A new study on fruitflies might radically advance how we treat humans for disease. That’s according to Manolis Kellis, a computer scientist at MIT. Over the past four years, Dr. Kellis worked with a team of about 100 other scientists – experts ranging from geneticists to biologists to computer experts like himself. Together, they created an ultra-sophisticated map of the fruitfly genome. Now, they’re attempting to make a more definitive map of the human genome, to help scientists pinpoint where disease originates. Dr. Kellis told EarthSky:
The reason why we started with the fruitfly was to really be able to develop the methodologies in order to be able to apply them to the human… By starting with a model organism, we were able to work on a genome that’s smaller, and more accessible.
What’s a genome? Dr. Kellis explained that all living organisms have a one. A genome is like a book that contains all our hereditary information. There’s a book in every cell, and that book is made up of letters. Dr. Kellis said those letters represent nucleic acids, which are a blueprint for DNA – the building block of life. But, he said, those same letters can also cause disease.
When one of these letters goes wrong, you could end up having a disease, or you could have a predisposition for a disease, you may be much more likely to get cancer if one of those letters changes.
And that’s where the fly genome comes in handy. While the human genome has 3 billion letters – we’re pretty complicated – the fly’s genome only has 160 million letters. It’s a playground for scientists – a place where there can experiment with different kind of methods to understand how genes are linked to the disease process. For the first time, he said, scientists – with the help of powerful computers – were able to classify the function of 80% of the genes in the fly genome. Before this, scientists just knew the location of the genes. Now, Dr. Kellis said, his team is turning its attention to the human genome, using the powerful techniques of genome analysis they’ve been practicing on the fruitfly. He’s hoping that, in 2011, scientists will be able to figure out – down to the letter – where certain diseases originate. Remember: our genome – what enables life and also encodes disease – is made up of billions of letters.
If you have say, a mutation, or a change in the letter… we can now say, aha! That letter falls in this region which we know carries out that function and we know is interacting with that other gene far away… and therefore make a prediction about what genes to target with a particular drug when you have a particular disease.
Dr. Kellis said that his team, better known as the modENCODE consortium, also worked on the genome of earthworms. A major player in the effort was Mark Gerstein, an expert in bioinformatics at Yale University. Dr. Kellis said that one of the biggest challenges of this project was getting a hundred scientists all over the world to work as a team. He explained how much work is involved in deconstructing a genome – the level of complexity involved:
There’s various tools. You can measure [genetic] expression, you can measure bindings of different regulators, there’s next generation sequencing, there;s antibody pulldowns…it’s very multidisciplinary, and everybody’s an expert in a particular experimental technique or computational technique and basically part of the challenge was getting people to work together, exchange data openly. To work as a team. To exchange and analyze the data in a coherent fashion.
He added that not only are they able to compare our results to all the existing bodies of knowledge for all these model organisms, and actually go back an intervene – by having an experimentally tractable species, they can go much deeper into the science.
And we know what to expect in the human when we see similar things.
If you’re interest is piqued, you can actually examine all the fly genome data sets, and the worm genome data sets, too. Everything is at modencode.org. The modENCODE team reported their findings on the fly genome in December 2010 in the journal Science.
Beth Lebwohl researches, writes and helps produce science content in audio and video formats for EarthSky. She is one of the authors on EarthSky.org, a script-writer for our podcasts, and helps host our English science podcasts in 90-second, 8-minute and 22-minute formats. Beth came to EarthSky in 2006 from the American Museum of Natural History's Department of Astrophysics, where she was surrounded by some of the greatest telescope-building, equation-wielding, code-writing physicists of our time. And they made her think . . . this science thing . . . it's pretty cool.