When we entered the Biosafety and Environment laboratory, we went straight to the incubator and observed the culture media we inoculated yesterday. We observed what we expected that was that the last line of streaking had the thinnest lines and many isolated colonies of bacteria can be observed. These colonies can be further described by using some specific terminologies. First is the form or the basic shape of the colony such as circular, filamentous, etc. The size or the diameter of the colonies can also be measured using a ruler. Some also measure the side view of the colonies or their elevation viewed when the petri dish is turned on one end. On a closer look, the margin or the border of the colony can be magnified and observed as well as for its surface (smooth, glistening, rough, wrinkled or dull). Other colony characteristics that can be observed are its opacity (transparent or clear, opaque, translucent, etc. ) and the pigmentation or color (white, red, purple, etc.).The colonies we observed were similar in overall morphology which means that it is possible that they are of the same group. When colonies are distinct, each colony will represent an individual bacterial cell group.
We then proceeded to the microbiology room and made stock cultures of the colonies in our culture media. These will be kept so that the microorganisms will be in viable condition or so that there will still be a source of the microorganisms if they will be needed. We observed aseptic techniques such as flaming the loops and then dubbing it on to a bacterial colony. The inoculationg loop or needle is then stabbed on to a small tube containing a culture media and then they will be stored in the refrigerator. Also, some colonies were placed using inoculating needles in small microcentrifuge tubes containing double distilled water. They were then placed in a 95 degrees Celsius water bath and this is the Boiling Method of bacterial DNA extraction.
While waiting for the microcentrifuge tubes with bacterial colonies, we helped in testing some blood samples sent to the laboratory for Brucella spp. using the RBPT.
For each of the organ sample’s (lungs, liver, mesenteric lymph node) culture media, 2 representative colonies were taken so there were 6 total samples. After boiling them to extract their DNA, they were then used for PCR mixture preparation. The master mix consists of 56.8 ul of double distilled water, 20 ul of buffer, 40 ul MgCl2, 24 ul dNTP, 8 ul each of forward and reverse primers and 3.2 ul of Taq polymerase. Five microliters of DNA for each sample was then mixed with a corresponding amount of the mixture.
The PCR tubes containing the PCR mixture were then placed inside the thermal cycler or the PCR machine and the run time was approximately 2 hours. Thermal cyclers are “DNA amplifiers” which regulate the temperature in different cycles (denaturation, annealing and extension). The following steps will not be done yet. Mam Noemi said that the PCR products will still be further processed, will be sequenced through an automated DNA sequencer and then the sequence results will be analysed by the BLAST search engine.












































































































































