Semester 4-Week 11- On Hold

Hello! Welcome back. Although last week I did promise to run some new experiments and continue primer testing, this week, like so many others do as the semester end approaches, I suddenly realized that we have three weeks of school left before finals. This means I have some catching up to do on course work, which I have spent all week doing. Additional experiments are therefore on hold, probably for the remainder of the semester.

The reason for the crunch is that I am taking a most excellent philosophy course on Bioethics, which requires that I write four essays worth 80% of my overall grade. Due to this being a late start class, the course schedule is compressed, and due dates for the papers are coming sometimes only a few days apart. So I have been knee-deep in position papers on the ethics of passive vs. active euthanasia, patient informed consent requirements, and animal research. It's a bit heady, and I am enjoying it.

There was one exciting development this week, and I must give my public thanks to S-STEM Director Amanda Chapman for making it happen. She has been in continual meetings with the ASU West faculty facilitating the transfer of S-STEM scholars into their NCUIRE program, which allows non-university undergrads the opportunity to either do authentic S-STEM experiences at ASU or begin internships at ASU as the student prepares to transfer to university. Last week, a group of PC faculty and S-STEM students toured the ASU West research labs and received an introduction to the program from Dr. Todd Sandrin, Associate Dean. It was an amazing experience.

As a result of Prof. Chapman's efforts, I met with Dr. Becky Ball, assistant professor of Sustainability Studies at the ASU West campus. Dr. Ball is a biogeochemist who studies soil conditions in multiple ecosystems (I have included a link here to her bio page). Long story short, I was offered and have accepted an internship with Dr. Ball, (contingent upon grant approval-fingers crossed!). Very exciting stuff!

The internship is not part of the NCUIRE program, however it will still provide me with the hands-on training and mentoring that I will need to continue my education and career.

Thank you, Amanda Chapman. For S-STEM, for the support you have given me over the course of this program, and for connecting me with the next stage of my development. I am in your debt.

Until next week, here is something that I hope you all enjoy:

Semester 4-Week 10- Primers and ASU West

Hello! Welcome back.

I spent lab time this week running gels on my primers to see if my initial dilutions had degraded and therefore affected my PCR results. The gels showed clear presence of nucleotide primers in my initial dilution of dry primers with TE buffer; however, results were negative for the new dilution I had made with sterile molecular-grade biology water. This result is a good indication of where I need to proceed from here, so next week will see me making new primer dilutions and doing another PCR.

The remainder of my time this week was spent attending a presentation at ASU West. We were introduced to the NCUIRE program, which allows undergrads to gain lab internship experience while receiving one-on-one mentoring (and a stipend, I might add). We were also graciously treated to a tour of the research labs, and we had the opportunity to meet with faculty researchers and question them about the parameters of their research projects.

It was an incredibly exciting experience for this uber-nerd. I am looking forward to pursuing an opportunity with the program, as this is my last semester with PC S-STEM.

Until next week, then. Happy Science! And please enjoy this brief article about mitochondrial DNA analysis that was conducted using a tissue extract from a ritually-sacrificed Incan child, circa 14,300 years ago. Click the link here.

Photo credit: Gόmez-Carballa et al./ Scientific Reports 2015. Incan child mummy.

Semester 4-Week 9-A Step Back

Hello! Thanks for joining me again.

This week, I needed to collect data on PCR amplification of the gram-negative species used for my study. Amplicons were detected post-PCR in multiple previous experiments; however, over the summer an anomaly arose after a PCR when two of the targeted species failed to amplify. This anomaly caused me concern, so I decided to re-test to see if the negative result could be repeated.

The original DNA samples I used for that PCR have degraded, so I had to perform new extractions. This is not optimal, of course. I would have preferred to re-test all of the original components, as it would be the only certain way to control the experiment, but too much time had passed since the original extraction. Additionally, I did not have enough of the original primer dilution to re-test all nine species.

From inception, the re-test was not a repeat of the original conditions that resulted in the anomaly. So while with new ingredients I could attempt to narrow down the reason for the amplification failure, there was too much variability from the summer procedure to be certain as to the cause.

This was borne out by the new PCR I ran. For the first time testing the set of PCAT-4 primers I designed for this study, amplification was unsuccessful on five of the nine tested species. I am stymied as to the reason why; there are simply too many variable changes to immediately ascertain a cause. I will have to repeat the experiment, changing one variable at a time, until I isolate the reason for the results.

That was my week. I have not had negative results for some time, and I was a little surprised (possibly even vexed) by the results. But as a wise wag (Josh James) once told me, "In science, there are no wrong answers, only new directions to explore." So I will simply explore those new directions and go where the science takes me until I find the answers I am looking for.

Cheers! See you in the lab.

PS: I just ran across a study that purports that humans emit a personalized microbial cloud that can be used to identify the unique individual. Researchers measured microbial emissions from a series of individuals and then used 16s gene sequencing to identify bacterial contributions from those subjects. It's worth a read, so I have included a link here to the published study. Enjoy!

PPS: One of the species I am targeting for amplification, Serratia marcescens: