a good way, not in the derogatory way the kids are using the term these days). Most of us start life out thinking that we’re unique and the more we learn about life, and the more it kicks out asses we become so disillusioned that we cease believing we’re really all that special.

But, new data generated by the 1000 Genomes Project recently confirmed that our parents have been right all along. The 1000 Genomes Project is an effort to sequence the genes of 2,500 people from around the world in an attempt to fill the gaps in the draft sequence of the human genome left by genetic variation. 
The draft sequence was established in 2000 by teams led by J. Craig Venter and Francis Collins. While that was a breakthrough moment in the field of genetics because it enabled the study of diseases caused by changes in our DNA, it only took us so far. 
Genetic variation refers to the differences in the human genome between individuals (ie: if my code is AGTCAGTC, yours might be AGCCAGTC). That kind of a difference can have a huge impact on how disease manifests itself, therefore studies looking for treatments for genetic-based disorders (Alzheimer’s, Parkinson’s Disease, Cancer, etc.) are hindered by these variations. 
The new data obtained by the 1000 Genomes Project, is a 95% map of human genetic variation. The results of the study show that each individual person has an average of 75 variations (single nucleotide polymorphisms, or SNPs, which are changes in the code like I described above). These variations are essentially what makes each of us different from everyone around us. My parents were right, I am special, but something tells me they weren’t referring to my genes. 
This is exciting for a few reasons:
1. Millions of dollars have been invested in this project, it is good to see something actually come of it. 
2. A better understanding of variation can enable more progressive research on genetic disease, from causes to treatments. 
3. Genome sequencing technology is advancing quickly, and making interesting research like this a reality. Expect more projects like 1000 Genomes, it’s definitely about to get ambitious in here. 
4. A project like this sets important standards for open access information and data sharing among researchers for genetic studies at this scale. 
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