Science in the City

 After hundreds of steps and five weeks of effort, today we anxiously awaited the results from the sequencing lab, which would be the final arbiter of the success or failure of our efforts so far.  As it was pointed out to me today, there are a number of things one has to do between the last checkpoint (PCR gel) and the final product.  The closest analogy I can think of is making a soup you don’t get to taste before serving it to the guests.  There’s simply a great deal that must be done without knowing if it’s gotten disastrously off track somewhere along the way.  Although the sheer volume of material sent to the unit suggested we’d get something back, I wasn’t especially optimistic about generating any useful data at this point of the project.  As we headed to the Genetics Analysis Facility, I half expected to see a wisp of smoke rising from my 96-well tray and a message reading ‘Surrender Dorothy.’

As I watched the sequencer, I saw several ‘Failed’ sequence reads, but many more which appeared to be going smoothly.  After eighty minutes of individually reading the labels I placed on each small bit of DNA in the sequencing reaction, the machine must use an internal statistical algorithm to indicate which DNA base is at each of the 500 or so positions on the gene I’ve targeted.  This last compilation step alone took several minutes to compute.  Finally,we were able to move the data over to a desktop computer to read with sequence alignment software.

The first file we opened was promising.  There were no egregiously bad segments along the gene sequence, and most of the arcs which represent the machine’s read of each DNA base looked clear and unambiguous.  ”This is a textbook sequence” I was told, but in all likelihood it was one of few such clear sequences in the batch, and that I shouldn’t expect too many more as good as that first one.  Leaving out the few (4) which failed to read altogether, there were over 90 more to go through, for two different genes.  But file after file, we were all impressed and excited at the clarity of the results.  Samples that came from different individuals of the same species bore the same sequence.  Samples from different, dissimilar species were different, more so than  samples from closely related species.  Before I could process what I was seeing, the other researchers were congratulating me on the lab equivalent of a home run in my first time at-bat!  Between strong protocols, close and patient supervision, constant care and a bit of luck, I’ve managed to generate useful sequence data for 11 species of seagrass for two internationally recognized DNA barcode loci.  As of 3:39 am EST, I’m the first person to ever do this.

It may not seem like much, but I’m overwhelmed an extreme sense of gratitude and humility for the small success this accomplishment represents.  My family made many sacrifices to spare me the opportunity to work here, and I wanted whatever I did here to redeem at least part of that gift.  The labs that have hosted me invested time and money to train and equip me.  Other people wanted the chance to be here, too.  Doing my best was the least I felt I could do, and getting such a strong result is an affirmation that all of this was the most it could be.

With two complete, tomorrow I will use my waning time here to attempt to process a third gene through cleanup and sequencing to join those which I have finished.  I’ve got to start learning to manipulate my results in sequence analysis programs, and generate phylogentic trees from the data.  It’s the end of the beginning of this effort, which will continue with or without my help, though I’d very much like to keep involved in whatever way I can going forward.