Grad Student Life Beyond Fieldwork: Part 4 (Our Labs)


Today’s post is the last installment of my series “Grad Student Life Beyond Fieldwork.” Take a look at Part 1 (Classes), Part 2 (Teaching) and Part 3 (Our Offices) to read about other facets of grad student life. Part 4, the post you are reading now, is about the labs where we produce and analyze data.


Some measurements we use for our research, like water temperature and salinity, can be measured directly in the field. Other more complicated things like “cyanobacteria community structure” involve taking field samples back to a lab (or multiple labs) for extensive analysis. Below I have posted a “virtual tour” of the lab I work in, the Microbial Ecology Lab at FIU, to give readers an idea of what grad students and scientists do other than walk around wearing lab coats. 


Above is the door to the lab. It basically says, “Welcome! You are about to encounter biological materials, carcinogens, flammable materials and high voltage equipment! You should probably turn around.” All of these dangers are necessary to understand what microscopic organisms live in water samples from the Everglades and Florida Bay. Although this sign implies that you might die upon opening the door, our lab is generally safe as long as you use common sense and have a little bit of lab safety training. 


Next we enter the lab. Note that just like my office, it has no windows. All scientists are allergic to sunlight.

One line of research conducted in this lab is determining cyanobacteria community structure. While one could look under a microscope at a water drop and take a guess at what kinds of cyanobacteria are in it, genetic techniques have been developed to give a much more accurate picture of what species are in a water sample. Understanding cyanobacteria community structure and factors that impact it is important for Florida Bay water samples because Florida Bay often experiences cyanobacterial blooms. Below is some of the equipment and tools we use to determine community structure.


This is the PCR (polymerase chain reaction) thermocycler, which amplifies segments of cyanobacteria DNA. An extremely small drop of a water sample and several reagents are added to tiny vials then placed in this machine. The machine then repeatedly heats and cools the vials so copies of the desired DNA segment can be made.

How small of a scale are we talking about? Above are the pipets that we use. Notice that they are set in microliters.

Not all laboratory equipment is highly advanced and specialized. While the DNA is synthesized, agarose gels are prepared using the microwave shown above. Since ethidium bromide, a probable carcinogen, is used in the gels, this is not the best place to heat up your lunch. 

After the gel is prepared and solidified, we pipet 5-10 microliters of the amplified DNA into tiny wells in the gel (I am probably really good at the board game “Operation” after doing this hundreds of times). An electric charge is then run across the gel in the gel electrophoresis machine shown above, which moves the DNA down the gel. The distance the DNA travels tells us how long the segment of DNA is. With a few more lab procedures and hours of analysis on Excel, we can determine what species of cyanobacteria were in the original sample.

FCE Grad Students: How much time to you spend in your lab? What are some things you like or don’t like about your lab work?

Other Readers: Do you have any questions or comments about our lab work?  Do you have any questions remaining about grad student life (classes, teaching responsibilities, etc.)?

Comments

  1. It is amazing how much information a few drops of water can tell!

    Haha I spend way tooo much time there. I process fish samples for my lab work... It can be relaxing, I get to sleep in,listen to music and count and ID fish. I do not like the smell of formalin however!

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