DO NOT READ!

I sometimes wonder if certain hormones increase in levels during night time. I have come across an article which explains oxytocin levels rising during sleep, but I still haven't found the article which explains why I'm feeling emotional right now. (I shall update you all when I do :D )
As an INTJ, most of you know this by now, I like planning everything ahead. So when I joined S-STEM during my last semester, all I had planned was being focused on learning as much as I can before transferring, completely neglecting the fact that other scholars would be there too.
But things don't always turn out as planned, sometimes they turn out for the better. (sorry I sound like a fortune cookie). 
Long story short, I enjoyed every minute with you guys! I have never felt this accepted in a group for me to feel as comfortable as I've felt with you guys. Sammie, I've enjoyed every one of the chess games I have lost to you; gave us time to bond and I am so grateful I met another INTJ who understands how I function. It's always been easy to talk to you. Jazzie, I still dream about that pecan brownie... JK. In all seriousness, you're one of the strongest young women I've ever met. We didn't talk much, but when we did, we talked about pressing matters which convinced me of your strength. I am sincerely proud of you, Jazzie. Brenda, you being super focused and goal-oriented, I never got the chance to really talk to you...until that day you helped with the video making. Thank you so much for your assistance that day. And thank you for being patient with my nervously stuttering self. Brian, it's always been a pleasure talking to you about all those physics matters and whatnot. I also thank you for listening to me as I blab about the brain :D . And Maricruz, I don't think I would have talked to you as much had it not been for that trip to the biosphere, and am I grateful! I enjoyed every minute of our conversation, and I wish I had more time to have more of those conversations with you. 
A friend of mine used to say, "regret is for the weak." I am not regretting, but if I had the chance to do it all over again starting from August, I would put more time into getting to know each one of you. The lab was a safe haven for me, and you guys had a part to play; starting from opening the door as I bang on it, to being nagged by me to either be the president, vice president or the photographer of a certain robotics club (you know who you are :D )
I'm going to miss you guys SO much, and what better way to say it than on a blog? Thank you all for making my last semester here in PC memorable. 
The first thing I wrote on my blogs, the about me section, ended in a quote. So it's only fair I adjourn my blogging using the same quote...
"Nam et ipsa scientia potestas est!"

Mirror Mirror on the wall, who's the blackest of them all?

.....cumin seeds are.
For the last two weeks, I have been keeping myself occupied with a side project I had assigned myself. 
Black cumin seeds are known in my religion, Islam, as the seeds which can cure anything besides death. As a child, being told such things with the addition to "because God said so" or "because It's in the bible/Quran" meant you should believe it by default. However, I now have the means to try if it has an effect. Granted I don't have access to a virus or a cancer cell, but I have something that could be as exciting; I have cultures of bacteria! Okay, maybe not that exciting. But it is something to see how effective the seed is. I was going to go through the process of boiling the seed in water, but I found some cold compressed oil made of 100% black cumin seeds making the experiment easier. 
I picked three kinds of bacteria to work with from toughest to treat to simplest. I decided to work with Bacillus subtilis (toughest), S. aureus (intermediate), and E. coli (simplest). However, my sample bacteria were not growing so I decided to work with an already cultured bacteria I found from the water filter at home. 
After streaking on a Kerby Bauer plate, then placing sterile disks in the oil, I placed the damp disk on the plate. I then parafilmed the plate and left it to incubate overnight. The next day, the results were staggering! The zone of inhibition, which is the zone where there was no growth of bacteria, showing the effectiveness of the oil, was enormous!

The three bacteria were treated with the oil as well but had relatively smaller zones of inhibition. Nonetheless, we should acknowledge that this oil had an effect on an endospore-forming bacteria, Bacillus subtilis. The chances of it working on other forms of bacteria are high. Pictures of Kirby Bauer plates of the three bacteria shall be uploaded next week.

Moreover, I'm not the only one who's interested in black cumin seed and its benefits. Apparently, research has shown that black cumin seed and its derivatives have antibacterial, antiviral, anti-fungal and anti-cancer properties. 
so, maybe, the blackest of them all could have saved Cinderella instead of the prince? 

Additional information for the curious:
-https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3252704/
-https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3642442/
-https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583426/
-https://www.omicsonline.org/open-access/study-of-antimicrobial-activity-of-black-cumin-seeds-nigella-sativa-lagainst-salmonella-typhi-in-vitro-.php?aid=73188

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.