A toast to MS Word

I would like to thank MS Word for bearing with me this week as I overuse it to write my research draft for both WAESO and S-STEM. Regardless of how unfortunate I was regarding both being today, I had MS Word with me throughout the journey. Whether I decide to wake up at 2 AM in the morning to finalize, or I choose to be more efficient as I type in the bus, MS word was by my side correcting my spelling, grammar and punctuation errors. Not only those, but it provided me with synonyms to sound a bit more sophisticated. I mean, I don't see google docs helping me change 'always' to 'frequently'. Therefore, for all the promised and delivered assistance, I dedicate this blog post to MS Word.

Disclaimer: Google docs was not harmed in the name of this post. Google docs is much appreciated as well, and should not be deemed unworthy of praise.  

 

I pinky promise I did not stain it!

A series of fortunate events led to an unfortunate event. I will admit, the unfortunate event worked in my favor. The journey began when Dr. Cotter informed us that we will need to add our plastics and our bacteria in small, capped test tubes. We gladly complied assuming it would be an easy task. We were terribly wrong. We first had to weigh our tubes, zero our weighing machine, then add approximately 15 milligrams of our plastic using forceps. It was a challenge, but we managed. The next task was to add our bacteria to different types of the plastic (plastic type 3, 4,5 and 6). After giving them about 4 solid days, we filtered the excess liquid found in the tubes using the filtering machine. And as always, extreme precaution was taken so that there would be no contamination. Next, we placed the filtered paper in a PIA plate to observe if there will be growth on the plastic. Less than 24 hours later, the result...

P. stutzeri on styrofoam

The results shocked me and excited me a little. Next week, we are planning on doing the same experiment, but using larger tubes. I pinky promise not to stain that one as well. 

Just another background...

Degradation of plastic within the environment is an important biogeochemical process worth pondering upon due to the various effects it has. In our environment, degradation of plastic has proven to be a potential threat due to its ability to be digested by fish, which later are consumed by us. In addition to that, Pseudomonas stutzeri is a microbe which is found in water and soil, and is known to cause sever illnesses to immunocompromised individuals.

Pseudomonas stutzeri is a gram-positive aerobic bacteria which forms a very slimy biofilm. This biofilm nature of its aids it in adhesion to certain types of objects, such as plastics. Moreover, Pseudomonas stutzeri biofilm characteristics is what causes breakdown of plastic over time.

            Regardless of its severe consequences, our society is not aware of the damage it causes directly or indirectly. Thus, we as a research group decided to come up with a strategic plan to find out if a specific plastic can be degraded by a particular Pseudomonas species. That way, with reliable results we will have, we can educate our society as much as possible to hopefully decrease the effects that are caused by our actions.

            Of all the variety of plastic provided to us, we had decided to settle for plastic number 3, 4, 5 and 6. Plastic number 3, also known as PVC, is commonly found in building and houses for water pipes. Plastic number 4, also known as low-density polyethylene (LPDE), is used to make garbage bags, squeeze bottles, etc. Plastic number 5, also known as Polypropylene (PP), is used to make lunch boxes, straws, etc. Finally, plastic number 6, also known as Polystyrene (PS) or extended- Polystyrene (PS-E), which is commonly and widely used to make Styrofoam.

Currently, we I am observing how much degradation could there be on plastic number 3, commonly known as PVC, which will be treated with Pseudomonas stutzeri to observe the rate of change on a weekly basis.

Pseudomonas Stutzeri, like other Pseudomonas spp, causes illness when ingested by means mentioned above. Moreover, it has been shown that most of the diseases caused by Pseudomonas stutzeri are infective endocarditis, vertebral osteomyelitis, and meningitis, which are often observed in immunocompromised individuals. Also, Pseudomonas stutzeri has been found in six patients undergoing hemolysis. They had frequent symptoms of fever, shaking chills, nausea, and vomiting. After careful considerations and methods to figure out the cause, it is now known that the infection was caused by the deionized water that is combined with the liquid concentrate to form the dialysate. Therefore, we can conclude from the latter statement that Pseudomonas stutzeri can be found in water systems found at home or in hospitals; which could compromise our health as well.

            From all the research done thus far, we have found different causes and effects from Pseudomonas as a whole. However, our research is focused solely on identifying the relationship between the plastic type and the specific bacteria that could grow on the plastic. This understanding could help us determine which plastics to replace so that a certain bacteria would not affect us as it grows on the plastic. For example, we could analyze the type of bacteria that could grow on plastics in healthcare facilities so that we can change the types of plastics that are available there.  Moreover, by educating our society about the effects of improper disposal of plastic has on us, we could decrease the amount of illness recorded due to this.

 Finally, after all the research done, I have hypothesized that there will be a significant change in degradation of plastic number 3, also known as PVC, when exposed to Pseudomonas stutzeri.

Fee fi pho fum...I sense there's more to our tap water scum

Everything around us can provide us answers to questions we choose to ponder on. The objects we prefer to rely on to help us during a critical situation could be another source of hurt. Within the week, we have collected water samples from the eyewash found in DB building. This particular eyewash is meant to help us rinse out any dangerously foreign substance that might have gotten in our eyes. It is meant to be clean and safe. However, after our thorough filtration process (using the apparatus shown in the first picture), we have managed to find bacteria within the water used to rinse out our eyes. We used PIA and PF plates, which are used to isolate Pseudomonas bacteria (shown in the second and third picture below)

Tiny is not so tiny

Perception has an impact in so many ways. At times, we can easily say that our five senses have a way of deceiving us. We can not rely on them completely. Now you might ask, "what led her to think in such a way"? Besides being bombarded by such ideas in philosophy class, the microplastics we thought were so micro are, in fact, enormous...depending upon what you are viewing them under. 
Take this fellow, for instance (image below). It is so minute that its weight is almost negligible. 
However, when looked under an electron microscope...

The image is extraordinarily precise, I can not wait till I observe the bacteria growing on these plastics. The process wasn't difficult either. We asked Dr, Abeer to assist us with it, and she quickly proceeded to coat it with gold to minimize scattering as observed in the image below. As a conclusion, it's safe to say that this week was a wonderful experience.

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...