Difference between revisions of "Team:Oxford/Test/Beads"

Aim

To improve on last years Oxford iGEM team biobead design, using agarose to make up beads and then coating them with a ethyl acetate and polystyrene mixture.

Method

In a fume cupboard, break up a standard (polystyrene) petri dish into small pieces and dissolve in the minimum amount of ethyl acetate.

Prepare a 150 mL 1.5 % Agarose solution in beaker with screw cap. Microwave on high for 2 minutes and then cool to 40 °C in water bath. When microwaving ensure the screw cap is placed on loosely.

Remove agarose solution from water bath and bring to laminar airflow cupboard. Pour the agarose into petri dish to a depth of 1cm. Allow to set; this should take roughly 15 minutes.

Still under laminar flow, use an autoclaved 1 cm diameter hole borer to core out the required number of identical agarose cylinders and place in a second petri dish and leave to dry.

Bring uncoated ‘beads’ to fume cupboard. Using autoclaved needles, pick up individual beads and dip in ethyl acetate-polystyrene solution, stand each bead on a needle upright in fume cupboard on blob of blu-tac to allow ethyl acetate evaporation and the coating to set. When the coating is almost set the beads should be able to be handled through gloves without damaging the coat. Remove needle and mould the polymer coat over the needle hole, sealing them.

Control of substances Hazardous to Health (COSHH) Assessment

Agarose

• Not a hazardous substance

Ethyl Acetate

• H225 – Highly flammable liquid and vapour.
• H319 – Causes serious eye irritation.
• H336 – May cause drowsiness or dizziness.
• P210 – Keep away from heat, hot surfaces, sparks, open flames and other ignition sources. No smoking.
• P261 – Avoid breathing vapours.
• P305+P351+P338 – IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do so. Continue rinsing.

Ethyl acetate poses the biggest safety hazard in this experiment so therefore do all steps involving it in the fumehood. Be careful of cutting self when breaking up the Petri dish, as the pieces can be sharp.

Write Up

150mL of 1.5% agarose was made up using 2.25g of agarose powder and 150 mL of MilliQ.

In a fumehood, one standard petri dish was broken into small pieces and placed into a 500mL beaker. To this, 50 mL of ethyl acetate was added along with a stirrer bar and the mixture was left to stir for 10 minutes. After 10 minutes the petri dish was still not dissolved so a further 10 mL of ethyl acetate was added and left to stir again.

The agarose was then poured into a petri dish to a depth of 1cm and left to set for 15 minutes. After this was set, using an eppendorf tube with the lid cut off cylinders of agarose were cut out and placed into a second petri dish.

After the agarose was left to dry it was taken to the fumehood, to be coated. The agarose beads were placed onto the end of pipette tips and then dipped into the ethyl acetate-polystyrene mixture. These were then left to dry standing up on the pipette tips.

The beads were left to dry overnight and it was found that the coating did not stick sufficiently to the agarose.

Findings

• Beads are far too big to fit into a catheter, but could be used in larger pipes.
• It is very hard to get an even coating of the ethyl acetate-polystyrene mixture around the bead and it would tend to slide off.
• Ethyl acetate-Polystyrene mixture was difficult to clean up.
• Is the coating actually porous?

Aim

Try and make some beads out of alginate instead of agarose and see if we can make them smaller and more suitable to be placed inside a catheter.

Method

Make the 30ml of 1.2% alginate solution in dH2O with 0.9% NaCl, add 0.36g of alginate slowly to hot water followed and add a magnetic stirrer bar. Then leave to stir until all solid is dissolved.

To compare, make up 30ml of 1.2% alginate solution in dH2O. Add 0.36g of alginate slowly to hot water and add a magnetic stirrer bar. Then leave to stir all solid is dissolved.

Transfer this mixture in a 2mL syringe with a needle attached and drop the mixture into a solution of 0.1M calcium chloride. Vary the size of the syringe and height from which you drop and record the effect on the beads. Leave the beads in the CaCl2 solution for 5 minutes and then filter the beads out.

Control of substances Hazardous to Health (COSHH) Assessment

Sodium Aliginate

• Not a hazardous substance

Calcium Chloride Solution (0.1M)

• H319 – Causes serious eye irritation
• P305 + P351 + P338 - IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing.

The calcium chloride poses safety hazards therefore when doing steps involving it make sure you are wearing safety goggles and gloves.

Write Up

Sodium Alginate, mass = 0.36g

Milli-Q Water, volume = 30mL

Used hot plate to heat the water. Then while stirring slowly added the sodium alginate. The mixture was left to stir. Once the solid had all dissolved the mixture was a gloopy gel.

Using a 5mL syringe without a needle attached the sodium alginate solution was dropped into 0.1M calcium chloride solution, which was already made up in the lab.

The beads were then filtered using filter paper and placed into a petri dish and the process was then repeated using a syringe with a needle.

Without a needle

• Inconsistent size
• Fewer beads produced

With a needle

• Consistent size
• More beads produced
• Preferred method

Tests

Beads from the with needle trial were placed into 3 eppendorf tubes. One was placed at room temperature, one at 4 °C and one at -20°C.

Aim

Attempt to encapsulate cells inside of the sodium alginate beads. To test whether the cells are inside of the bead and to see if they are still alive we will use fluorescent bacteria and then measure the fluorescence of the beads under difference conditions.

Method

Take 1mL of cells in culture medium. Spin down in a centrifuge at maximum speed for 1 minute. Remove the culture medium. Re-suspend cells in 1mL of sodium alginate.

Make beads using the same method as above.

96-Well Plate

To attempt to see whether the cells are alive inside of the beads we will use a 96-well plate with different varieties of beads/medium/etc and then use a plate reader to measure the fluorescence.

	1	2	3	4
A	Bead with no bacteria	Bead with MG(-)	Bead with 20k MG	Bead with 20K DH5
B	Bead with no bacteria	Bead with MG(-)	Bead with 20k MG	Bead with 20K DH5
C	Bead with no bacteria	Bead with MG(-)	Bead with 20k MG	Bead with 20K DH5

Control of substances Hazardous to Health (COSHH) Assessment

Sodium Aliginate

• Not a hazardous substance

Calcium Chloride Solution (0.1M)

• H319 – Causes serious eye irritation
• P305 + P351 + P338 - IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing.

The calcium chloride poses safety hazards therefore when doing steps involving it make sure you are wearing safety goggles and gloves.

In this experiment you are working with live bacteria therefore make sure everything used its sterile and you wear gloves.

Write Up

First 30mL of Sodium Alginate solution was made up using the protocol from 14/08/2015.

Then taking the 3 bacteria being encapsulated (MG(-), 20K MG, 20K DH5 a 1mL portion was placed into an eppendorf. These were then spun in a centrifuge at maximum speed for 2 minutes. The cells were then resuspended in 1mL of sodium alginate solution by pipetting up and down several times.

Beads were then made from the same method as in 14/08/2015.

To see whether any bacteria had been encapsulated the beads were viewed under a microscope. However due to problems focusing the microscope this was only completed for the first 2 beads.

Then the 96-well plate was made up and the fluorescences of each bead measured.

The wells that contained a bead that should have fluorescent bacteria encapsulated was much higher than the two controls. From this we could assume that the bacteria had been encapsulated inside of the bead however more analysis would be needed to study whether they were still alive.

Results

	1	2	3	4
A	164	152	1475	670
B	170	155	2082	794
C	163	155	1744	750

From the data we can make the assumption that the bacteria have been incorperated into the beads.

Column 1 contained no bacteria and has a low reading. Also column 2 contained bacteria that should not fluorsece which again had a low reading.

However column's 3 and 4 contained bacteria that should fluoresce, therefore we can conclude that the fluorescent bacteria are in the beads. This will be repeated over two more days to see if the results are consistent.

Aim

Repeat results from 17/08/2015 to check whether we get consistent results. To make a batch of beads that can be frozen and then tested for the bacteria viability at a later date.

Method

Repeat protocol from 17/08/2015

Freeze a couple of each beads:

• No bacteria
• MG (-) (if we overnighted any, if not ask if we have an equivalent)
• 20K MG
• 20K F
• 20K DH5

Control of Substances Hazardous to Health (COSHH) Assessment

This experiments has the same hazards as in 17/08/2015

96-Well Plate

In order to get a greater set of data than in 17/08/2015 the fluorescence of more beads to be tested.

	1	2	3	4	5	6	7	8	9	10
A	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5
B	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5
C	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5

Write Up

30mL of sodium alginate made up using 0.36g of sodium alginate and 30mL of Milli-Q.

From this the 5 different sets of beads were made up:

• No bacteria
• 20K MG
• 20K F
• 20K DH5
• MG(-)

The beads were then washed with Milli-Q and the fluoresnces was measured.

The rest of the unsued beads were then placed into the -20°C freezer to be tested at a later date.

Results

	1	2	3	4	5	6	7	8	9	10
A	131	131	1703	2339	557	131	130	1531	2158	443
B	126	132	1263	3960	311	129	131	1113	3766	411
C	130	131	774	2113	603	132	133	551	1401	260

Method

Make up one set of each type of bead listed below:

• No Bacteria
• MG(-)
• 20K MG
• 20K deltaF
• 20K DH5

Measure the fluorescence.

	1	2	3	4	5	6	7	8	9	10
A	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5
B	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5
C	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5

Control of Substances Hazardous to Health (COSHH) Assessment

Same hazards as 17/08/2015.

Write Up

1mL of each bacteria in LB was placed into an eppendorf and spun down at max speed for 2 minutes. The media was then swapped for M9 and diluted 1/20 in M9 in conical flasks.

• Cells = 1mL
• M9 = 19mL

However no MG(-) was overnighted so they could not be made into beads.

These flasks were then left in the incubator at 37C.

OD measurements were taken at regular intervals and when the reading reached 0.4-0.7 the flasks were taken out of the incubator.

Time passed	Bacteria	OD	Ready?	Time passed	Bacteria	OD	Ready?
2 hours	20K MG	0.110	No	3 hours	20K MG	0.13	No
	20K F	0.136	No		20K F	0.19	No
	20K DH5	0.096	No		20K DH5	0.112	No
Time passed	Bacteria	OD	Ready?	Time passed	Bacteria	OD	Ready?
4 hours	20K MG	0.126	No	5.5 hours	20K MG	0.203	No
	20K F	0.267	No		20K F	0.488	Yes
	20K DH5	0.093	No		20K DH5	0.148	No
Time passed	Bacteria	OD	Ready?	Time passed	Bacteria	OD	Ready?
6.5 hours	20K MG	0,230	No	7.5 hours	20K MG	0.270	No but used
	20K F				20K F
	20K DH5	0.203	No		20K DH5	0.246	No but used

Beads made up from 2mL of the M9 and bacteria being spun down and resuspended in sodium alginate solution.

Fluorescence was measured in the same was as before:

	1	2	3	4	5	6	7	8
A	No	20K MG	20K F	20K DH5	No	20K MG	20K F	20K DH5
B	No	20K MG	20K F	20K DH5	No	20K MG	20K F	20K DH5
C	No	20K MG	20K F	20K DH5	No	20K MG	20K F	20K DH5

Results

	1	2	3	4	5	6	7	8
A	154	4439	2830	1180	151	2385	3507	3121
B	153	5157	2743	958	156	3218	2474	781
C	148	3479	3886	1852	151	3425	4099	2019

Method

Media swap and dilute to 1/20 in M9, leave in the incubator until the OD reads 0.4-0.7.

Make up beads using each of the bacteria.

Measure fluorescence and then freeze what is left.

Control of Substances Hazardous to Health (COSHH) Assessment

Same hazard as 17/08/2015.

Write Up

Media changed to M9 using 1mL of the overnight cultures from each bacteria and then diluted 1/20 in M9 in conical flasks. These flasks were then left in a 37C incubator.

The OD was measured at regular time intervals until they reached between 0.4-07.

Time passed	Bacteria	OD	Ready?	Time passed	Bacteria	OD	Ready?
3 hours	20K MG	0.170	No	3.75 hours	20K MG
	20K F	0.212	No		20K F
	20K DH5	0.126	No		20K DH5
	MG(-)	0.298	No		MG(-)	0.439	Yes
Time passed	Bacteria	OD	Ready?	Time passed	Bacteria	OD	Ready?
4.5 hours	20K MG	0.224	No	6 hours	20K MG	0.375	No
	20K F	0.414	Yes		20K F
	20K DH5	0.130	No		20K DH5	0.209
	MG(-)				MG(-)
Time passed	Bacteria	OD	Ready?	Time passed	Bacteria	OD	Ready?
6.75 hours	20K MG	0.418	Yes	7.5	20K MG
	20K F				20K F
	20K DH5	0.207	No		20K DH5	0.273	No but used
	MG(-)				MG(-)

The fluorescences was then measured according to before.

	1	2	3	4	5	6	7	8	9	10
A	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5
B	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5
C	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5

All unused beads were frozen.

Results

	1	2	3	4	5	6	7	8	9	10
A	145	155	5598	2511	1498	148	154	3432	1679	1629
B	147	155	6504	1642	2096	147	154	5920	2355	4107
C	146	152	4315	1990	677	145	151	2970	1382	1428

Method

Media swap the overnights from LB to M9 and dilute in M9 1/20 in conical flasks. Leave these flasks in the 37 incubator and measure the OD as regular intervals, until it reaches between 0.4-0.7 then remove the flasks.

Make up a fresh batch of 1.2% sodium alginate solution making sure the process is as sterile as possible.

Make up a set of each beads using sterile technique.

Measure the fluorescences of the beads.

	1	2	3	4	5	6	7	8	9	10
A	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5
B	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5
C	No	MG(-)	20K MG	20K F	20K DH5	No	MG(-)	20K MG	20K F	20K DH5

Place 1mL of LB + Chl into 5 test tubes. In the a test tube place one type of bead and then repeat with the other 4 test tubes.

Freeze any unused beads, labelled with the date.

Control of Substances Hazardous to Health (COSHH) Assessment

Same hazard as 17/08/2015.

Write Up

Media was swapped and diluted to 1/20 and then flasks left in the 37 incubator.

OD measured at regular intervals.

Time passed	Bacteria	OD	Ready?	Time passed	Bacteria	OD	Ready?
4 hours	20K MG	0.179	No	5 hours	20K MG
	20K F	0.311	No		20K F	0.500	Yes
	20K DH5	0.135	No		20K DH5
	MG(-)	0.633	Yes		MG(-)
Time passed	Bacteria	OD	Ready?	Time passed	Bacteria	OD	Ready?
6.5 hours	20K MG	0.306	No	7 hours	20K MG	0.351	No
	20K F				20K F
	20K DH5	0.210	No		20K DH5
	MG(-)				MG(-)
Time passed	Bacteria	OD	Ready?	Time passed	Bacteria	OD	Ready?
7.5 hours	20K MG	0.401	Yes	8 hours	20K MG
	20K F				20K F
	20K DH5	0.258	No		20K DH5	0.285	No but used
	MG(-)				MG(-)

30mL of 1.2% sodium alginate was made up.

• Milli-Q, volume = 30mL
• Sodium alginate, mass = 0.36g

Beads of each type were made up trying to be as sterile as possible. The beads were not filtered out of the excess CaCl2 but instead it was poured off, this was to avoid any contamination from the filter paper.

The fluorescence was then measured.

Results

	1	2	3	4	5	6	7	8	9	10
A	154	153	5122	3148	1057	148	151	4039	1382	1735
B	147	151	2702	2668	1776	148	152	1990	3089	2239
C	150	150	2411	2460	2699	147	149	1990	3089	1113

Update

Stop using 20K DH5, just takes too long to grow, it can be left for 7 hours and only reach OD measurement of 0.285. However it should reach 0.4 at least.

Beads left in the broth over the weekend did go cloudy in the end. Not the best results. Is the bead actually containing the bacteria or is this from contamination?

Control of Substances Hazard to Health (COSHH) Assessment

Same hazard as 17/08/2015.

Method

Media swap from LB to M9 using a 1/20 dilution.

Make up a set of beads of each type.

Measure the fluorescence.

	1	2	3	4	5	6	7	8
A	No	20K MG	20K F	20K DH5	No	20K MG	20K F	20K DH5
B	No	20K MG	20K F	20K DH5	No	20K MG	20K F	20K DH5
C	No	20K MG	20K F	20K DH5	No	20K MG	20K F	20K DH5

Write Up

Instead of giving up on DH5, a 1/10 dilution was made up to speed up time to reach log phase. Therefore check OD in 2 hours.

OD’s were measured at regular intervals until it reached between 0.4 - 0.7.

Write Up

20K MG, 20K ∆F, and MG(-) were media swapped (1mL) into M9 and diluted 1/20, these flasks were then left in the 37C incubator. 20K DH5 was media swapped (1mL) into M9 then diluted 1/10 and the flask left in the 37C incubator.

The OD was measured at regular intervals and the flasks removed from the incubator when the OD had reached between 0.4-0.7.

The 4 different bacteria were encapsulated into Sodium Alginate solution and beads were made up.

The beads were then placed into a 96-well plate according to the layout:

Fluorescences measured using the GFP protocol.

Results

Raw data that was collected from the plate reader. From this the graph was created in order to be able to analiysis the data more effectivly.

From the results all of the beads that were frozen showed very little fluorescence greater than those with no bacteria. Therefore we can conclude that freezing the beads would not be a suitable storage method.

The only beads that showed greater fluorescence was those that were made on the day.

There is a large peak for 19/08/2015 MG(-), this could be an annomaly or experimental error as all other beads with that bacteria have very little fluorescence.