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Papers by Pasindu Chamikara
Advanced Study on selected taxonomic groups of Bacteria and Archaea
This paper helpful to study of Domain Archaea.
Conference Presentations by Pasindu Chamikara
The atmosphere of the earth is divided in to layers as troposphere, stratosphere, mesosphere and ... more The atmosphere of the earth is divided in to layers as troposphere, stratosphere, mesosphere and thermosphere. Each of these layers contain different types of airborne microorganisms owing to their physical and chemical characteristics such as types of gases, temperatures and atmospheric pressure. These microorganisms may have the ability to tolerate low O2 conditions, high temperature levels and survive even under UV rays. Therefore, isolation of these microorganisms can be useful in identifying the microbial diversity. Therefore, a 'water-boost rocket' method was developed to collect air samples from different layers of the atmosphere, where it can be used to isolate beneficial microorganisms from different layers of the atmosphere. The water-boost rocket consists of two main parts: the main rocket and the sample collecting part. Rocket is powered by water and compressed air. It is made out of a 1.5 L capacity plastic bottle. Four fins were attached to the bottom of the bottle using a plastic board. These fins help the rocket for its flight on a straight line. The nosecone of the rocket was made by using another 1.5 L plastic bottle. The neck and the bottom part of the bottle was removed to preserve the cone shaped part of the bottle. Then 50 g of clay was pasted on the top of the cone shaped part. This adds weight to the nose cone and the center of gravity is moved higher, thus making it more stable. The prepared nosecone was attached to the top of the rocket by gluing and taping. The nozzle of a size of 0.6 cm was prepared using a PVC pipe. The rocket launcher wad made up of wood. A separate pipe line was used to fill air to the rocket. Rocket can be filled with water through the nozzle. To launch the rocket, it has to be placed on the launcher and air should be pumped to the rocket by air pump or compressor. After pumping air, launcher can release the rocket. Normally this rocket flies up to 100 m of height. This height can be extended up to around 500m, if it is prepared with several stages by joining several bottles together. If we can use another type of gas instead of normal gas, it also can increase the height. The volume of water in the bottle and the pressure decides the maximum height that it can fly. A petri plate can be attached to the rocket using another nosecone, which can be attached over the pre-attached nosecone. Between two nosecones medium containing petri plate was placed. Then a timer circuit is placed on the first nosecone. This circuit helps to open and close the secondary nosecone at a specified time. When the nosecone is opened plate is exposed to the environment and then it should be closed within a predetermined time period (3 sec.). After the rocket is landed, we can take the plate, incubate it and isolate the microorganisms. Different types of media can be used to isolate diverse groups of microorganisms.
Phosphorus (P) is an essential element which is next only to nitrogen, influencing plant growth a... more Phosphorus (P) is an essential element which is next only to nitrogen, influencing plant growth and productivity. Unlike nitrogen, this element is not acquired through biochemical fixation but comes from other sources to meet plant requirements. Phosphorus compounds in the soil can be categorized into 3 groups including inorganic phosphate compounds, organic phosphate compounds of soil humus and organic/inorganic phosphate compounds associated with cells of living matter. Some of these are in insoluble form and some of them are in soluble form. Plants can absorb only the soluble part and soluble form infrequent than insoluble form in soil. Phosphate Solubilizing Bacteria (PSB) can convert either insoluble organic phosphate or insoluble inorganic phosphate into soluble orthophosphates. They make Phosphorus available for plants from insoluble organic and inorganic complex Phosphorus sources by solubilizing and mineralization. PSB were isolated from Aloe vera and Vigna unguiculata Rhizosphere soil collected from Kuliyapitiya. Visual detection and even semiquantitative estimation of the phosphate solubilization ability of microorganisms were carried out using serial dilution and spread plate method using Pikovskaya's Agar (PVK agar) medium. It showed clear zones around the microbial colonies in media containing insoluble mineral phosphates as the single P source. PVK agar plates were observed after 5 days incubation and selected the PSB strains. Then selected strains were re-cultured in PVK agar medium. Then plates were observed after 5 days incubation and confirmed the PSB by halo zone formation. Morphological characterization of colonies was done by observing the appearance of colonies in PVK agar medium. Microscopic characterization was accomplished by Gram staining, motility test and endospore staining. Further biochemical tests and molecular biological tests were performed for further identification. Here, twenty-nine biochemical tests were carried out according to Cowan and steels’ manual. And molecular biological 16s rRNA sequencing was carried out for confirmation of identified strains from biochemical tests. According to the tests isolated strains were Pseudomonas aeruginosa, Achromobacter xylosoxidans from Aloe vera and Pseudomonas fluorescens, Bacillus subtilis from Vigna unguiculate.
For more Information – https://globescience.net/what-are-microbes/
Various types of solid surfaces are used by the manufacturers to carry out packaging of their hea... more Various types of solid surfaces are used by the manufacturers to carry out packaging of their healthcare products. In order to control microbial hazards, these surfaces are subjected to de-contamination processes to avoid cross-contamination of the products and to improve product safety. The preventive approaches have resulted in the use of microbiological analysis of surfaces of the working areas as one of the tools to control the hygiene of products. The surface sampling method or their modifications are generally carried out for this purpose. The objective of this study is to validate a modified surface sampling method against the conventional method. The surface sampling method, i.e. conventionl swabbing test was performed to asses the quality of the work areas. This method was used in specific locations in the work surfaces and microorganisms in the selected area (100 cm 2) was taken, using a sterile swab. The swab test is based on the serial dilution technique (10-1 to 10-7) and 1 ml of each dilution was plated with Tryptic Soy Agar (TSA). In the modified method, 1 ml from each prepared dilution was transferred to the selected area of the surface. After 2 minutes, the surface was rubbed with a sterile swab. Each swab was then tranferred into a buffer solution contained in a universal bottle and 1 ml from each dilution was plated with TSA. All prepared plates were incubated at 32 ° C for 3 days. Three trials were conducted for each method as stated before and the results were calculated as cfu/ml. The results were subjected to paired-samples t-test using MINITAB programme to compare the two methods. There was no significant difference in conventional swab sampling method (m= 192, SD = 129) and the modified method (m=190. SD = 130); t (6) = 2.08, p= 0.083 (Table T value = 2.45, p=0.05). Both surface sampling methods successfully swabbed all bacteria in the selected area to be tested. Therefore, both methods can be performed to analyse the microbiological quality of working surfaces.
Optical microscope is an instrument, which uses visible light to magnify small objects that are n... more Optical microscope is an instrument, which uses visible light to magnify small objects that are not visible to our naked eyes. A typical light microscope used in our laboratories, can be very expensive and difficult to handle due to its weight. A maximum magnification limit of this instrument is ~1500X. An attempt is made to develop a small optical microscope that is very easy to handle with low production cost. The base of the microscope was made by an outer cover of a hard disk drive. Then a 15 cm long PVC pipe was attached to the base by gluing. A glass piece of 2cm × 2cm was placed on the top of the PVC pipe. It acts as the stage of the microscope. The prepared slide can be placed on this stage. A normal glass slide cannot be used here due to its size and thickness. Therefore, instead of the slide, a 2cm × 2cm size phone screen protector can be used. The specimen can be placed between the two layers of screen protector. Because screen protector consisted of the glass and a protecting film over that. Small earphone clip was used as the stage clips to hold the slide rigidly. The lense of a web camera was set to the top of the PVC tube above the glass stage. It was a 5 Mp camera lense with 30 mm radius of curvature. This lense act as the objective lense of the microscope. This lense gives nearly 40X-60X magnification. A white color bright Light-Emitting Diode (LED) was placed under the stage as the light source. It was powered by a 3.1 V phone battery. The intensity of LED can be controlled by using a volume controller. It can change the resistance (R) of the LED. Therefore, current (I) is changed. (V=IR) Thus intensity is controlled. So it acts as the condenser of a normal microscope. As there is no need of electricity power to this microscope, it can be easily used as a mobile instrument. The eyepiece was prepared by using a laser lense. It gives 10X magnification. The tube was attached to the PVC tube by using a spring. So it can be moved very easily. Focusing of the eye piece can be controlled by turning it around. It is the fine focus of this microscope. The movement of the objective lense around, acts as the coarse focus of this microscope. A total magnification of 400X-500X could be achieved using this microscope. The total cost of production was around LKR 1500. This mobile instrument has potential to deliver better magnification with few improvements, without spending huge amount of money on other kinds of microscopes.
For more information - https://globescience.net/rocket-science/
Teaching Documents by Pasindu Chamikara
Advanced Study on selected taxonomic groups of Bacteria and Archaea
This paper helpful to study of Domain Archaea.
The atmosphere of the earth is divided in to layers as troposphere, stratosphere, mesosphere and ... more The atmosphere of the earth is divided in to layers as troposphere, stratosphere, mesosphere and thermosphere. Each of these layers contain different types of airborne microorganisms owing to their physical and chemical characteristics such as types of gases, temperatures and atmospheric pressure. These microorganisms may have the ability to tolerate low O2 conditions, high temperature levels and survive even under UV rays. Therefore, isolation of these microorganisms can be useful in identifying the microbial diversity. Therefore, a 'water-boost rocket' method was developed to collect air samples from different layers of the atmosphere, where it can be used to isolate beneficial microorganisms from different layers of the atmosphere. The water-boost rocket consists of two main parts: the main rocket and the sample collecting part. Rocket is powered by water and compressed air. It is made out of a 1.5 L capacity plastic bottle. Four fins were attached to the bottom of the bottle using a plastic board. These fins help the rocket for its flight on a straight line. The nosecone of the rocket was made by using another 1.5 L plastic bottle. The neck and the bottom part of the bottle was removed to preserve the cone shaped part of the bottle. Then 50 g of clay was pasted on the top of the cone shaped part. This adds weight to the nose cone and the center of gravity is moved higher, thus making it more stable. The prepared nosecone was attached to the top of the rocket by gluing and taping. The nozzle of a size of 0.6 cm was prepared using a PVC pipe. The rocket launcher wad made up of wood. A separate pipe line was used to fill air to the rocket. Rocket can be filled with water through the nozzle. To launch the rocket, it has to be placed on the launcher and air should be pumped to the rocket by air pump or compressor. After pumping air, launcher can release the rocket. Normally this rocket flies up to 100 m of height. This height can be extended up to around 500m, if it is prepared with several stages by joining several bottles together. If we can use another type of gas instead of normal gas, it also can increase the height. The volume of water in the bottle and the pressure decides the maximum height that it can fly. A petri plate can be attached to the rocket using another nosecone, which can be attached over the pre-attached nosecone. Between two nosecones medium containing petri plate was placed. Then a timer circuit is placed on the first nosecone. This circuit helps to open and close the secondary nosecone at a specified time. When the nosecone is opened plate is exposed to the environment and then it should be closed within a predetermined time period (3 sec.). After the rocket is landed, we can take the plate, incubate it and isolate the microorganisms. Different types of media can be used to isolate diverse groups of microorganisms.
Phosphorus (P) is an essential element which is next only to nitrogen, influencing plant growth a... more Phosphorus (P) is an essential element which is next only to nitrogen, influencing plant growth and productivity. Unlike nitrogen, this element is not acquired through biochemical fixation but comes from other sources to meet plant requirements. Phosphorus compounds in the soil can be categorized into 3 groups including inorganic phosphate compounds, organic phosphate compounds of soil humus and organic/inorganic phosphate compounds associated with cells of living matter. Some of these are in insoluble form and some of them are in soluble form. Plants can absorb only the soluble part and soluble form infrequent than insoluble form in soil. Phosphate Solubilizing Bacteria (PSB) can convert either insoluble organic phosphate or insoluble inorganic phosphate into soluble orthophosphates. They make Phosphorus available for plants from insoluble organic and inorganic complex Phosphorus sources by solubilizing and mineralization. PSB were isolated from Aloe vera and Vigna unguiculata Rhizosphere soil collected from Kuliyapitiya. Visual detection and even semiquantitative estimation of the phosphate solubilization ability of microorganisms were carried out using serial dilution and spread plate method using Pikovskaya's Agar (PVK agar) medium. It showed clear zones around the microbial colonies in media containing insoluble mineral phosphates as the single P source. PVK agar plates were observed after 5 days incubation and selected the PSB strains. Then selected strains were re-cultured in PVK agar medium. Then plates were observed after 5 days incubation and confirmed the PSB by halo zone formation. Morphological characterization of colonies was done by observing the appearance of colonies in PVK agar medium. Microscopic characterization was accomplished by Gram staining, motility test and endospore staining. Further biochemical tests and molecular biological tests were performed for further identification. Here, twenty-nine biochemical tests were carried out according to Cowan and steels’ manual. And molecular biological 16s rRNA sequencing was carried out for confirmation of identified strains from biochemical tests. According to the tests isolated strains were Pseudomonas aeruginosa, Achromobacter xylosoxidans from Aloe vera and Pseudomonas fluorescens, Bacillus subtilis from Vigna unguiculate.
For more Information – https://globescience.net/what-are-microbes/
Various types of solid surfaces are used by the manufacturers to carry out packaging of their hea... more Various types of solid surfaces are used by the manufacturers to carry out packaging of their healthcare products. In order to control microbial hazards, these surfaces are subjected to de-contamination processes to avoid cross-contamination of the products and to improve product safety. The preventive approaches have resulted in the use of microbiological analysis of surfaces of the working areas as one of the tools to control the hygiene of products. The surface sampling method or their modifications are generally carried out for this purpose. The objective of this study is to validate a modified surface sampling method against the conventional method. The surface sampling method, i.e. conventionl swabbing test was performed to asses the quality of the work areas. This method was used in specific locations in the work surfaces and microorganisms in the selected area (100 cm 2) was taken, using a sterile swab. The swab test is based on the serial dilution technique (10-1 to 10-7) and 1 ml of each dilution was plated with Tryptic Soy Agar (TSA). In the modified method, 1 ml from each prepared dilution was transferred to the selected area of the surface. After 2 minutes, the surface was rubbed with a sterile swab. Each swab was then tranferred into a buffer solution contained in a universal bottle and 1 ml from each dilution was plated with TSA. All prepared plates were incubated at 32 ° C for 3 days. Three trials were conducted for each method as stated before and the results were calculated as cfu/ml. The results were subjected to paired-samples t-test using MINITAB programme to compare the two methods. There was no significant difference in conventional swab sampling method (m= 192, SD = 129) and the modified method (m=190. SD = 130); t (6) = 2.08, p= 0.083 (Table T value = 2.45, p=0.05). Both surface sampling methods successfully swabbed all bacteria in the selected area to be tested. Therefore, both methods can be performed to analyse the microbiological quality of working surfaces.
Optical microscope is an instrument, which uses visible light to magnify small objects that are n... more Optical microscope is an instrument, which uses visible light to magnify small objects that are not visible to our naked eyes. A typical light microscope used in our laboratories, can be very expensive and difficult to handle due to its weight. A maximum magnification limit of this instrument is ~1500X. An attempt is made to develop a small optical microscope that is very easy to handle with low production cost. The base of the microscope was made by an outer cover of a hard disk drive. Then a 15 cm long PVC pipe was attached to the base by gluing. A glass piece of 2cm × 2cm was placed on the top of the PVC pipe. It acts as the stage of the microscope. The prepared slide can be placed on this stage. A normal glass slide cannot be used here due to its size and thickness. Therefore, instead of the slide, a 2cm × 2cm size phone screen protector can be used. The specimen can be placed between the two layers of screen protector. Because screen protector consisted of the glass and a protecting film over that. Small earphone clip was used as the stage clips to hold the slide rigidly. The lense of a web camera was set to the top of the PVC tube above the glass stage. It was a 5 Mp camera lense with 30 mm radius of curvature. This lense act as the objective lense of the microscope. This lense gives nearly 40X-60X magnification. A white color bright Light-Emitting Diode (LED) was placed under the stage as the light source. It was powered by a 3.1 V phone battery. The intensity of LED can be controlled by using a volume controller. It can change the resistance (R) of the LED. Therefore, current (I) is changed. (V=IR) Thus intensity is controlled. So it acts as the condenser of a normal microscope. As there is no need of electricity power to this microscope, it can be easily used as a mobile instrument. The eyepiece was prepared by using a laser lense. It gives 10X magnification. The tube was attached to the PVC tube by using a spring. So it can be moved very easily. Focusing of the eye piece can be controlled by turning it around. It is the fine focus of this microscope. The movement of the objective lense around, acts as the coarse focus of this microscope. A total magnification of 400X-500X could be achieved using this microscope. The total cost of production was around LKR 1500. This mobile instrument has potential to deliver better magnification with few improvements, without spending huge amount of money on other kinds of microscopes.
For more information - https://globescience.net/rocket-science/