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Preparation Of Agar Plate Biology Essay

Samples from flower of the Ixora javanica and fruit of the Mimosa Diplotricha have been grinded into powder form by Dr. Zazali. 30g of the ground plant material was dissolved in 250ml dichloromethane and shake overnight at 150rpm in room temperature at 25oC by using shaking incubator (SI-900R). Then, the solution was filtered by using Whatman filter paper and the residues are collected and dried under fume cupboard (FUMETEC). The residues are transferred into the conical flask and 250ml of 50% ethanol is added and shake overnight at 150rpm, 25 oC. Then, the mixture was filtered. Filtrate was collected and poured into a separation funnel. Dichloromethane is added into the separation funnel and shake the mixture of dichloromethane and ethanolic solution. The bottom layer of the dichloromethane is extracted out as waste. This is repeated for several times to remove the lipid of the plant material. Then, the ethanolic phase is collected. The ethanolic solution is then undergone evaporation by using rotary evaporator to evaporate the ethanol. The concentrated plant extract is then undergo freeze-dry and keep at -20 oC.

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3.2 Column chromatography

Polyacylamide column is packed by added amide 6 that dissolved in the 2% acetic acid to the column bit by bit. 50centimeter of the amide is packed. Then, the column is connected to the akta prime plus fraction collector to calibrate the column with 2% acetic acid by setting the flow rate as 0.1ml/min and run overnight. Then, 1g of Ixora javanica extract was dissolved in 2ml 2% acetic acid was injected into column through the akta prime plus fraction collector. The flow rate was set to 1.5ml/min. The pressure was ensured not to more to 0.4 atm. The fraction was collected when the absorbance was increased dramatically. The colour pigmented compound was not collected although it will raise the aborbance.

3.3 Preparation of agar plate

Agar plates were prepared by using Mueller-Hinton agar. 20g of Muller-Hinton agar was suspended in 1000ml of distilled water in conical flask. The mixture was stirred until it completely dissolved in distilled water by using glass rod. Then, the mixture was sterilized by autoclave machine (Tomy SS-325) at 121 oC for 15 minutes. The mixture is then cooled to 40 oC after sterilized and poured into petri dishes and solidified became agar. The agar plates were incubated overnight in the incubator at 30 oC to ensure no any contamination occurred. The agar plates is keep in refrigerator for prolonged usage.

3.4 Cultivation of bacteria

Gram-positive (Bacillus subtilis, Bacillus cereus, Staphylococcus aureus) and gram-negative (Plesiomonas shigelloides, Escherichia coli, E.coli 0157:H7, Salmonella sp., Salmonella typhi) bacteria were given in glycerol stock solution. Each bacteria species was streaked on the agar plate by using a loop. Cultivation of bacteria has done in laminar flow to ensure the surrounding area always in sterile conditions. The wire of the loop was heated until red-hot and cooled it before picking up bacteria. The bacteria were streaked on the agar surface using dilution streaking method. The loop was cleaned by glycerol 20% and heated red-hot each time before used or for the different species of bacteria to be cultivated. This is to prevent growth of other bacteria and contamination. The agar plates were then incubated in the incubator at room temperature for 24 to 48 hours.

3.5 Screening for antimicrobial activity of extracted protein from plant

Single colony of the B.subtilis was taken from the agar plate and transfered and streaked homogenously on a new agar plate by using a loop. 40µl of protein extracts were pipette dropped onto the agar plate that have been make 4 holes for the input of protein extracts. The agar plates were incubated in the incubator at room temperature for 24 hours. The same procedure was repeated for other bacteria. Another set of agar plates were used for antibiotics such as amphicilin, kanamycin and streptomycin. The result was observed.

3.6 SDS-PAGE (Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis)

SDS-Page is method performed based on the discontinuous buffering system by Laemmli (1970).

3.6.1 Discontinuous Polyacrylamide Gels

The stacking gel and resolving gel solutions were prepared as below:


Stacking gel (4%)

Resolving gel (17%)

30% Arylamide/Bis



0.5M Tris-HCl, pH 6.8



1.5M Tris-HCl, pH8.8



10% SDS



18.3 MΩ-cm H2O






10% APS

50 µl

50 µl

Total volume



Overlay solution was prepared as below:



10%(w/v) SDS


Distilled water


The resolving gel solution was prepared by mixing all the reagent except 10% APS and TEMED in a flask. The solution was degassed for 3 minutes. 10% APS and TEMED were added after degassed and swirled gently to mix and were poured in between the glass plates by using pipette. The solution is poured gently to prevent it from mixing with air and avoid formation of bubbles. The resolving gel is overlaid with 0.1%SDS or distilled water. The gel was allowed to polymerize for 1 hour. After polymerization, the overlay solution was poured.

The stacking gel monomer solution was prepared by mixed all the reagents as shown in the table except 10% APS and TEMED. The solution was degassed for 5 minutes before the 10% APS and TEMED were added. The solution is swirled gently after 10% APS and TEMED is added and poured on top of the resolving gel until the top of the plates by using pipette. The comb as inserted slowly and gently. The stacking gel was allowed to polymerise for 30-40 minutes. The comb is removed gently when it is to be used.

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3.6.2 Sample loading

Sample buffer was prepared as shown below:



0.5M Tris-HCl,pH 0.25ml




10% SDS




0.5% bromophenol blue


Distilled water




Running buffer was prepared as table shown below:



10X Tris/Glycine/SDS


Distilled Water




The assembly was filled with running buffer until the below the edge of the outer gel plate. Sample is added with sample buffer with ratio 1:4 and heated at 95oC for 5 minutes. Samples and molecular weight markers were loaded slowly into the wells and allows them to settle at the bottom of the well. Electrophoresis was performed at a constant voltage of 120 V for around 2 to 3 hours. The electrophoresis was stopped when the tracking dye front was around 1cm from the bottom of the gel. The gel was stained with Coomassie Brilliant Blue.

3.6.3 Colloidal Coomassie Staining

Staining solution

5% (w/v) Coomassie Brilliant Blue G-250 0.1g in 2ml or 1.0g in 20ml

Phosphoric acid, H3PO4 11.8ml

Ammonium sulphate, (NH4)2SO4 100g

The staining solution prepared by the 5% (w/v) Commassie Brilliant Blue separately. 100g ammonium sulphate dissolved in distilled about 500ml. Phosphoric acid is added. 5% (w/v) Coomassie Brilliant Blue is added little by little. Then, the mixture is top up to 1L.

Destaining solution

Methanol 40ml

The staining solution was topped up with distilled water to make a total volume of 200ml.

Protein can be visualized directly in gel by Coomassie staining. Before staining, methanol is added to staining solution with the ratio 1:4. The gel immersed into the staining solution and shake overnight. The gel is destained in destaining solution with gently agitation on the shaker. The destaining solution was replenished several times until the background of the gel become clear and fully destained. The result is observed.

3.6.4 Silver staining

Silver staining was used to visualize the bands on the gel which the band is not clearly shown by colloidal coomassie staining. The protocol was modified from Heuckeshoven and Dernick (1985). The solutions were prepared according to the measurements given below:

Fixing solution

[40% (v/v) ethanol, 10% (v/v) acetic acid, 150ml]

Ethanol 60ml

Glacial acetic acid 15ml

Top up with distilled water to 150ml

Sensitizing solution

[30% (v/v) ethanol, 0.5% (v/v) glutaraldehyde, 8mM sodium thiosulphate, 0.5M sodium acetate, 150ml]





Sodium thiosulphate

Sodium acetate

Top up with distilled water to




Silver solution

[0.04% (v/v) formaldehyde, 150ml]

Silver nitrate


Top up with distilled water to




Developing solution

[0.24M sodium carbonate, 0.04% (v/v) formaldehyde, 150ml]

Sodium carbonate


Top up woth distilled water to




Stop solution

[ 40mM EDTA-NA2 . 2H2O, 150ml]


Top up with distilled water to



Preserving solution

[30% (v/v) ethanol, 4.6% (v/v) glycerol, 150ml]



Top up with distilled water to





From the coomassie staining, the gel was immersed in sensitizing solution for 30 minutes. The sensitizing solution is discarded. Then the gel was washed. The gel washed 3 consecutive times with distilled water. Each wash lasted for 15minutes. The gel then was incubated in a silver solution for 20 minutes. The gel was washed twice with distilled water for a length of 1 minute per washing. After that, the gel was incubated in a developing solution and the gel is immersed in stopping solution after the desired band intensity is obtained. Stopping solution added for 10 minutes then the gel is again washed with distilled water for 3 times with each last for 10 minutes. After washed, the gel was preserved in preserving solution. The silver staining procedure was carried out on an orbital shaker which was shaked about 50 rpm.

Summary of the sequenc used in staining by the silver method

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Duration (min)



















15 (3 times)




10 (3 times)

Few months

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