Describing a “typical” day in the Buchler lab is difficult, as my agenda for any given day depends on the tasks required to advance my research project to its next step. That being said, there is a general pattern to what I do, although this pattern does not apply to a “typical” day, but rather to a typical “stage” of my project, the completion of which may be spread over a few or several days, depending on what the stage of the project. As such, in order to give as descriptive and revealing a look into my work as possible, I will thus devise a hypothetical agenda (comprised of tasks that I may not all actually complete on a given day) that illustrates what each of these stages may involve.
Most days begin with a meeting at 9 am for all of the Howard Hughes fellows where we either discuss important aspects of being a researcher or enjoy a presentation by a member of Duke’s faculty on the research that she or he is performing. Once these meetings are over, and usually after a quick stop at Twinnie’s Cafe for some coffee or a bagel, I arrive at lab around 10 am. Upon arriving in lab, I set up my little section of a desk with my laptop, important papers, and my lab notebook, and then walk over to my secondary mentor’s desk to discuss with him what we need to accomplish during that day. Once we have a tentative schedule of tasks laid out, it’s off to the races. Almost inevitably, this means beginning with a mini-prep (which is scientific jargon for saying that I begin the day by extracting the plasmid DNA of bacteria that have been growing overnight). This step is almost always the first thing on the agenda, regardless of what type of “stage” my research is in. This is because I almost always have to grow a fresh batch of the plasmid that I am working with for the procedures of the day.
Once I have my plasmids, my next step is almost always to run an analytical digest and analysis (I mix a portion of my plasmids with enzymes that cut the plasmids into segments that I can evaluate by length after running them through a gel that separates the segments by length) to see if the plasmids that I have just obtained are the plasmids that I want. Although–in order to keep this post relatively short and (hopefully) interesting–I will not discuss the specifics of each procedure, I will give a brief description of the specifics of this step in order to give readers who are unfamiliar with research procedures a small, descriptive sample of a typical procedure for synthetic biology.
Performing a digest and subsequent analysis involves three basic steps:
1. Mixing solution from several different vials through a lot of pipetting and letting the mixture sit in warm water for about an hour.
2. Mixing agarose with hot water and pouring the mixture into casts to make a gellatin-like substance that can be used to separate segments of DNA by length
3. Putting the gel (with digested DNA inside) into a machine that runs an electrical current through the gel for about 20 minutes (which, simply put, is what drives the DNA to be separated by length within the gel.)
In other words, much of the time I spend in lab is used pipetting, mixing, pouring, placing, and waiting. In fact, almost every procedure is a sequence of mixing solutions from several different vials, placing the new mixture into a machine that serves a specific function (be it analytical or procedural), waiting for the machine to work, and then either analyzing the output or using the output in the next sequence of pipetting, mixing, etc.
After completing my daily miniprep and digest, my agenda may look something like this:
3. Isolate a segment of DNA that I want to insert into a plasmid (I do this through a miniprep and a digest as described above)
4. Prepare the plasmid into which I want to insert the segment from step 3 so that it is ready to accept that segment.
5. Insert the segment from step 3 into the prepared plasmid from step 4 via a ligation reaction (a reaction where enzymes attach the insert to the plasmid so that it becomes one whole unit)
6. Isolate the new plasmid that I created in step 5
7. Insert the plasmid that I isolated in step 6 into a strain of bacteria
8. Grow the bacteria from step 7 overnight so that I have a fresh supply of my new plasmid to work with the next day
9. Repeat this process all over again (staring from a miniprep) with a new segment of DNA to insert
Each of these steps is part of what I call a “stage” of my research (a stage might be, or instance, taking plasmid A and making it into plasmid B) and involves procedures very similar to that for running a digest (i.e. pipetting solution together, mixing, etc.) All in all, there are probably 8 stages to my project, meaning I have to start from plasmid A and get to plasmid I by going through plasmids B, C, D, etc. If I’m lucky, I can compete maybe two stages in a week, altho0ugh that is an ambitious estimate given that I didn’t include all of the analytical steps that I have to do to make sure my synthetic steps are going as planned.
Now I know what you’re thinking…”that sounds so boring.” And, indeed, performing a miniprep for the twentieth time is not what I would call the most exhilarating experience. But I enjoy each step none-the-less, regardless of how many times I have done it. I find it stimulating to consider the theory behind the procedure itself (i.e. considering how the reagents used in a mini-prep actually serve to isolate the desired DNA). But what’s even more exciting and rewarding is to consider that every mini-prep I do, every digest and gel I run, every ligation, every step that does not lead directly to data takes me one step closer to getting results that I can see and analyze and apply. In this light, I find even the most repetitive tasks to be fulfilling. They are an essential and inescapable part of being a researcher and I spend 10:00-5:00 each day completing as many of them as I can, all so that I can be that much closer to completing my goal.