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Algae genome model developed by NYU Abu Dhabi team

By Luke Geiver | August 17, 2011

The United Arab Emirates may be the next location for algae research by Kourosh Salehi-Ashtiani, but his previous work in New York City should be on his mind for a long time to come. Salehi-Ashtiani, a faculty member at New York University Abu Dhabi, helped create a genome-scale metabolic model of the algal species Clamydomonas reinhardtii and completed the majority of his work at the New York campus. “This will allow us to make more accurate and in-depth predictions as to how the systems (algae strains) behave,” he said. The work, he explained, will help the entire algae research community understand how the strain will react to the practice of gene manipulation, allowing the researchers to predict what the strain will do given certain light conditions and nutrient allowance.

The genome model isn’t the only work Salehi-Ashtiani and his team of researchers completed. With the help of Jason Papin, a member of the biomedical engineering faculty at the University of Virginia, the team also created a set of clones for several of the genes in the model to allow researchers to physically test any hypothetical tweaks they made to the genome model. “At the end of the day when all of this is done with the network model that guides us computationally,” Salehi-Ashtiani said, “we have a set of clones that corresponds to each set of genes that are described in the network that we can actually do experiments with. We can see if gene knockouts or knockdowns can integrate well with the computational models.”

Not only does the work of Salehi-Ashtiani and his team provide the combination of computational modeling and the cloned apparatus for real-world testing, he also said the model will drastically reduce the amount of time needed to perform experiments. “If there were specific metabolites you wanted to look at, you can use the model to make predictions…for a gene or a set of genes so that if you did a knockout you might be optimizing production of that desired metabolite.” These types of experiments, he said, are hard to do. “If you want to know if there is a double knockout that can basically yield an increase in the metabolite that you are interested in,” he said, “you have about a thousand genes in the network, so a double knockout would be a thousand times a thousand, so basically a million experiments.”

Although the strain the team modeled isn’t generally used by commercial companies for large-scale commercialization, he said, the model can be adapted or used to generate metabolic models for these other species. “It kind of paves the way for moving forward and working with other algae species.” One of the benefits of the model that can directly help with the commercial use of algae for biofuels is linked to model’s ability to make predictions of strain behavior based on light fluctuations and exposure.

While the work at NYU is mostly complete, the team will continue to refine the model. Salehi-Ashtiani has plans to return to the UAE at the NYU-Abu Dhabi campus (there is also an NYU-Shanghai campus) to study how the algae species used in the genome modeling interacts with the environment there, all in attempt to map that out in terms of “evolutionary relationships,” he said. “There is a lot of work to be done, but there is a lot of excitement in this field. It is really an exciting time to be doing this kind of work.”

 

 

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