Tuesday, May 24, 2016

ASU internship-2016

Hello! Welcome back to my blog.

Since this blog went on hiatus least December, I completed my time at PC and was offered (and accepted!) a research internship working for Dr. Becky Ball @the School of Mathematics and Natural Sciences, ASU West. Dr. Ball is a sustainability scientist and biogeochemist whose research is focused on the relationship and role of microbial and invertebrate organisms to carbon and nutrient dynamics in soils. Pretty exciting stuff!

I have included a link here to Dr. Ball's bio, lab info, and publications: .

As I am a research assistant, I will be working on part of an ongoing project of Dr. Ball's that is studying the changes in chemistry during the decomposition of plant detritus. This project aims to identify how changes in chemistry during decomposition affect the overall process; more specifically, myself and Miranda, the other assistant assigned to this project, will be measuring hemi-cellulose, cellulose, lignin, and phosphorous levels in leaf-litter samples obtained from various locations around North and Central America. Analysis of the samples will be conducted using a number of methods, including a thermal reduction method as well as sequential acid digestion. Details on the processes and how the data obtained relates to the project to follow on a later blog, as that portion of the study is set to begin later this week.

My first week in the lab was comprised of various activities. Miranda and I prepped litter samples for both distribution to other labs, as Dr. Ball's study is a cooperative one, and thermal reduction for our own later analysis. I also assisted on two other projects working out of the lab. The first, a leaf-litter decomposition project, is being conducted by PC's Dr. Elena Ortiz and Matt Haberkorn. We constructed a number of leaf-litter bags of various mesh sizes, packed them with sycamore tree leaf detritus, and installed them in a compost bin at PC; Elena and Matt will be extracting and analyzing the microbial and invertebrate organisms from the samples as the project progresses.

Nikita, another research student, is doing a project that studies how nitrogen and phosphorous deposition affects microbial communities in soil. To that end, I was invited to join Nikita and Dr. Ball for some field work around the Phoenix area. We spent a full day taking soil core samples from two desert research sites that have plots that have been treated with a nitrogen additive. We also took samples from adjacent control plots that have been left untreated. Nikita will later compare these samples in the lab for their N, P, and microbial content.

The work this first week was, simply put, fun. I love doing field work. Being outdoors and getting down in the dirt in pursuit of knowledge is my idea of heaven. The work done off-site was productive and was also notable for how many times I was able to get a cholla burr embedded in my skin (including my achilles tendon-ouch!), so it looks like I will be investing in a pair of hiking boots rather quickly.

By the way, thanks to Dr. Ball for having the foresight to bring a pair of pliers. They came in handy for doing cholla spine extractions from various parts of my body.

Thanks for checking in with me. Talk to you soon!

All photos: Usery Mountain Park. Credit: Paul Cattelino

Wednesday, December 9, 2015

Semester 4- Week 13- The End.

Hello! And welcome to this, my final edition of this blog.

It has been an amazing ride these last 4 semesters in S-STEM. I have learned an incredible amount about science, but more importantly, I have made a number of great, soon-to-be-lifelong friends.

I will never forget the day I first interviewed for S-STEM. Anil Kapoor had recommended me for the program, but despite the endorsement of such a brilliant instructor, I was nervous. I felt out-of-place, and I was certain that I did not belong in such a prestigious program. My nervousness was only compounded when Matt Haberkorn inexplicably left the room during my interview, leaving me alone with Josh James. I thought for certain that I had screwed up somehow, and that Matt leaving the room was somehow a dismissal of my application.

Little did I know that Matt would turn out to be the kindest, gentlest person I would ever meet, and that he was incapable of that kind of insensitivity.

So there I was, face-to-face with Josh and his poker face. He asked me a question: "Who would you most like to have dinner with?" In a flash, I said. " I know a lot of people would say Jesus, but I want to meet .....". Josh's face was inscrutable, and again I thought I had flubbed the interview.

After what seemed like hours and a thousand other questions from Josh, Matt walked back into the room. Josh turned to him, and with that mischievous grin that I have seen a million times since, he spoke two words: "Jane Goodall." It was my answer to his question.

I then watched as these two guys silently communicated in the way that only two people who have known each other for years can do, with mouths silent but their eyes full of knowing; and I suddenly realized that I hadn't screwed up. In fact, I realized I had just met two people who understood me, for possibly the first time in my life.

In that moment I realized that I not only belonged, but that I had found a home. And the lab has been my home ever since- through good and bad, easy times and tough, even after I had my stroke and became a real pain in the ass, the Biosciences team has been there for me every step of the way. We have laughed together, expressed frustration, then laughed together some more-and through it all, I have felt love.

Thank you Josh, Matt, Dijana, Amanda, Cori, Ana, Kim, and Anil, along with all of the scholars that have befriended me along the way. My life has been forever changed for the better because of the home you have given me.

Live long, and prosper.


Photo credit: Paul C. Selfie the day I got my shirt.

Wednesday, December 2, 2015

Semester 4-Week 12- Field Trip!

Hello all! Welcome back.

I am currently taking BIO 182, as apparently it was the only biology course I have NOT taken at Phoenix College, and it is required for my major. It is an interesting course, made even more so by the fact that I have an excellent instructor, John Schampel.

Recently, we were able to take a field trip to the Phoenix Mountain Preserve, aka the location of Piestewa Peak, and do some field work surveying dispersal patterns of ambrosia deltoidea. This lovely little shrub is commonly known as triangle-leaf bursage, and is an important Sonoran Desert native species that is related to sunflowers. See below.

 Photo credits: Bursage plants.

One of the benefits that this plant provides to the desert is its status as a microbiome. Bursage prefers to grow in open areas that receive a lot of sunshine, and therefore is one of the first plants to colonize hot, open spaces that are too hot for other plant seedlings. Its dense branch canopy also prevents herbivory. Bursage thus acts as a "nurse species" for other plant varieties. Over time, seeds from other species will germinate in the shade of a bursage shrub; this leads to a variety of plant species colonizing formerly open areas after bursage has taken root.

The purpose of our field trip was to survey the number of bursage plants in 81 square-foot plots, the distance from each bursage to its nearest neighbor, and the species of that nearest neighbor. To do so, we marked off the plot with flags and hand-counted/measured distances between the applicable plants. Our hypothesis was that bursage would be found to be predominantly sheltering other plants, rather than be the sole organism in its root zone, and that those plants would likely be another species.

My plot happened to be on a hillside with a lot of loose shale, so it was a little tricky to keep my footing and not pitch off into a ravine, but with the assistance of my lab partner we were able to get the survey done fairly quickly. After analyzing the results, we determined that we had 21 bursage plants in the measured plot. Of those 21 plants, 17 of them were found to be adjacent to another plant, which is an 81% rate of adjacency. Of those 17 plants,  5 were found to be another species that appeared to have germinated within the bursage canopy, which is a 24% sheltering rate. That sheltered species was exclusively creosote bush. This low sheltering rate did not support our hypothesis, yet procedural error cannot be ruled out as a factor in this result.

Above photo credits: Paul Cattelino. Phoenix Mountains preserve.

The dominance of bursage in the adjacency rate may be an indication of an inaccuracy in the count procedure and may have resulted in a conclusion error regarding our hypothesis. We counted each distinct crown of bursage leaves as a separate plant; however, we could not determine with 100% accuracy if each plant was a unique individual without removing the plants and conducting an analysis of the root zone(s). Thus the rate of bursage-to-bursage adjacency may be inaccurate. However, as it is already known that bursage has a distinct alleopathic root zone that prevents other plant growth when it is found to be sheltering creosote, the creosote adjacency rate appears to be accurate.

Further data is required to make an informed conclusion. Unfortunately for our lab group, only five of us showed for the field trip, so we could only make two groups and survey two plots. This makes the data we collected statistically insignificant. Nonetheless, it was fun. I enjoyed being out of the classroom for the afternoon and getting a taste of fieldwork.

That's all for now. Have a Great Week!

P.S. According to some web sources (indicated below), bursage can be used to relieve menstrual cramps and allergies. Creosote has applications, as well; it can be used as an anti-oxidant, antiseptic, and an anti-bacterial for use in minor cuts and scrapes.

Website sources to check out:

United States Bureau of Land Management

United States Department of Agriculture: Plants

Desert Eye Education

PVCC publication

Thursday, November 19, 2015

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:

Thursday, November 12, 2015

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.

Thursday, November 5, 2015

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:

Thursday, October 29, 2015

Semester 4-Week 8

Hello! Thank you for joining me.

This week, I have been busy putting together various elements of my research paper. I had to start working on this paper at the beginning of the semester, as I needed to identify any potentially weak or missing data so that I could have time to repeat certain experiments for data clarification.

I also spent some time this week working with a fellow S-STEM scholar, Mitra. I was asked to share my extraction and gel protocols with her and give some guidance as she implemented them into her own project. We did a couple of bacterial extractions and then ran gels; unfortunately, the experiment did not yield DNA. I am not sure why this occurred. It is a procedure that I have done repeatedly in the past, so my conclusion is that there must have been an unaccounted for error in the process, and we must simply re-do the experiment. More on that on another blog.

In the meantime, I am including a link here to an article published in Yale News about the prevalence of bacteria in the indoor environment. I am also including a link here to the original paper by J. Qian, et. al, that was published in 2012. I hope you enjoy them both-they are quite interesting!

Have a Great Week!

Here's another picture of my favorite bacteria, E. coli. 

Photo credit: Centers for Disease Control,