Nav: Home

New software improves ability to catalog bacterial pathogens

June 27, 2016

PULLMAN, Wash. - Washington State University researchers have developed a new software tool that will improve scientists' ability to identify and understand bacterial strains and accelerate vaccine development.

RepeatAnalyzer is able to track, manage, analyze and catalogue the short, repeating sequences of bacterial DNA.

The researchers used the software to characterize Anaplasma marginale, a tick-borne bacteria that affects cattle, and published their work in the journal BMC Genomics. The research team includes computer science student Helen Catanese; Kelly Brayton, Department of Veterinary Microbiology and Pathology; and Assefaw Gebremedhin, School of Electrical Engineering and Computer Science.

Like many types of bacterial pathogens, A. marginale has a huge variety of strains and is widely distributed geographically, which makes vaccine development challenging. Scientists use short repeating sequences of DNA, called repeats, to understand the bacteria, its heredity and geographic distribution and to determine how harmful it is.

But for A. marginale, for instance, researchers have found more than 235 short, repeating DNA sequences. Without any kind of database, researchers had to mine published literature to keep track of the sequences. The task is also error prone when done manually, said Brayton.

"We developed RepeatAnalyzer precisely to bridge that gap," said Gebremedhin.

They developed the software for A. marginale, but it can be extended to any other species with similar repeating DNA sequences. It also provides a visualization tool so researchers can track strains on a world map, said Catanese.

"This reliable software tool can fuel research and collaboration and accelerate the path to the discovery of a vaccine," said Gebremedhin.

RepeatAnalyzer has garnered significant interest, and Brayton's collaborators in South Africa and China are already using it, she said.

"Here is something that was overlooked and didn't exist,'' said Gebremedhin. "More than anything, it will help people. When you have a tool, and the right metrics and analysis, you may find things you might not have known before.''

The researchers are working to extend the software to collect and handle similar datasets on other bacteria, as well as expanding on the visualization and analysis functionalities.
The work was supported by Gebremedhin's National Science Foundation CAREER award, which supports development of fast and scalable algorithms for solving problems in data science.

The research is in keeping with WSU's Grand Challenges, a suite of research initiatives aimed at large societal issues. It is particularly relevant to the challenge of sustaining health and its theme of changing the course of disease.

Washington State University

Related Bacteria Articles:

Conducting shell for bacteria
Under anaerobic conditions, certain bacteria can produce electricity. This behavior can be exploited in microbial fuel cells, with a special focus on wastewater treatment schemes.
Controlling bacteria's necessary evil
Until now, scientists have only had a murky understanding of how these relationships arise.
Bacteria take a deadly risk to survive
Bacteria need mutations -- changes in their DNA code -- to survive under difficult circumstances.
How bacteria hunt other bacteria
A bacterial species that hunts other bacteria has attracted interest as a potential antibiotic, but exactly how this predator tracks down its prey has not been clear.
Chlamydia: How bacteria take over control
To survive in human cells, chlamydiae have a lot of tricks in store.
More Bacteria News and Bacteria Current Events

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Teaching For Better Humans
More than test scores or good grades — what do kids need to prepare them for the future? This hour, guest host Manoush Zomorodi and TED speakers explore how to help children grow into better humans, in and out of the classroom. Guests include educators Olympia Della Flora and Liz Kleinrock, psychologist Thomas Curran, and writer Jacqueline Woodson.
Now Playing: Science for the People

#535 Superior
Apologies for the delay getting this week's episode out! A technical glitch slowed us down, but all is once again well. This week, we look at the often troubling intertwining of science and race: its long history, its ability to persist even during periods of disrepute, and the current forms it takes as it resurfaces, leveraging the internet and nationalism to buoy itself. We speak with Angela Saini, independent journalist and author of the new book "Superior: The Return of Race Science", about where race science went and how it's coming back.