Week 9

Welcome back and I hope everyone is doing well as well as we enter these final weeks of our Senior Projects!

This week was my final week at the lab because I do not have enough remaining time to run more trials. I am so happy that my experiment was finally able to produce results. Though the data that I gathered was minimal and did not answer my hypothesis, I was still able to produce something that shows my project had some progress and at this point with all of the setbacks, I will take anything that I can get. Usually I would be mad or disappointed with not accomplishing everything that I told myself that I would, but I’m just relieved and happy to have something. One of the lab assistants that I was working with told me that I accomplished more than what most bio undergrads there have done which made me laugh a bit (and then I realized that they apparently couldn’t follow instructions which means those lab assistant jobs are mine).

My data at the lab is small and probably won’t produce any waves in the scientific community but I can use the data and experience along with my connection with Mr. Tahmahkera to try more ambitious research projects at ASU in the future. That and I can learn fun new things at the lab while working with the people there. For example, I found out that you can make glow-in-the-dark plants with the materials at ASU’s labs from Brandon which is something that I look forward to doing.

Now that I was finally able to get data from my experiment, I remembered that I had other parts of my project that I needed to do other than the PowerPoint presentation. I have been so absorbed with trying to produce results at the lab that I forgot that I had to also work on a research paper. I decided to start working on the paper this week but I remembered that I rushed the research for this second project and forgot to save the research papers that I used. So, I had a fun time doing a scavenger hunt through my internet history looking for the research papers that I used to come up with my project and yes it was as painful.

My time at ASU’s labs have been fun and frustrating but I am grateful for the experience.

- CJ Pimentel

Week 8

Hello, I hope everyone is doing well and welcome back!

This week has been an interesting one as I have been hit with drawbacks in my project that I did not see coming. Last week, I got a minor cold (could be from the bacteria I’m working with or maybe flu season is here already) and that cold spread to the rest of my family this week. I was unable to go to Arizona State University and continue doing my research due to the fact that my mom was sick and that I needed her to be with me at the lab (one of the drawbacks of being under 18 while working in research). I’m not sure whether to laugh or be mad at the irony of being set back by bacteria while working with bacteria but I now better understand the reason why universities provide so much health services after experiencing just how much being sick can set one back on their work.

My inability to go to the labs gave me the opportunity to think about my senior project presentation. I will not be able to talk in depth about the data and results for my project because of the setbacks and the fact that my project required much more time than what I was given to produce significant results. I decided that I would focus more on the experience and how research really is as a career or for graduate students. I hope that I will be able to produce even the smallest results when I return to the labs to run my final trial next week. Mrs. Nath brought up an important point in my meeting this week which was that there is the possibility that the general public, who does not understand the difficulties of research, may view my lack of results as a product of laziness or incompetence. I hope that I will be able to produce results so I can at least show that some progress was made in my time at ASU’s labs.

This week was uneventful compared to my previous weeks but it gave me the breathing room to think about my project’s presentation and what I should do in the the very real case that I did not produce any results in my remaining time at the ASU labs.

I will see you all next week where I will hopefully have at least the smallest bit of data.

- CJ Pimentel

Week 7

Hello and welcome back everyone!

In one of my first posts I stated how I looked forward to genetically modifying bacteria because one can not control the outcomes and the possibility of finding something new. I also said how I would probably regret regret saying that in the future and it is starting to look like I was right.

My current research is looking into how efficiently bacteria can take free floating genetic material from the environment and integrate them into their own genetic makeup to see if the rise of genetically modified organisms from companies pose an imminent danger as sources for genetic material which could lead to uncontrolled pathogenic bacterial evolution.

I am comparing the efficiency of bacteria who are induced into transformation with calcium chloride and comparing it to bacteria who are left to take in plasmids by themselves. My experiment is basically a modified version of the pGLO gene experiment (a simple experiment you can Google).

As you all know, every experiment needs a control group in order to see if the results of the experiment are actually significant. This week, my project’s control groups failed because the bacteria did not grow in the way that I needed them to and so the experimental group’s results couldn’t be verified. I had to completely start over and remake my plates because it seems that the ampicillin in the plates denatured (having to start over repeatedly seems to be a common theme).

Thanks to my experience in research, I learned a valuable yet frustrating truth. One person can run thousands of trials before their experiment actually produces presentable results because success is low especially when it comes into delving into an area that no one else has worked on (and when working with something fickle like life).

The silver lining in all of this is that the constant restarts have given me the chance to become familiar with the lab equipment. I can now operate most of the equipment and perform all of the mandatory lab practices without needing constant reminders of what to do which is going to save me time if I have to redo something in the future (which i probably will).

I hope that my project will be able to produce presentable results by the end of my Senior Project but if it doesn’t then I will at least have the skills and experience that I picked up working at the labs. See you all next week.

- CJ Pimentel

Week 6

Welcome back everyone!

This week has been very exciting for me because I got to spend a lot of time working in the lab with my on-site advisor and his lab assistants.

In one of my previous posts, I stated my anxiety over working with undergraduate seniors and being intimidated by them; however, I found out that working with them can actually be fun and helps alleviate the boring nature of research (turns out research is eighty percent cleaning and preparation and not nearly as exciting as what you see in movies). One of the lab assistants, Miguel, talked to me about college life and was the reason why I decided to apply to Arizona State University out of nowhere. He also gave me a tour of the dorms and campus after I was done for the day at the lab. Brandon, another lab assistant I worked with, talked to me about the fun side of student life at ASU and I now know which clubs to join for parties. My project at the lab is meant to be solo and the lab assistants are there to supervise my project. I learned that working solo on a research project can become boring when most of the project requires you to wait before you can move on (not like Ms. Vo’s labs where everything was fast paced and on a time crunch). If I’m going to pursue another research project in the future, I would probably do a group research rather than doing it solo.

My previous experiences with Ms. Vo’s labs did a good job at preparing me for working at ASU’s labs, but there were things that I had to learn. One, I had to learn how to work with an open flame to sterilize my materials which was fun until I accidentally tipped over the bunsen burner (which isn’t as solid as it looks) and suddenly had flames bursting at my chest. I also learned how to operate an autoclave. An autoclave is used to sterilize materials for use and biohazard waste before it is thrown out. It’s basically a giant steamer that looks like a massive oven that is inserted into the wall. I had to put on a lot of protective wear while working with the autoclave. The last skill I learned was how to use a fume hood properly. At BASIS, we used fume hoods to store waste from experiments, but they are supposed to be aseptic (free of contamination from microorganisms) environments for experiments.

Overall, working at the lab has been a fun experience so far and I will see you all next week.

- CJ Pimentel

Week 5

Hello and welcome back! I hope everyone enjoyed their Spring Break.

I spent my break coming up with a new Senior Project experiment as my last one had to be completely scrapped. It was a stressful and enlightening experience to the reality of research because I learned that a single mistake can lead to an entire project’s failure regardless of the amount to work or research that went into it beforehand. I also realized that being overly ambitious can be a problem but if you’re going to dream, you might as well dream big (just be prepared for failure).

As I was trying to come up with a new experiment, I wanted to try and address another significant problem but not have to project be too ambitious like the last one. I decided to go off of one of the concerns raised over my last project: the danger of creating new harmful bacteria in the environment. Companies today are becoming more and more reliant on biotechnology as seen with all of our genetically modified crops and animals. These are easily accessible sources for genetic information for bacteria who are able to evolve by taking in genetic material floating in the environment. We have seen infectious bacteria in the past evolve by taking in genetic material from various other species as seen with the swine flu virus evolving through the genes of pigs and birds. Today, these sources for bacteria have been improved with genes that cause them to grow and breed faster and these genes could be copied by infectious bacteria to create a deadlier new species.

My new project will look into how efficiently bacteria can take in genetic material from the environment. Unfortunately, I will not be able to look into how bacteria can copy genes from a live host. Instead, I will be looking into how efficiently can bacteria take free floating genetic material in the environment to replicate the scenario of an infectious bacteria taking genes from a dead host. For this new experiment, I will be testing common bacteria like E. coli and C. freundii because these bacteria are the ones that are most likely to evolve from the DNA of genetically modified organisms due to the fact that they are everywhere. Also, these bacteria are opportunistic and can still be infectious. For the genetic material, I will be using pGLO (the gene that makes jellyfish glow) because I can easily tell if the bacteria successfully took the gene.

Hopefully this new project will turn out well and I will see you all next week.

- CJ Pimentel

Week 4

Welcome back to the blog!

This week has been a very interesting one for me. Some good news is that my on-site advisor recovered from his pneumonia this week so I was finally able to meet him in person at ASU and hear his thoughts on my experiment. Unfortunately, more problems were raised during my meeting and my experiment had to be completely scrapped.

In my previous two posts, I talked about how seriously the government controls the experimentation of bacteria and the fact that I was not able to get access to the plasmids that I needed for my experiment (the most important and irreplaceable part). These problems came back to haunt me this week when my advisor said that he would not be able to purchase the plasmids because the government requires him to send an approved list of materials that he will be using at his lab a year in advance and the campus will not purchase any new materials that he is not using for his classes. If I were to use the plasmids in my experiment, I would have to do a lot of paperwork beforehand and gain approval from both the government and the university and I would be under constant surveillance from government officials during my experiment (my on-site advisor stated that he would be uncomfortable with having cops roaming his labs constantly). I would also have to familiarize myself with the long list of laws regarding experimentation on bacteria because if I were to unknowingly break any of those laws (i.e. if there was a breach in containment and some of the modified bacteria got out of the lab) then I would be in trouble with homeland security and be labeled as a biological terrorist.  Due to all these complications, I had to completely abandon my experiment and try to come up with a new one. The good news is that I will be able to reuse my original experiment in college.

For my new experiment, my on-site advisor gave me a list to bacteria and the pGLO plasmid to work with. The pGLO plasmid is the plasmid that makes bacteria glow under UV light (we did the same experiment in Mr. Gilbride’s biology class). My task is to make an original idea by twisting some aspect of this basic experiment. The hard part is that this experiment has been reinvented so many ways because of its simplicity and so coming up with an original idea will be a challenge. Hopefully I will have a finished plan for my new experiment soon.

Next week I will be taking a break so there will be no new posts, but I will be posting the week after about how my experiment is going. See you all next time and hope you are all having a wonderful time.

- CJ Pimentel

Week 3

Hi and welcome back everyone!

In my last post, I stated how my on-site Senior Project advisor was sick and this week I found out that his flu turned into turned into bacterial pneumonia causing him to be sent to the hospital and preventing him from being present at the lab. Fortunately, I was able to go to the lab this week and finish my lab orientation with one of his lab assistants. I am excited because I am now able to begin my experiment at the lab now that my training is done; however, I am also a bit nervous and slightly intimidated because I’ll be doing my project under the supervision of lab assistants (Seniors at ASU) when my on-site advisor is not there. Honestly, I really don’t know how I feel about doing my project alongside other ASU students while they are doing their own thing, but I guess I will just have to wait and see how things go.

Unfortunately, I found that concerns will be raised with every step of progress that I make. I planned to have started my experiment week 1 but I experienced some unforeseen delays (the irony of being delayed by bacteria while I’m working on them). The delays were a serious concern for my project because of the amount of time my project needs and so I decided to talk with my BASIS advisor, Mrs. Nath, to see what I could do about the problem. We decided that I would need to cut off the last two thirds of my project (the parts where I test out how efficient my new bacteria is at degrading plastic) and just focus on the first part (the part where I try to create the bacteria). I can’t say that I didn’t see this coming because my project was very ambitious and I anticipated that I would have to cut out a lot of parts because of the time constraints.

Access to materials is another concern that was raised this week. I found out that the lab I am working at does not have the plasmids (the DNA I will use) or competent cells (the bacteria I will insert the DNA into) that I need for my experiment. I was able to find where I could buy the competent cells but I was unable to find where I could get the plasmids that I needed. I might have to completely change my experiment to another one that is currently available at ASU if I am unable to find the plasmids that I need soon. Hopefully, these problems will be solved by the end of next week.

I will see you guys next week and thanks for stopping by!

- CJ Pimentel

Week 2

Welcome back readers!

The second week of my project has mostly been a continuation of the first week. I have continued reviewing literature on genetic transformation of bacteria and on successfully growing bacteria cultures.

In my last post, I said that I would be stepping into the microbiology labs at Arizona State University to begin my project. Unfortunately, my on-site senior project advisor was out with the flu for the entire week and I was unable to come in for lab orientation. On the bright side, I was able to visit Arizona State University’s Tempe campus and take a small tour. I was able to locate where I would be doing my project so now I don’t have to worry about being lost on campus looking for where I will be doing my internship.

In addition to continuing last week’s literature review, I also began looking into the legality of using genetically modified bacteria for industrial purposes and for using those bacteria to clean up the environment. I found that using genetically modified organisms for industrial and economic purposes is relatively easy as long as the organism is contained and does not pose a threat to the surrounding environment. If my experiment is successful, I will be able to integrate it into the recycling industry without legal barriers.

However, legal issues began to crop up when I started looking into genetically modified organisms and their potential use for environmental mitigation. Genetically modified organisms are by no circumstances allowed to be released into the environment because they have the ability to disrupt the balance and potentially ruin the surrounding flora and fauna. Genetically modified microorganisms are given the strictest rules which is understandable. Bacteria have the ability to pass on their genetic information to surrounding bacteria and this could lead to an uncontrolled emergence of new bacteria. Some of these new bacteria could be harmful to humans and the environment. Another issue with releasing a genetically modified organism into the environment is the fact that these organisms tend to die off quickly in uncontrolled environments.

If I am going to use my bacteria to clean up the plastic in the environment, I would have to either remove my bacteria’s ability to transfer genetic information and give it the ability to survive in the wild or develop a machine capable of extracting plastic efficiently from all types of environments without harming the surrounding area. Both are extremely difficult because one requires me to combat the randomness of nature and to counteract one of nature’s mechanisms for evolution while the other would require me to have an in-depth knowledge of engineering which I don’t have. Luckily, I won’t have to face these problems until my project turns out to be a success.

Thanks for stopping by and I will see you all next week.

- CJ Pimentel

Week 1

Hello readers!

This first week of my research project has been dedicated to reviewing the research papers that I have used when I constructed my experiment. I have been focusing on Shosuke Yoshida’s team’s papers on I. sakaiensis’ discovery and other publications commenting on their breakthrough. I hope that my research has fully prepared me for my experiment before I step into the lab next week.

I am glad that I spent the time to review my research and experimental design before I got into the lab because I was able to catch a concerning detail in the first part of my experiment.

As I mentioned in my earlier post, I will be genetically modifying bacteria for my experiment. In order to get V. natriegens to accept new genetic material, I need to use a thermal shock on the membrane to open up the bacteria. I realized that I based the temperatures of the thermal shock on the ones used for E. coli because I could not find the temperature range for V. natriegens. I believe that the thermal shock temperatures for the two bacteria are relatively the same but if anyone knows what the ideal thermal shock temperatures for V. natriegens are, then please let me know in the comment section below.

Reviewing my experiment also allowed me to make a few adjustments. Originally, I was planning to modify V. natriegens by inserting DNA from I. sakaiensis. Now I am planning to also modify I. sakaiensis by inserting DNA from V. natriegens. I hope that increasing the pool of hosts and DNA donors will increase the probability of creating my targeted bacteria by the end.

Playing with DNA and life in general tends to lead to unpredictable results so this will probably be the first in a series of revisions to my experiment. I love the unpredictable nature of my experiment (Watch me retract this statement later on). Who knows? Maybe I will end up discovering something bigger while I play with DNA in the lab.

Next week, I will be going to Arizona State University’s microbiology labs at their Tempe campus. I will be doing lab orientation and safety training before I begin the first part of my experiment.

I look forward to conducting my experiment and keeping all of you up to date on my research project. Best wishes and I will see you all next week.

- CJ Pimentel

Introductory Post

Pollution is undeniably one of the most prevalent problems facing modern society and plastic makes up a considerable portion of said pollution. Plastic's versatility, light weight, flexibility, moisture resistance, strength, and relatively low cost is what drew the world to develop a massive appetite for plastic goods; however, these aspects which we praised are being turned against us and our environment as tons of  plastic debris is being thrown into our lands and oceans. These slowly degrading piles plastic are destroying ecosystems, killing marine life and in turn decreasing our food supplies from the ocean, and poisoning the meats that we consume as animals ingest the plastic floating in our environment.

Recycling plastic is currently inefficient and doesn't reduce the amount of new plastic that our modern society needs to produce. For example, plastic used for making a chair is recycled and the plastic is weakened during the process which means that the plastic cannot be used to make another chair because it is too weak and must be used to create something weaker such as a plastic bottle. This scenario shows that we would have to constantly input resources into the making of plastic because recycling is not effective enough. In order to reduce the amount of plastic in our environment, recycling plastic must come close to one hundred percent efficiency so that companies will be drawn to reclaim plastic rather than produce more because recycling will become the more economically viable option.

My research project seeks to create a true circular flow in the recycling of plastic and remove the need for new materials to create plastic. I will be working to create a genetically modified species of Vibrio Natriegens capable of degrading plastic at a lab in Arizona State University. I will be focusing of the degradation of polyethylene terephthalate (PET) because it is one of the most commonly used plastics. I will be the taking genes from Ideonella Sakaiensis and inserting them into V. Natriegens. I. Sakaiensis was found to be too slow at degrading PET to be put into practical use. I hope that by taking V. Natriegen's PET degrading abilities and combining it with V. Natriegens' fast growth rate, I will be able to create a bacteria capable of breaking down PET efficiently.  These basic components that PET is broken down into can be reused to create new plastic with strong bonds and this process can be continued without the risk of the bonds weakening.