Week 5-02/25/2014

Week 5 is upon me, and this is the week that my research begins in earnest. My primers will be arriving from the suppliers on Thursday, so on that date I will be able to begin the process of testing my hypothesis regarding universal primers for the 16s rRNA identification of common bacterial species.

Until then, I will continue electrophoresis gels on the DNA I extracted from Escherichia coli during my last laboratory session, and continuing to raise my awareness of basic laboratory processes. To that end, today another intern instructed me in the production of TSA plates for use in culturing by the Microbiology students.

Last week, the S-STEM students and faculty members were the lucky recipients of an expense-paid field trip to the Wildlife World Zoo in far-west Phoenix. While I am not  proponent of zoos in general, preferring the observance of wildlife in its natural habitat to captivity for the collection of data, the excursion was an excellent opportunity to witness a number of species that are not endemic to the desert Southwest. I particularly enjoyed the albino alligators and white tiger; one could make an argument that these creatures will have a longer lifespan in captivity than in the wild, due to the likelihood of predation in the wild as a result of them lacking the natural camouflage present in their non-albino brethren.

Here's a shot:

 

 

What is outside the frame of the shot is the bar and grill located directly next to the very small tank containing this endangered individual, where zoo patrons could order Pabst Blue Ribbon beer in cans for only $2.00 and ogle him from the comfort of their bar stools. Incongruous, to say the least.

Week 4: 02/19/2014

Week 4.

Last week, I completed my first DNA extraction on the common bee, then processed an electrophoresis to verify DNA presence. Initially, the EP was unsuccessful, and much time was lost as I focused on the equipment itself as the source of the failure. Further review revealed that my mathematical calculations were in error when I created the buffer solution for use in the EP. As a result the equipment would not conduct the electrical charge. Once the solution was changed to the appropriate percentage of ingredients, the EP was completed and a UV photo was taken. See below. Lesson: Check, then double-check all calculations before proceeding to the next step of an experiment.

 

This week, I am focused on researching universal primers for the identification of bacteria that are commonly stocked in college-level labs. The intent is A) identify usage patterns of primers in existing published research to indicate if universal primers exist, B) to verify the universality of specific primers by replicating results of that existing research, using those common laboratory bacteria, and C) determine if usage of those primers can be adapted into a student lab protocol that will accompany the standard clinical format of bacterial culturing and thereby introduce the student leaner to elementary DNA identification technology.


As I review publications for source material, I will also be learning additional DNA extraction methods. Updates to follow. In the meantime, please enjoy the following:

 

Week 3: 02/12/2014

e. Coli.

Week 3 (Already??!):

Still working on the unknown bacteria identification. Results of the lactose test were negative, but the glucose came back bright-yellow positive and presenting a gas bubble. The next step was to inoculate a TCB tube and incubate for 24 hours, so the waiting game continues. This is taking some time, due to the intervals between my scheduled lab times, but I am still having fun with this initial project.

I have settle into this semester's routine, which is basically: school, work, school, work, ad infinitum. Somewhere in there I do get to sleep a few hours, but my social life is gone, so what interaction I get with other creatures outside those two venues consists primarily of talking to my dog and cat. I'm loving every minute of this process, however, and more importantly- I am learning, almost every moment of the day. I am also building valuable relationships with the other STEM students that I hope will be long-lasting and thus continue beyond my time here at PC.

No progress yet on beginning the secondary, larger project of the semester. Currently, I am in the research phase, which essentially consists of me educating myself on some of the terminology and procedures I will be using for the research into a universal primer for 16s DNA sequencing, as the subject is new to me. I'm out of my comfort zone on this, and that's GOOD, as it means I exploring unfamiliar territory and am positioned to advance my learning process. We'll see what tomorrow holds. Until then- here's an image of my first DNA extraction and electrophoresis:

Week 2: 02/05/2014

Week Two. Hard to believe that we are already nearly 20% of the way through this semester.
Today in day 2 of lab, I began the identification process for the unknown bacteria given to me for my first project. Having already incubated it for 24-hours, I pulled the culture and did the basic Gram-stain test. Initial results are a Gram-negative bacilli, presenting singly under the microscope. Colonies are circular, raised slightly from the plate, and white in color. There is little odor. Tomorrow, Day 3, I will complete the identification process, and later I'll update this blog to reflect my results.

P.S. Kudos to the immediate response from the lab team today after an emergency arose with a student during a lab. There must have been either a fireman's pole between floors in the Dalby building, or Josh and Matt jumped from a second floor window to the labs, because it seemed like only seconds after a request was made for help that both were on the scene. Good to know that I am in such good hands.

Update 02/07:

Did an oxidase test on the unknown and results indicated a negative response, so I made three cultures (single- and double-strength lactose and glucose broths) at once so I could lessen the time it's going to take to complete this project. No I'm not skipping any steps, but since the results of the glucose MIGHT send me to do a lactose next, I thought- let's cover all my bases.

Here's a little something for you to enjoy:

 

Week 1: 01/29/2014

Hello, and welcome to my blog! Please feel free to contact me with any comments or feedback.

It has been a challenging month-to-date, but I am looking forward to it heating up as the semester continues and all of my late start classes kick in. Next Monday is D-Day for me, as that is the day when I am officially carrying the weight of a full class load (four of them), the S-STEM program and attached internship/class, my tutoring commitment to the Success Center and the English 101 class that I am attached to, along with my role as a full-time retail manager. My motto this semester is, "Who needs sleep, anyways?"

I am looking forward to interning in the Bio labs and getting to see things from the other side-as a student, I have previously done lab assignments for multiple classes, including Micro and A & P's 201 and 202. I am excited to get a different perspective on the department; I am even more excited to have the opportunity to do the research projects that are available as part of the S-STEM program and to actively practice the discipline of science.

I love learning and welcome each new opportunity with welcome arms. I am looking forward to getting to know each of you in a professional capacity. Cheers!

PS: Here's a well-known pic of the human whose example has inspired me since my childhood to question what I am told, always remain inquisitive and skeptical of the status quo, and never be afraid to endure hardship in the quest to acquire knowledge and understanding.