NEWS FROM BIOFRONTIERS - July 2015
Driving innovation without boundaries
A member of Sara Sawyer's lab at BioFrontiers holds a sample of yeast infected with a virus. 
Bioinformatics answers questions of cancer and career path

 

At some point in school, we were taught that humans are a diploid species, made of cells with two sets of chromosomes - one set contributed by each parent. This idea neatly packaged the way we believed cells carried on with dividing themselves and creating more cells, but it isn't the only way. Polyploidy occurs when cells have more than two complete sets of chromosomes. Polyploids are common: Plants, some fish and amphibians are polyploid. Aneuploidy is yet another chromosomal mix - one where there is an abnormal number of chromosomes in a cell due to extra or missing chromosomes. While being diploid looks much simpler on paper, recent research points to the chromosomal flexibility of the ancestors of many diploid species, because as it turns out, polyploidy and aneuploidy appear to be pretty helpful in smoothing out the evolutionary ride.

 

In a recent paper in Nature, BioFrontiers Institute faculty member, Robin Dowell, an assistant professor of Molecular, Cellular and Developmental Biology, describes the influence that polyploidy has on accelerating evolutionary adaptation. By studying Saccharomyces cerevisiae, a helpful species of yeast well-known in winemaking, baking and beer brewing, Dowell was able to show that many individual strains can switch between polyploidy and aneuploidy, and they do so to adapt to evolutionary and environmental changes.

 

Dowell's lab is, in part, focused on studying how chromosomes influence adaptation and how these adaptations affect cellular processes. These processes are poorly studied because genetic data creates huge datasets and many labs lack the computational tools and abilities to dig through them. Dowell's lab, in the Jennie Smoly Caruthers biotechnology building, blends a biological wet lab with a computational dry lab resulting in research that has the capability to look deeply at bioinformatics.

 

Phil Richmond is part of Dowell's lab and a co-author on the Nature paper. He did much of the groundwork for this research as an undergraduate in the Department of Molecular, Cellular and Developmental Biology at CU-Boulder. His job was to comb through the data of 130 genome-sequenced strains, narrowing the dataset to 78 that were of acceptable quality to study.

 

"One of my biggest contributions on this project was benchmarking a way to track mutations in the genes," says Richmond. "Everything was built for humans with a diploid assumption and the current tools couldn't find mutations in polyploid yeast. This was my first really cool experience in digging into genomics."

 

Polyploidy and aneuploidy become interesting study subjects when it comes to cancer. From a cancer standpoint, polyploidy is a mistake in replication of chromosomes, and the odds of a polyploid cell becoming cancerous are increased. Some cancers appear to start when the cell divides and extra chromosomes go into one cell instead of splitting evenly between two. As this happens over and over, a cell can quickly become what scientists call "self-interested" and become a soft tumor.

 

Genetic sequencing is showing promise as a powerful tool for learning about different types of cancers. Richmond started at CU-Boulder as a pre-medical student and quickly fell in love with biology. Dowell hired him into her lab as a sophomore where he filed papers and washed glassware, but it wasn't long before Dowell recruited him for a programming project. Read more

New BioFrontiers lab uses evolution to fight disease

by Paul McDivitt

 

Ebola comes from bats, HIV from primates, and new strains of influenza from birds and pigs. With zoonotic diseases - those capable of transmission from animals to humans - grabbing headlines across the globe, understanding how they work has never been more important.

That's the mission of a new team of researchers led by Dr. Sara Sawyer at the BioFrontiers Institute. By analyzing the genomes of hosts and viruses alike, Sawyer and her team hope to shed some light on why humans are resistant to most animal viruses, and how animal viruses evolve the ability to overcome these obstacles and infect humans.

 

"These are exactly the kinds of targets that we're after - mammalian genes that determine why viruses infect the species that they do and why they don't infect the species that they don't," said Sawyer.

 

One example of the work that Sawyer's lab does is a project studying how HIV - the virus that causes AIDS - jumped from primates to humans, and why the virus affects humans differently than some primates.

 

"Chimpanzees and humans only differ in their genetic code by two percent, yet HIV doesn't make chimpanzees nearly as sick as it makes humans," said Sawyer. "So somewhere in that two percent difference in their genetic code may lie the answer to surviving this devastating disease."

 

Sawyer's team, which moved to Colorado from the University of Texas at Austin, works primarily with HIV, dengue (the virus that causes dengue fever) and influenza.

 

They utilize samples from a variety of primate, rodent, bat and other mammalian species in order to understand the genetic reasons why some species are susceptible and others aren't.  Genetics may provide the answer to how viruses evolve to infect new species. One of the specialties of this lab is bringing wildlife samples into the lab rather than relying on materials from model organisms (the lab recently received part of a wolf heart in the mail).

 

The lab, which is housed in the Jennie Smoly Caruthers Biotechnology Building on the CU-Boulder east campus, operates at biosafety level two, which required a substantial retrofit before Sawyer's team could move in. (The lab does not work with live strains of Ebola, which is highly regulated and requires a biosafety level four lab.)

 

Sawyer is carving out a niche in the field of virology thanks to her background in evolutionary biology. By applying techniques from evolutionary biology Sawyer hopes to better understand interactions between viruses and their hosts, which could lead to novel methods for preventing future outbreaks. For example, by predicting when and where viruses could transfer to humans, we could implement simple public health measures to protect people - an intriguing prospect given the rapid proliferation of deadly viruses such as Ebola. Read more

 

 

UPCOMING EVENTS AT BIOFRONTIERS
2nd Annual Women in Bio Symposium
The Women in Bio Symposium will again be held at the Jennie Smoly Caruthers Biotechnology Building. This year's event will feature a keynote by Amy Millman, CEO of Springboard Enterprises. This event is hosted by the Colorado Bioscience Association.
July 21 - 2:00 to 6:00 pm
JSCBB-Butcher Auditorium
Students can save 50 percent off their registration using code: WSYMP15. 

Technology Transfer Office Hours at JSCBB - First Wednesday of every month
Visit with experts from CU's Tech Transfer Office to discuss all your tech transfer and intellectual property issues, 8:30 to 11:00 am in the JSCBB Cafe area on these dates:
Wednesday, August 5
Wednesday, September 2
Wednesday, October 7