Blog Post Week 10 12/02/16

This week the group needed to pour and run gels for the following samples:

Monday 205 lab (10 samples:  5 biofilm & 5 water)

Tuesday 205 lab (Cori 12 samples)

Wednesday day 205 lab (10 samples: 5 biofilm & 5 water)

Wednesday night 205 lab (12 samples:  6 biofilm & 6 water)

We also had to make gel maps in order to determine the number of gels we needed which we needed to pour gels once again on Thursday before our meeting. We made a total of 8 gels because we were screening multiple samples. We started to make the gels the day before to make it a little easier for the team and use our time more efficiently to progress on our data and project.

Sample of our gel using the Gel doc EZ imager that
shows us the bands of DNA and base pairs to see
which ones turned positive.

UV light through gels to see DNA

Blog Post Week 9 11/25/16

This week is Thanksgiving week so we did not meet on our regular scheduled day but did meet and come in during the weekday. The microbiology labs have done DNA extraction for their samples and we followed by nano dropping. The microbiology classes also ran a PCR and we were in charge of nano dropping that as well and screening them through gel electrophoresis.

This week the group set up PCR for the following samples:

Monday 205 lab (10 samples:  5 biofilm & 5 water)

Wednesday day 205 lab (10 samples: 5 biofilm & 5 water)

Wednesday night 205 lab (12 samples:  6 biofilm & 6 water)

Samples from the classes with their zones, sites and sources

Blog Post Week 8 11/18/16

This week we Nano dropped DNA samples from the Mon, Tues & Wed 205 labs before Friday. We also screened the gel results from the Mon, Tues & Wed 205 labs. The next step was determining which samples to run for DNA sequencing. Lastly, we began organizing data from Mon, Tues & Wed 205 labs into a table and created a composite of plate images from samples testing positive and the data should be organized by Zone, Site and Source. In addition, the microbiology classes have started collecting water and bio-films samples. Our team is now in charge of using the class samples and taking the data and compile it with ours. This week we took pictures of the plates and began to organize a file that will include the classes data. 

Some samples from the MicroLab courses.

Blog Post Week 7 11/11/16

Due to Veterans day, our research team did not meet, however, some of us throughout the week ran PCR once again and analyzed data to see if what we have has matched our previous results.

Blog Post Week 6 11/04/16

This week as a grade we were assigned for the independent research projects. We got to choose from three being: 1) Continuing collecting water samples, and completing steps as previously performed 2) Going to ASU West and using their equipment to find specific proteins 3) developing protocols for removing micro-plastics in the water using Pseudomonas. For the reason being that I am doing a project and poster for my honors class, and having a second person, I was required to stay with the 1^st independent research project. It is also crazy to think that from here there is only 1 month left to collect and analyze water and bio-film samples for the project. We also analyzed the PIA and PF filtration plates from 4 lab sections and inoculated TSB broths for all samples testing positive.

Pseudomonas Isolation Agar (PIA)

Pseudomonas Florescence (PF)

Blog Post Week 5 10/28/16

This week we poured and ran the gels for our positive controls, ran PCR on our positive controls and screened the positive controls to choose the best ones to create more positive controls to test the Pseudomonas (PA) and (PS) control samples. The PA samples are those of Pseudomonas aeruginosa and the PS samples of Pseudomonas species. We also learned how to do DNA extraction from the gels by cutting the bands out which is something new that I hadn’t done before nor did I perform this on my last project working with the protocols for E. coli. So definitely it was fun learning a new procedure that can be done to keep on confirming our DNA and positive controls.

Our tubes needed to perform PCR containing the primers.

Bog Post Week 4 10/21/16

This week for the Pseudomonas project we ran PCR on Pseudomonas aeruginosa DNA to create more positive controls for ourselves and the microbiology labs and as well performed PCR on the Pseudomonas control DNA using PA primers. So what is very interesting as well for this project and term is that three courses this semester are getting together to test the water and biofilm samples as well, which means more collection for us and more DNA data that we can use for consistency. This is a very first-time experience because the classes will have an opportunity do to real life undergraduate research and have that experience and a little taste to what researches do on a day to day basis. We also assisted with the “Creating Undergraduate Research Experiences Workshop,” which was for faculty only, but because we were part of the internship team, we got to help out, and therefore be a part of this great starting opportunity for undergraduate research at the community college level. 

The thermocycler  that allows for PCR to be ran by three important steps.

Blog Post Week 3 10/14/16

Continuing from last week the DNA extraction, was performed by following a protocol that was made during the summer by another intern. One way that we can quantitatively see and confirm how much DNA was actually in the tubes and shown in the gels is by Nano dropping. This shows a couple of numbers that let us know exactly what is DNA and what is just junk. Following the Nano drop, we proceeded to do PCR. PCR is an amplifier for our DNA using primers that are specific to the pseudomonas species we are looking for. However, there were troubles with the PCR because some of the samples didn’t have the full 25 microliters that were needed for the PCR so we had to rerun PCR on all of the samples. The goal was for the ones that turn out positive from the DNA gel extraction, then we are to send the positives to perform DNA sequencing at Arizona State University. 

Gels running for electrophoresis

Blog Post Week 2 10/07/16

This week for the Pseudomonas project we prepared and learned how to pour gels using the powdered agarose to create the gels to perform gel electrophoresis on our samples. (Since it is a team research project and Daisy and I are in this team and in STEM, feel free to look at both to learn more of what we do.) We have done water and bio-film collection from different sites and zones from our map. We have moved on to do filtration, using a filtration apparatus to trap any bacteria onto a filter. That filter was then transferred onto a plate to allow for us to culture the bacteria. The growth was then transferred into broth to allow to proceed into DNA extraction.