Aptamer Selection against Burkholderia pseudomallei to improve diagnostic procedure for Melioidosis

Here is the link to my full proposal with complete images.

The final report is here

Abstract:

Burkholderia pseudomallei is a rod-shaped bacterium that causes melioidosis in humans and animals. Melioidosis’ symptoms may contain significant variance between cases, many possessing similarities to tuberculosis and some strains of pneumonia (Melioidosis 2011). The disease in endemic to northern Australia and southeast Asia, which draws concern towards the eradication of the disease, which is primarily passed through exposure to contaminated soil and water (Pathema 2011). Incubation periods vary anywhere from two days to several years, considering the possible dormancy of the bacteria. Overall, the mortality rate of the disease varies from 20-50% across all areas (Whitlock, Estes, Torres 2007). A cause to the high death rate, diagnosis of the disease is particularly cumbersome. Lower income areas, such as the endemic geographies of B. pseudomallei infection, have low access to full system scans or the serological test required to correctly diagnose the melioidosis, leaving many individuals without proper treatment.

Melioidosis diagnosis is marked by the presence of B. pseudomallei in the body. Bacteria taken from the bodily fluids must be cultured and detected as the causative strain before proper diagnosis can be obtained. Aptamers are nucleic acid chains that bind to specific targets, especially proteins. Through the SELEX process, aptamers can be partitioned from large pools of randomly generated nucleic acid strands to bind to a single protein target (Turek and Gold, 1990). The use of an aptamer would permit a relatively inexpensive test that could be used to diagnosis melioidosis more accurately and quickly, thus leading to faster application of treatment.

Specific Aim 1: Selection of RNA aptamers against Burkholderia pseudomallei.

B. pseudomallei is the cause of the disease melioidosis in humans and animals. This disease has a not insignificant mortality rate among infected individuals and current procedure for diagnostic tests are costly, in both time and financial areas. An aptamer that could bind to a surface membrane protein (for instance one of OM proteins targeted in vaccination development) would lessen the time and money needed to determine presence of B. pseudomallei in and individual (Gotoh 1994). Particularly pertaining to the lower GDP areas of endemic status, a cheaper avenue for diagnosis would greatly improve survivability.


Figure 1: The diagnosis of melioidosis using an aptamer-target-marker complex as the diagnostic tool will increase the efficiency of diagnosis for the disease (specific aim 1).

This bacterium can be obtained from Dr. Katy Brown, who has the targets already prepared.

Works Cited

§ Gotoh, N. et al. (1994) “Isolation and characterization of the outer membrane proteins of Burkholderia (pseudomonas) pseudomallei.” Microbiology. 140: 797-805.

§ ”Melioidosis: signs and symptoms.” Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Division of High-consequence Pathogens and Pathology. May 2011. http://www.cdc.gov/melioidosis/symptoms/index.html

§ Pathema: Bioinformatics Resource Center “Burkholderia pseudomallei.” Institute for Genomic Research. May 2006. http://pathema.jcvi.org/pathema/b_pseudomallei.shtml

§ Tuerk, C., Gold, L. (1990) “Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.” Science. 249: 505-510.

§ Whitlock, G., Estes, D., Torres, A. (2007) “Glanders: off to the races with Burkholeria mallei.” FEMS Microbiol Lett. 277:115-122.


Jake Van Fleet


For a link to my first progress report blog post, click here.


6 comments:

Zoe White said...

We are sort of doing the same target. Look forward to working with you.

-Zoe White

Austin Rezigh said...

Nice protocol. Very succinct. Go through and re-read though as there are a few grammatical errors.

Any ideas on what you are going to tag the aptamer with in order to use it as a diagnostic?

Arsany Gadallah said...

I did the same thing! and nice abstract! Hopefully, it works because I'm excited to see some positive outcomes.

Arsany

Alec Rezigh said...

Nice job Jake. Your abstract is very concise and straight to the point. Watch out for run-ons and other grammar errors. Best of luck!

Michael Ledbetter said...

Good abstract. Like Austin and Alec said, there are some gramatical erros that should be fixed, but overall well done. I noticed that you didn't mention a specific protein. Your probably still waiting on that information from Gwen, but you should try and find out something about its function when you decide. That is important to know whether the developed aptamer could potentially work as a therapeutic or solely a diagnostic.

umar.ahmad said...

Think you have an excellent proposal. Hopefully since we now have more specific info on the target we can probably better understand the exact goals.