Three Birds with one stone

The week started off pretty interesting. We ran PCR of our assigned bacteria (Pseudomonas stutzeri). But first, Amber taught us how to run PCR gel by following the protocol provided to us by Dr. Cotter.
 

I shared a gel with a teammate, Jasmine, who's assigned bacteria is Pseudomonas putida. Unfortunately, I had made a mistake of pouring pipetting my DNA on the wring pool; I should have pipetted on pools number 6 and 7 instead of 5 and 7. after running our PCR, this was the band we observed.
  
Later that week, we sterilized the ground plastic we had prepared. We had a number 3 (PVC), a number 4 (LDPE), and a number 5 (PP). The processes wasn't complicated, but it did require careful handling to avoid contamination. We first put some plastic in small, autoclaved beaker after labeling the beakers. Then, 40 ml of 100% isopropanol was added to them in the fume hood then left them in there till we decide to use them during our next research meeting. 


Finally, today, we inoculated from our plates to thioglycollate tubes to identify if our bacteria is an aerobe, an anaerobe, facultative, or aerotolerant bacteria and left three tubes in incubation (bacteria PA, PP, and PS), and left PF at room temperature. 

Hopefully, we shall see some results from our tubes tomorrow. 

One step closer...

This week, the team had the opportunity to extract DNA from their bacteria. During the first week, we had to pick the bacteria we want to work on throughout the semester, and I had picked Pseudomonas stutzeri. Right now, the goal of the extraction is to run a PCR so that we could have our PCR primers to later try and culture some bacteria from specific types of plastic so that we can see if a specific type of Pseudomonas does, in fact, grow and degrade that form of plastic. 
In addition to that, this week, I was asked to prepare a ground form of plastic number 6, which we decided to use styrofoam for. To grind it, we used a blender. Seemed like a good idea until blending it became a disaster when static electricity chose to be a part of the blending. I couldn't get the styrofoam to stay in the blender. the more I blended and opened to check on it, the more of a mess I made. However, in the end, I asked if water can be added while blending so that it could get rid of the static electricity. After blending using water, Matt agreed to evaporate the water to leave us with our plastic. 


So far, my week has been very productive and successful. Hope the next week is as successful...

The grinding has begun...

I will admit, last week when Brian was showing me how to grind plastic, I was a little hesitant and nervous. It looked like a job for the strong, and I was completely doubtful of such strength residing within me. I made sure I understood all there is to do before trying the machine. I asked about the cleaning process, and even Dr. Cotter and Matt helped come up with better ways to save plastic and prevent excessive messiness in the lab when grinding. 

The first day I tried grinding, I realized my assumptions were on point. I was shaking as I turned it on to grind! However, after the first try, I got the hang of it. And with the aid of music, the second and third try was a breeze…

This week, after finding out the type of plastic I should be working on (which is PVC), I proceeded with learning how to grind it. Brian, who’s an expert at grinding any plastic, showed me the process of grinding, how to use the tools correctly and carefully, and even gave me easier methods to get maximum results. At that day, Brian was grinding the bottle seen below. However, Before the grinding process, Dr. Cotter had asked me to disinfect my PVC. So after spraying my PVC with ethanol and wiping it, I sprayed it with the ethanol again and left it there to dry. I performed this cleaning process one more time even if I was informed that there is no point and that I’ll have to disinfect the PVC after grinding it. I believe it made the job less taxing by 2% :D

Last week, I had to leave my microbe in the glucose tube and MSA plate so I could be 100% sure it’s a gram-positive bacterium. After the 24 hours, my results were confirmed. My bacteria was a gram positive bacterium known as Bacillus subtilis. 
After figuring out the bacteria, my next mission was to pick the type of Pseudomonas bacteria I want to work with for the WAESO project. The WAESO project is concerned with the role Pseudomonas bacteria plays in the breakdown of micro plastics, and how micro plastics affect us. For this session in the WAESO project, I will be working with Pseudomonas stutzeri. Pseudomonas stutzeri is the bacteria that breakdown bio-plastics, which are used in the medical industry. Therefore, by understanding how these bacteria break down the plastics and the effects it has, we can come to a conclusion that will prevent other complications. Below are the Pseudomonas bacteria we will be working on throughout the semester.

Let the games begin. May the odds be ever in our favor *mockingjay whistle*...

This week was a lot more of a challenge than it was last week. After being provided with an unknown bacteria, I proceeded with the streaking method to figure out what my bacteria is. After leaving it in the incubator for 24 hours, I inoculated from the Petri dish to a microscope slide. Before that, however, I first drew a circle on the slide with a wax pencil, then made a drop DI water inside the circle. After that, i mixed the inoculated bacteria with the DI water. Then, I covered the slide with a paper towel and using wooden tongs, placed the slide on boiling water for 6 minutes; making drops of Malachite Green every 30 seconds. Malachite green is used to stain the potential spores of the bacteria, and the heat is needed to open up the spores. After the 6 minutes were up, I picked the paper towel up from the slide and rinsed the slide with DI water, then proceeded to add the Safranin and leave it for 60 seconds. The next step was to observe the slide under a microscope. After confirming the microbe had endospores, I used a MAC plate to confirm it is in fact gram positive bacteria. I did that by smearing some bacteria on the plate and leaving it in incubation for 24 hours. After confirming, I had to find out what the bacteria actually is so I Needed to perform one last test on a glucose tube and an MSA plate. Unfortunately, I wasn't able to find out today as I have to leave the microbe in the glucose tube and MSA plate for 24 hours in incubation. So stay tuned for final results...

This week was my first week in STEM. I haven't done much besides watch a lot of videos regarding safety and whatnot; along with reading some modules about research. Those above took me two sessions in the lab, and tomorrow will be my first day working on actual lab work. I have been assigned an unknown bacteria, and my first job, after reading the lab manual, is to do some streaking. Hopefully, a lot will be done by next week. I have also been given a notebook where I’ll record everything I do in the lab. Josh and Matt warned me to record EVERYTHING in a hilarious way. I doubt I will forget now J