Friday, May 13, 2016

The Last of the Last (Legionella pneumophila Blog Week 12)

Wow oh wow this semester felt like a whirlwind! With classes, the S-STEM program and work it feels like the semester barely started yesterday yet here we are at finals week.  I just want to express my gratitude for all of the opportunities that this program has afforded me. Not only did I learn various lab techniques but I also had a taste of what research was actually like in a real life lab.  When we went to the ASU sequencing lab it really hit me that we were actually conducting the same research that you often hear of in the news.  Beyond the academic gains I have earned I also had the pleasure to meet some amazing people such as, my research team, the mentors and the people that are part of S-STEM. Thank you everyone and I hope that all of your academic and career aspirations come to fruition.

Estrella Mountain Community College Presentations (Legionella pneumophila Blog Week 11)

Hello everyone!  This week was presentations week at the Estrella Mountain Community College conference.  The conference was largely attended by people in the soft sciences so it was a little funny to see how technical all of our S-STEM posters where compared to what everyone else was presenting.  Despite the fact that we had really technical content we had a couple of our Phoenix College students win 2nd and 3rd place for poster presentations, congratulations to Beth and Oliver! Daisy and I also presented and I think it was a great experience to be able to talk to people about all of the work that we have been doing all semester long.  Here is a picture of Daisy, our poster and me!

Thursday, April 21, 2016

Lab work on top of lab work (Legionella pneumophila Blog Week 10)

This week feels like we've been in the lab non-stop.  Tuesday our team finished filtrating 3 samples that we had not been able to filter last week because we ran out of autoclaved vacuum filtration glassware. Once we finished filtrating our samples we began DNA extraction from the filtered samples.  The only problem we had was that we were not using the usual DNA extraction kit that we had been using.  Instead we used a kit by Omega bio-tek. This kit used a pretty extensive protocol (roughly 30 steps) and it took our group a while to work through the extraction.  Wednesday we worked on our poster fine tuning what we think was wrong with it. I will post it here and would love to hear any feedback you guys may have on the poster.  Today also ran four Agarose Gels with the PCR product from our last PCR procedure in order to see if ASU's DNA Lab will be able to sequence these bands once we extract them.  We have our fingers crossed since we would really love to know through genomic sequencing that we found L. pneumophila in these samples.

Oh the Stress (Legionella pneumophila Blog Week 9)

Oh the stress, this week was pretty rough.  We had to get a great deal of work done in the lab plus we had to re-run gels and re-do some PCR on the samples we gathered because the sequencing lab at ASU was not able to sequence the samples that we extracted from the Agarose gels.  On Friday we also re-collected 8 samples in order to analyze them and see if they would test the same nearly a year later.

Despite the fact that we have had these setbacks I think that it has been a great learning week.  We got a chance to know what it is like to try to find results with an impending deadline (the Estrella Conference) looming over our heads.

Thursday, April 7, 2016

Almost Through An Entire Cycle (Legionella pneumophila Blog Week 8)

I view our work in the detection of Legionella p. as a cycle.  First we must collect the samples, then we have to filter out the DNA, next is the extraction of the genetic material.  Once the genetic material is out, we amplify the DNA we want through PCR with primers specific to a gene in Legionella p. Once amplified we perform electrophoresis with a positive control and a molecular weight marker to screen for our suspect.  After all of this has been done we finally cut out the genetic material out of the gel, extract it and send it off for genomic sequencing at ASU. Then we start with gathering samples all over again.  This week we are supposed to send 4 of our samples off to ASU to get tested to see if we can absolutely identify the bacteria.  I can not wait to drop off our samples and see what we get.  Getting those results back would finally complete a cycle of research!

I'll post a picture of our group at ASU tomorrow when we go!
So here is the picture of the lab, I didn't want to take pictures of people so I tried to avoid them and this is all I could get.  

Thursday, March 31, 2016

Even more PCR and Electrophoresis (Legionella pneumophila Blog Week 7)

Hello everyone, this is week 7 of our journey through the S-STEM internship!  This week for our Legionella p. project, we had to run PCR on 10 different samples.  We ran the PCR on Tuesday and today we ran the amplified DNA in the Agarose Gel. Unfortunately, I goofed on 4 samples that I loaded (I loaded the gel wells with 7 microliters [μL] of material instead of 12μL).  Our mentor, Robin Cotter, advised us that it would be wise to run the PCR again on these samples and do the electrophoresis again in order to verify our results.  The reasoning is that; if the Legionella p. bacteria are present but there was not enough genetic material in the 7μL then it may not be visible when looking at the gels.  As for the remaining 6 samples that did run and ran well, we will be cutting out the clearly visible bands and performing a DNA extraction process from the gels so that we can send the samples to ASU for genomic testing. Once we know the sequence of the nucleotides, we can compare that to the known sequence of Legionella p. and know for sure that the bacteria were present in the samples that we collected.

That is all for now! Above is a picture of me on my birthday with Daisy one of my group mates.

P.S. Today is my birthday!

Thursday, March 24, 2016

1st Agarose Gel Pour/Run (Legionella pneumophila Blog Week 6)

Spring Break, short are thee
In your midst I wish
to be.  Once more free
from the petri dish

Yet here I am at,
close to the midnight.
Had I not laid flat
I'd be far from plight.

Hello everyone, that was my sadness from the end of spring break coming through.  I'll jump right into it since there is no better way to do work.  This week in the Lab our team ran PCR on nine samples some of which had been collected nearly 6 months ago.  I'm sure many of you are familiar with this process but after the PCR had been run. We poured 3 gels and ran our samples through 2 of them.  This was the first time I had ever poured the Agarose Gel and it being my first time it did not go well at all.  Luckily Daisy poured the other two and those were the ones we were actually able to use.  Below is an image of the water samples collected.  According to the banding size it appears as though we actually got a positive for the Legionella bacteria, on the first go around!  We didn't have enough time to scan the second gel but once I get the picture I will upload it onto here.  Coming back hasn't been so bad after all!