Modeling Arabidopsis Responses to Microgravity

Dr. Sarah Wyatt and graduate student researcher Marilyn Hayden are converging their knowledge of genetic research and computer-assisted network analysis to build a novel computer model. The model will collectively present International Space Station (ISS) plant experiment data from the past 10 years. The meta-analysis will provide plant geneticists with a visual, interactive network model of the genes acting and interacting across the genome in response to microgravity conditions.NODEs

The network model is part of the Wyatt Lab’s current space-based research experiment, known as BRIC-20, and will include 47 space-based plant research projects conducted by international researchers aboard the ISS. Many international scientific journals have published some of the data, but a large portion of it has never been publicly available.

Since the data results from a variety of plants, space-flown treatments, and different test hardware, all of which impact the kind and quality of data collected, Hayden must carefully normalize the data across all 47 experiments before it can be modeled. This requires parsing long, disparate lists of genes, annotations and associations, normalizing them through an extensive pipeline of applications, and then importing them into a database as well-ordered and correlatable information.

Once Hayden has the information in the database, she will use the space-flown data to filter a separate foundational network simulation of the entire Arabidopsis genome that she created by piping in information from several comprehensive and publicly available data centers. By applying the data from the meta-analysis to the foundational network, Hayden will create the first network model of the plant’s adaptive response to microgravity conditions.

The model will show which biomolecular responses are specific to a plant experiencing microgravity. “The visual interactive computer simulation,” said Hayden, “will allow bioinformation researchers to highlight a specific gene, visually see what other genes this gene is interacting with, and see relationships across the whole genome that were too complex to notice without the model.”

Once the computer model is complete and the results tested, the Wyatt Lab will share the model publicly to help other researchers studying plants in microgravity conditions.

Dr. Wyatt recently presented the network model at the annual meeting of the American Society for Gravitational and Space Research (ASGSR) in presentation titled, “Plant Gravitropic Signal Transduction: A Network Analysis Leads to Gene Discovery.”

Read the abstract here.

 

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