S-STEM Scholar Elijah Diaz Blog

  Introduction      Having successfully carried 3 way Gibson Assembly the prior week, the goal of this week was to further this effort by the use of Q5 Polymerase. Q5 Polymerase was used in hopes to amplify results.  Methods     PCR using Q5 Polymerase was run on both new Gibson PCR product as well as the prior week's Gibson Assembly. In addition to running PCR on these two products, long amp PCR was also run on PRAD 1 Plasmids in an effort to create more sample for eventual implementation in Gibson with the other three fragments. After having conducted PCR, a gel with 15 wells was run. There were a total of nine samples run (four Gibson PCR products, four long amp PCR products, and a 1kb ladder). Results     In the gel pictured below, the well layout is as follows: Well 1- 1kb ladder, Well 2, 3- PCR Gibson Products, Well 4, 5- Original Gibson Assembly Product, Well 6-9- Long Amp PCR. Conclusions     Contrary to what was expected, t...

  Introduction     Having gathered all of the materials needed the prior week, our group was able to continue working on our Gibson Assembly project. Our Gibson Assembly requires three fragments, two of which we had prior to our temporary hold on the project. More of our left fragment was needed in order to carry on with assembly. Methods     On Monday we streaked 3 plates of D. rad, PRAD 1, and PHRAM using freezebacs. From these plates, the bacteria was then streaked onto other plates due to their coming from freezebacs. PCR was then conducted on our three fragments needed for Gibson Assembly. Next a gel was run to determine whether or not our three way Gibson Assembly was successful or not. Were it to be successful, the size of the three fragments combined would be 2,527 base pairs. Results      On Thursday we ran our gel to see if our 3 way Gibson Assembly was successful. An image of the gel is shown below:  Gel Run on 4/25 Despite no band...

      This week was spent planning and prepping for future project work. Having wrapped up conferences, our group focused on our plans moving forward. Our plan is to continue our Gibson project which we were working on prior to conference work but put on hold temporarily. In addition to the Gibson project we also seek to continue working with D. metalli,  specifically with biofilm, throughout the summer. During this week we prepped for Gibson project work by making media. On Monday we made 100ml of TGY broth, 200ml of TGY agar, 200ml of LB broth, and 200ml of LB agar. Using this media, plates were then poured so that we would have all the materials necessary to continue the project the following week.

      This week our group prepared for the poster and presentation for the Arizona Nevada Academy of Science conference. Our group spent this week creating the poster which we were to also present and be judged on. Given the fact that this was my first time ever taking on such a project, it proved to be a great learning experience and left me with anticipation of further poster presentations like this one. Here is our completed poster

  Introduction     With the biochemical tests already conducted on D. Metalli, our focus on the bacteria was then shifted to its ability to form biofilm. Our goal was to bring about an even further understanding of the bacteria as well as provide potential follow up research on its biofilm in the future. Methods     Due to D. Metalli's growth of biofilm being more plentiful in nutrient rich environments, we inoculated the bacteria into 25 ml of TGY within a flask. This flask was then put inside of a non shaking incubator for 24 hours to best aid biofilm growth.  Results          After the 24 hours, there was the successful growth of biofilm, as shown below: In addition, we also gram stained D. Metalli with its biofilm growth, as shown below: Conclusions     The successful growth and observation of D. Metalli's biofilm proved to be very valuable information. We used this information for our conference poster and presentatio...

Introduction      This week we conducted biochemical tests on the bacteria D. Metalli in preparation for our conference presentation. These tests included the oxidase, urease, catalase, starch and SIM tests. These tests were conducted in order to better characterize the species.  Methods      In the beginning of the week we gram stained D. Metalli. Our results showed it to be a Gram positive rod shaped bacteria.  We then streaked our experimental plates, including R2A and TGY plates for catalase and oxidase tests, a Starch TGY plate for Starch hydrolysis tests, and 2 experimental Urease plates and SIM Test tubes for D. Metalli. In addition we also s treaked control plates/tubes with B. Subtilus, S. Epidermis, E. Coli, and C. Fruendii. The controls were incubated at 37℃ and the experimental groups at 30 ℃. The tests were then conducted on Wednesday. For the oxidase test, 2-3 drops of oxidase was put onto the plate. For the catalase test, drops of h...