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