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.
Stress may protect -- at least in bacteria
Antibiotics harm bacteria and stress them. Trimethoprim, an antibiotic, inhibits the growth of the bacterium Escherichia coli and induces a stress response.
'Pulling' bacteria out of blood
Magnets instead of antibiotics could provide a possible new treatment method for blood infection.
New findings detail how beneficial bacteria in the nose suppress pathogenic bacteria
Staphylococcus aureus is a common colonizer of the human body.
Understanding your bacteria
New insight into bacterial cell division could lead to advancements in the fight against harmful bacteria.
Bacteria are individualists
Cells respond differently to lack of nutrients.

Related Bacteria Reading:

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

Digital Manipulation
Technology has reshaped our lives in amazing ways. But at what cost? This hour, TED speakers reveal how what we see, read, believe — even how we vote — can be manipulated by the technology we use. Guests include journalist Carole Cadwalladr, consumer advocate Finn Myrstad, writer and marketing professor Scott Galloway, behavioral designer Nir Eyal, and computer graphics researcher Doug Roble.
Now Playing: Science for the People

#529 Do You Really Want to Find Out Who's Your Daddy?
At least some of you by now have probably spit into a tube and mailed it off to find out who your closest relatives are, where you might be from, and what terrible diseases might await you. But what exactly did you find out? And what did you give away? In this live panel at Awesome Con we bring in science writer Tina Saey to talk about all her DNA testing, and bioethicist Debra Mathews, to determine whether Tina should have done it at all. Related links: What FamilyTreeDNA sharing genetic data with police means for you Crime solvers embraced...