Purposes

In-field detection of aromatic compounds in environments has always been desirable, and convenience has always been an important requirement for in-field detection. To meet this requirement, the detection process should be fast and the result should be easily read by naked eyes. Furthermore, the device we design to realize all these should be readily portable.
When designing such a portable user-friendly device, the most challenging part would be developing the preservation method. As we choose Escherichia coli, which is unable to germinate spores, as our host strain, special method should be developed to protect the bacteria from temperature changes and physical stress while keeping them alive. We used alginate encapsulation as a basic solution to this problem and built advanced device based on such preliminary design to measure the concentration of aromatics in samples.^[5]

Alginate Encapsulation

Alginate is a polysaccharide consisting of β-D-mannuronic acid (M) and α-L-guluronic acid (G) residues. When exposed to calcium irons, G residues will immediately cross-link to form a gel-like material that may serve as a matrix to safely contain our biosensors.
Alginate has been frequently used as the biological encapsulation material for various organisms such as Saccharomyces cerevisiae, Escherichia coli and mammalian cells^[1][2]. It stands out because of several distinct characteristics^[8]:
(1) Stable and inexpensive, even edible.
(2) Does not interfere with biosensors we constructed.
(3) Ease to shape and manipulate.
(4) Provide reliable protection against environmental stresses.
The alginate encapsulation successfully solve the problem of lethal dehydration and oxidation stress upon our biosensor strains, so no recovering process is required.
If additional protective agents were applied, the biosensor strains may be preserved at 4℃ for more than a month.

Experimental protocol:
1.5% Alginate solution was boiled and kept warm in 40°C.
E.coli was grown overnight in LB medium at 37 °C in 15 ml Falcon tube, then were harvested by centrifugation at 4000 r.p.m. for 10 minutes and then resuspended in 500 μl of fresh LB media. mixed with 3 ml alginate solution, and dropped into 0.2M calcium chloride in room temperature(20 to 24℃) to form bead-like alginate encapsulation.
Alginate beads were washed in PBS to eliminate calcium irons and then stored in the solution with protective agents or drilled-water.

Protective Agents

Inositol

Bacterial under dehydration may face an increasing osmotic stress as the water activity decrease. A possible way to counteract the osmotic stress is to accumulate compatible solutes to maintain a high osmotic pressure in cytoplasm to stablize proteins and balance the dehydration in the environment^[4]. Inositol is highly compatible for this usage for its stability and hydrophilicity.
Previous work done by Aitor. et al. showed that inositol is highly efficient for preserving bacterial cells. (In that case, P. putida, which is the host of the transcriptional factors we used in our biosensors. )
The link to the original paper: http://link.springer.com/article/10.1007/s00216-010-4558-y

Trehalose

Trehalose has an advantage over other kinds of sugars for it has a relatively high glass transition, so the bacteria may maintain a glassy form with the temperature and humidity change.Additionally, high concentration of NaCl solution induces the expression of intracellular trehalose. ^[7]

To obtain a high validity maintainance, the protective agents’ we use were of ralatively high concentration, so we should test that the induction process was not interfered by the protecting agents. A series inositol and trehalose solutions of different concentration were tested.

Results

There is visible difference between the beads with and without induction. and it would be clearer under blue light.

For NahR, 3 hour induction was sufficient to discriminate the 100μM 4-MeBzO’s induction with the blank by naked eyes. The concentration of 100μM was chosen according to previous tests, indicating this concentration was to obtain highest induction ratio without noticable toxicity. (fig. 5b)
After 4 hours incubation, the fluoresence of NahR biosensor worked as expected, and 10μM of 4-MeSaA can be detected by this device. (fig. 5d)
Additionally, This experiment was done after 10-day-storage in the 4℃, so the bacteria were likely to survive for more than 10 days. According to the paper’s report, the maintenance of validity of the bacteria could be sure to meet the detection requirements in more than a month^[4].

Although the evidence of this device was inadequately rigorous, the actual products could be used in field to achieve a rough detection.

Advanced Design

Based on the alginate encapsulation method and previous test results, a hydrogel patterning and transferring method could surve our purposes. This method would be multi-purposes including aromatic detection in a quantitative view, possibility of the cell communication serving the idea of adaptor, and potential for the application of bandpass filter by constructing a inducer concentration gradient.

PDMS Template Design PDMS(polydimethylsiloxane) is particularly known for its unusual rheological (or flow) properties. PDMS is optically clear, and, in general, inert, non-toxic, and non-flammable. PDMS is a material with no marked harmful effects on organisms in the environment, which is frequently used in the microfluridic chips.
The parallel wells were etched on PDMS, using a PDMS template in which 500 μm×500 μm square patterns are microfabricated and equidistant from each other by 500 μm. The depth of the wells was 170μm. This design was aiming at prevent interaction of E.coli between different suqares, because the interaction may influence the diffusion process for constucting a concentration gradient. Addtionally, the shape could be altered according to the basal level and detection convenience^[5].
Pattern Transferring The alginate solution and bacterial culture mixture(described in the protocol of alginate encapsulation) was transferred in the wells. After treated with Calcium irons, the PDMS with the mixture was transferred to a agarose layer. (Its concentration is of 1.5% or 2%) In 5 minutes, the PDMS template was peeled off with the cell patterns left on the agarose substrate.
Improvements For adaptors, the adaptor E.coli cells could be encapsulated in the agarose layer. Then if the substrate of adaptor exist, it would be tranferred into the inducer which could be dected by corresponding biosensor.
For the bandpass filter, the agarose layer could be pre-treated, that sample and water was drilled on each side of the agarose layer. After 6 to 12 hours treatment, a concentration gradient would be constructed by diffusion. (The diffusion time could be calculated according to the mass of inducers and the concentration of agarose layer.)

Results

Potentials

The advanced device design has potentials for the entire aroamtic toolkit’s application. Various biosensors could be encapsulated by the same method, and the agarose layer may also encapsulate another kind of biosensor, or the adaptor bacterial cells. As the fact that the communication between the agarose layer and alginate is fast, it’s possible to conduct multi-sensor assay by this device. It’s also applicable for the adaptors.

Different concentration gradient could be constructed on the agarose layers. More tests are required to obtain the diffusion constant and this parameter could be used to calculate the diffusion time. After determine the pre-treating time, the alginate encapsulation of bandpass filter would be applied to this device. If the concentration of each square pattern could be calculated, then the bandpass filter would show response in different position. Then we may roughly read out the concentration by the response position. This approach would provide an opportunity for in field aromatic detection.

References
[1] Koch, S., Schwinger, C., Kressler, J., Heinzen, C. H., & Rainov, N. G. (2003). Alginate encapsulation of genetically engineered mammalian cells: comparison of production devices, methods and microcapsule characteristics. Journal of microencapsulation, 20(3), 303-316.
[2] Wang, N., Adams, G., Buttery, L., Falcone, F. H., & Stolnik, S. (2009). Alginate encapsulation technology supports embryonic stem cells differentiation into insulin-producing cells. Journal of biotechnology, 144(4), 304-312.
[3] Morgan, C. A., Herman, N., White, P. A., & Vesey, G. (2006). Preservation of micro-organisms by drying; a review. Journal of Microbiological Methods,66(2), 183-193.
[4] de las Heras, A., & de Lorenzo, V. (2011). In situ detection of aromatic compounds with biosensor Pseudomonas putida cells preserved and delivered to soil in water-soluble gelatin capsules. Analytical and bioanalytical chemistry, 400(4), 1093-1104.
[5] Choi, W. S., Kim, M., Park, S., Lee, S. K., & Kim, T. (2012). Patterning and transferring hydrogel-encapsulated bacterial cells for quantitative analysis of synthetically engineered genetic circuits. Biomaterials, 33(2), 624-633.
[6] Leslie, S. B., Israeli, E., Lighthart, B., Crowe, J. H., & Crowe, L. M. (1995). Trehalose and sucrose protect both membranes and proteins in intact bacteria during drying. Applied and environmental microbiology, 61(10), 3592-3597.
[7] Peking iGEM 2010 wiki
[8] iGEM: Imperial Collage/Encapsulation, 2009
[9] van der Meer, J. R., & Belkin, S. (2010). Where microbiology meets microengineering: design and applications of reporter bacteria. Nature Reviews Microbiology, 8(7), 511-522.