RNA Selection Against Burkholderia pseudomallei (BPM) to Accelerate Burkholderia Diagnostics and Aid in Treating Melioidosis

By: Arsany Gadallah

Melioidosis is a commonly misdiagnosed infection that can be presented as a fatal case of pneumonia or sepsis. The presence of melioidosis has been proven to be related to rainfall and extreme weather cases such as in the tropics (Baker and Tahani D, 2011). It has been spreading across the globe from northern Australia, several African areas and Asian countries to neighboring countries within the Americas at a fast rate. The causative agent of melioidosis is Burkholderia pseudomallei (BPM), which is a motile soil-borne bacterium that infects humans and animals, inducing symptoms such as chest pain and engendering cases of sepsis (Cheng and Currie, 2005). The disease has a mortality rate of 20-68% (White NJ and Dance DA, 1989), ranging from acute cases to severe and blood-borne cases. Both forms of the disease, acute and chronic forms, have called for attention from public health institutions, pointing out melioidosis as an endemic. Regarding the slow response to the current treatment of the disease, global researchers have been looking for faster, more responsive therapeutics to minimize the morbidity of the disease.

A vaccine, however, is being developed through extravagant, costly techniques, which would cause economic hardships to many infected areas (Cheng and Currie, 2005). Therefore, institutions are looking for cheaper and faster methods to treat melioidosis. One way to carry out such a task is to utilize nucleic acid oligonucleotides. Through the usage of aptamers, identification of the bacterium is possible. BimA, a trimetric Autotransporter/ macromolecule secreted by BMP (Brown and Iverson, 2011), which is an integral protein on the outer surface of B. pseudomallei, is functionalized with enough Histidine tags and actin-nucleating factors for a SELEX process using Nickel-NTA beads (Lazar and Stevens, 2011). Through selection, a fast therapeutic use of aptamers can help in treating the infection with accurate resources.

Specific aim 1: An aptamer, a precise nucleic acid sequence, is needed for selection against BMP through Nickel-NTA beads. The beads should help the protein and the RNA to meet and bind. The RNA sequence has to bind Burkholderia pseudomallei at the BPS site in order to activate a signal transduction that would aid in indentifying the bacteria and in accelerating the diagnosis and treatment of the infection (melioidosis). This therapeutic advantage of aptamers would be a congenial treatment, considering the precision and efficiency of SELEX rounds. If the selection is successful and the goals are achieved, inhibition of the Burkholderia bacteria would be easier and faster. Similarly, the same process can be applied onto Burkholderia mallei targets and similar results can be expected in treating glanders, since both B. pseudomallei and B. mallei are closely related.

Figure 1. An aptamer is needed to bind the Burkholderia pseudomallei (BPM) bacterium at the surface (BimA) for identification, which would later help identifying the bacterium and avoiding the enhancement of melioidosis.

***The target is on the “Recommended and Available” list of targets provided by Dr. Katy Brown, found in the -80⁰C freezer. The protein is sold by the company ATCC (ATCC.org) for $215 per 5 ug genomic DNA. Catalog # BAA-244D-5***


1. “Groundwater Seeps Facilitate Exposure to Burkholderia pseudomallei.” Appl Environ Microbiol. 2011 Aug 26, Baker A, Tahani D, Gardiner C, Bristow KL, Greenhill AR, Warner J.

2. PLoS Negl Trop Dis. 2010 Nov 30;4(11):e900: “The epidemiology and clinical spectrum of melioidosis: 540 cases from the 20 year Darwin prospective study. Currie BJ, Ward L, Cheng AC.

3. J Infect Dis. 1989 May;159(5):890-9. "Melioidosis: a major cause of community-acquired septicemia in northeastern Thailand." Chaowagul W, White NJ, Dance DA, Wattanagoon Y, Naigowit P, Davis TM, Looareesuwan S, Pitakwatchara N.

4. Faraday Discuss. 2011;149:23-36; discussion 63-77. "Development of reagents and assays for the detection of pathogenic Burkholderia species."Qazi O, Rani M, Gnanam AJ, Cullen TW, Stead CM, Kensing H, McCaul K, Ngugi S, Prior JL, Lipka A, Nagy JM, Gregory CW,Judy BM, Harding SV, Titball RW, Sidhu SS, Trent MS, Kitto GB, Torres A, Estes DM, Iverson B, Georgiou G, Brown KA.

5. Front Microbiol. 2011;2:151. Epub 2011 Jul 15. "Autotransporters and Their Role in the Virulence of Burkholderia pseudomallei and Burkholderia mallei. Lazar Adler NR, Stevens JM, Stevens MP, Galyov EE.

LINK TO PROPOSAL: http://dl.dropbox.com/u/42009520/Proposal%202.docx

LINK TO PROGRESS REPORT 1: http://aptamerstream.blogspot.com/2011/10/progress-discussion-problems-and.html

LINK TO FINAL MANUSCRIPT: http://dl.dropbox.com/u/42009520/Final%20Manuscript.docx


Santiago Diaz said...

Good job gathering information about your target and process conditions overall.

Shaan said...

I'm really interested in epidemiology and this seems pretty fascinating! Do you know more of the pathology of this disease? Interesting information gathered here though!

Alec Rezigh said...

Nice background information. Perhaps focus a little more on the signal transduction method you plan to inhibit. Overall well done, though!

Michael Ledbetter said...

Good work. Watch your use of abbreviations and make sure to introduce them before using them, namely BPS.

Jessica Beardsley said...

You have a lot of good background information about your target and methods for selection. Great job and good luck!

Jessica Beardsley said...

You have a lot of good background information about your target and methods for selection. Great job and good luck!

umar.ahmad said...

Since we have similar targets, I found your approach to the problem interesting. Regardless, still a great abstract.

John Ferguson said...

Your abstract is great. I also looked into your proposal, with your stated background information and methods it seems like your off to a good start. You know what your inhibiting, you just have to make it work now. This is very interesting and I wish you the best of luck on your research.

Jeffrey Chang said...

The information regarding how melioidosis affects people in lower socioeconomic regions sets up a good reason for the discovery of an aptamer against BPM. Good job!

Juan Herrejon said...

You have done a great job researching the background information and sounds like you know what you're doing! Keep up the good work!