Shadowing a Microbiology Lab

by Kaci Jones

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The following is stated by: J. Cameron Thrash, Assistant Professor in Systematics, Ecology, and Evolution at Louisiana State University. Thrash has a PhD in Microbiology at the University of California, Berkeley: graduated in 2009.

Thrash introduces us into the lab by giving general background information about what takes place in their lab. Thrash states that in the lab, they try to isolate microorganisms from the environment so that we have them in the lab to do experimental work with. Along with doing in lab work, they also work in the field to collect samples. This is so that they can examine the genetic information of each individual organism. This process is called the cultivation independence method.

Main machines that are used within this lab are: Flow Cytometry Machine, Cultivation Machine, and what they call “R2D2”.

This is a Flow Cytometry Machine.

This is a Flow Cytometry Machine, in perspective this cost more than a luxury car.

Flow Cytometry Machine- allows them to count cells in water at very low cell concentrations. This machine counts cells when they are extremely diluted, which are how they usually exist in system. This machine also allows them to count that are really, really small. The size that I’m talking about is about the size of a micron or sometimes even at sub micron levels.

The above link is showing how the Flow Cytometry opens. This is how they clean the tubes, put new tubes contain organisms in, and it shows the amount of tubes that can be inputed at one time.

An example of how small a micron level or a sub level is when thinking of a bicycle spoke. A bicycle spoke is usually around a millimeter in diameter. Picturing that, now slice your bicycle spoke into 1000 pieces; that is how small a micron is.

This is a

This is a containment hood.

The next machine was the cultivation machine, better known as the containment hood. This machine allows the lab workers to work in a mostly sterile environment, which helps avoid contamination while transferring organisms from one place of culturing gear to the next.

This is the  AKA "R2D2"

This is the liquid nitrogen dewar aka “R2D2”.

The last machine we went over is the “R2D2” machine, formally called the liquid nitrogen dewar. Within this dewar there are culture collection of all the organisms that they’re isolating from Louisiana’s coastline. The purpose of the dewar is to keep these organisms at extremely cold temperatures for indefinite storage.

Organisms only go into the dewar once they’ve been isolated. Well technically only some go in there. The other isolated organisms are cultivated and are continuously being worked with in the lab. Just incase any mishaps happen, they always save a few organisms.

For cultivation you can either place organism in a refrigerator or place the organism in a heated incubator. Within the two temperate designations, the organisms can either be placed in flasks, 96 well plates, or agar plates.

The different incubators are set up to cultivate the organisms at the temperature in the environment at which they were found in. For example, in the gulf it is really, really warm during the summer. So the organisms gathered over the summer in the gulf have been in an incubator at 31 degrees Celsius, which is how warm he water was out where they took the water samples. Normal body temperature is 37 degrees Celsius, so that’s a good comparison on how warm the water is out in the gulf.

There are multiple other benches in the lab, benches are areas within the lab. Some purposes for the other benches include isolating organisms and characterization of DNA and RNA from the organisms. The lab sends the DNA strands upstairs to the super computer so that they get a high performance computing clusters. They use those for all the sequence information once they extract it out of the organism.

This is Michael 'Mike' Henson, showing the DNA sequence from the super computer. Mike is a PhD Student at Louisiana State University.

This is Michael ‘Mike’ Henson, showing the DNA sequence from the super computer. Mike is a PhD Student at Louisiana State University.

Simple break down:

  • Growing microorganisms (in flasks)
    • Cultivation flasks with media in them
  • Incubators
    • Where they put organisms to grow
    • That way they are in their natural temperature
  • Media is being made within the lab
  • Counting microorganisms
    • Isolating them for genetic material

This is an overview of the lab; I really enjoyed going and learning more about what other people in the environmental field do on a daily basis. I also really liked how the research they’re conducting within their lab is in our backyard. All they’re research is done on organisms that are in the gulf off the coast of Louisiana.

For more information on the lab work, visits Thrash Lab at http://thethrashlab.com

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