A day in the life of… Sara

by Sara Thomas

Lab Environmental Sample Processor (ESP)

Mentor Post-doc Julie Robidart

A typical day in the ESP lab begins with loading a nifH template (nifH is a gene expression for nitrogen reductase) onto the Micro-Fluidic Block 2 (MFB2).  Although the MFB2 sits at my work station, its real home is on an ESP instrument.  The ESP will collect environmental water samples in-situ during deployment in micro-fluidic proportions which ultimately make its way to the MFB.  Once the sample reaches the MFB it undergoes a qPCR (quantitative polymerase chain reaction).  An in-situ qPCR experiment is exciting for micro-biologists and microbial oceanographers because it allows scientists to investigate marine biogeochemistry in near real time.  If it weren’t for the ESP, these samples could not be analyzed for their content for days after their collection.  My main task on the non-deployed MFB2 at my desk is to determine nifH standard curves for different groups of microbes.  I do this by loading known concentrations of templates and plotting the DNA amplification curves (fluorescence vs. cycle number) in Excel.  The process, run in triplicate, takes approximately 6 hours to complete.

Setting up a gel electrophoresis

After setting up the MFB2, I run over to the other lab and prepare what I call an “old- school” PCR where I test the primers I designed to target the idiA gene (expressed during iron deficiency) in the species Synechoccocus.  I prepare the appropriate master mixes and primer probes for my samples to prepare them for DNA amplification.  I can test for DNA amplification, and therefore if my primers worked, by running an agarose gel electrophoresis on the PCR product against DNA ladder standard material.  After sending an electrical current through my gel and buffer, I observe how chunks of DNA from the PCR product have moved (or raced) through the gel relative to the standards (I hope to see a tie at a certain ‘ladder step’ in each lane).

At this point in my day I secretly do a celebratory fist pump and heel click because my agarose gel has just told me that my PCR product is worthy of cloning which reinforces the success of my primer design.  I happily pull e-coli cells out of the -80°C freezer and introduce them to my PCR product via a cloning procedure.  Then I spread material onto an agar plate, throw them in an incubator at 37°C over night, and hope to see cultures waiting for me in the morning.

A bit about me!!

It wasn’t until recently that I discovered my interest in microbial oceanography.  I earned my B.S. in Global Environmental Science with a minor in Meteorology.  My major required an undergraduate thesis and so I performed a trace metal analysis where I investigated the spatial and vertical distribution of arsenic in soil cores collected from O’ahu- a project completely different from what I am doing now.  The C-MORE (Center for Microbial Oceanography; Research and Education) Scholar’s program provided support for this project and opened my eyes to the intriguing world of microbes through meetings and seminars.  My internship here is supported by C-MORE and I’m stoked to have a project that directly ties into research in microbial oceanography!

In Monterey with flatmates Izzy and Melissa

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