Oxalic Acid Gradient

Oxalic Acid Gradient:

1. In 15 mL falcon tubes, 5 mL of sulfuric acid, 2 mL of Potassium Permanganate, and x amount of oxalic acid.
2. The solutions would then sit for 10 minutes, being inverted every few minutes.
3. The optical density with a wavelength of 528 nm was taken for each falcon tube. The results were recorded.

The purpose of hospitals is to help people get better. However, in the United States, 2 million people are infected during their hospital stay and bacterial biofilms are responsible of 65% of all hospital acquired infections. A biofilm is a conglomeration of bacteria that is enclosed in a matrix of sugars and extracellular DNA, this helps to hold the bacteria together like a community. Biofilms can adhere to any surface and are commonly found in nature. However, biofilms can become problematic when they adhere to surgical tools such as catheters, endotracheal tubes, and scalpels. Currents methods used to destroy biofilms include antibiotics and biocides. These methods are often expensive, harsh, and ineffective; biofilms are notorious for developing resistance to chemical treatments. Instead of trying to kill the bacteria in the biofilm, we decided to degrade the matrix that protects it. We have created a cocktail of Nuclease and Dextranase to achieve this purpose. Once the matrix is degraded, the bacteria inside can be eliminated without the use of expensive chemicals.

What is nuclease? What is dextranase?
As mentioned earlier, one of the two targets for dispersing the biofilm is its extracellular DNA. To do so, we are using E.coli to secrete nuclease. A nuclease is an enzyme that catalyzes the hydrolysis of the phosphodiester bonds of nucleic acids. More specifically, the nuclease utilized by our team is a Micrococcal nuclease (Mnase) capable of cleaving single-stranded and double-stranded nucleic acids. The irony of the situation being that the nuclease bio brick (Part: BBa_K729004) being used is derived from Staphylococcus aureus. S. aureus biofilms are a major problem on medical equipment, and account for many infections. The S. aureus biofilm uses the Mnase for partial dispersal of its outer layer, so its inner colonies can spread outside and grow more biofilms. S aureus. Being a gram positive, ubiquitous bacteria, has one of the toughest biofilms. And hence, the strength of the Mnase is equally supplementary. Although the Mnase is derived from S. aureus, the function and the effect of the enzyme is not limited to that bacteria. Since extracellular DNA is component of almost every biofilm, the effect of the enzyme will not be affected by a change in the species/strain of bacteria. To further enhance the effects of Mnase, it will be applied in a mixture that also includes Dextranase. Dextranase is an enzyme that catalyzes the hydrolysis of bonds within dextran. Dextran is a component of the exopolysaccharide (EPS) matrix, common to many biofilms. The dextranase used for the construct, is an alpha-dextranase derived from Chaetomium gracile (a dematiaceous mold from the fungi family). Dextranase, by degrading parts of the EPS matrix would allow for Mnase to further seep into the biofilm, and thus increase the overall efficiency of the mixture

What we are doing differently
Past projects have targeted the bonds within the biofilm structure to disperse the biofilms, but since there is a variety of major bonds found within different biofilms, the effects of the construct have been limited to some bacterial species. But, by targeting the extracellular DNA and the exopolysaccharide matrix (common components of almost every biofilm), our aim is to create a general all-purpose dispersant, capable of working on a variety of biofilms, thriving in a variety of settings.

Extracellular Polymeric Substance Matrix: Sticky Stuff!
The bacteria in the biofilm are surrounded by an extracellular polymeric substance (EPS) matrix. This matrix is comprised of water, which hydrates the cells; various sugars, to provide nutrients and the sticky structure of the biofilm; proteins, which are typically enzymes; lipids; and extracellular DNA, which serves as a structural component of the biofilms. The EPS matrix constitutes 50-90% of a biofilm’s organic matter. The purpose of the EPS matrix is to adhere the bacteria to a surface and protect the biofilm against any harsh environmental conditions. The matrix also provides a “transport system” so that nutrients, water, and enzymes can move around the structure to meet the needs of each cell.

The production of the EPS matrix is, in part, regulated by quorum sensing; this is a way for bacteria to communicate with each other via chemical signalling molecules. Like a “quorum”, once there are enough bacteria, the bacteria are able to communicate with each other to collectively express a gene, in this is case they would be producing the EPS.