Am I running gels or are the gels running me?

Previous to my current experiences in the wet lab, I had envisioned the gel electrophoresis to only be a smaller part of the big picture of the paper I was reading. But after a month of lab, I would argue otherwise. The gel electrophoresis is a method used to visualize DNA based on molecular weight. Molecules with higher molecular weight travel more slowly through agarose gel than low molecular weight counterparts. The movement of DNA through the gel is powered by an electric current.

With flaviviridae (the family of viruses that are frequently carried by mosquitoes), the genome is often small enough to easily edit. This makes them an ideal candidate for a host of creative projects attempting to document their cytopathic effect. The cytopathic effect (CPE) is the resulting structural changes in a host cell brought on by a viral infection. So, we can alter the viral genome and observe the effect of induced “breakages” on CPE. But how do we even prove we made the gene editing change? In steps the gel electrophoresis.

The first step to gene editing is to isolate a gene is to clone the sequence you wish to edit on a plasmid. To determine if the plasmid we wish to replicate is pure, you run a gel to determine its purity. Then, after you’ve transformed your plasmid into your bacteria, cloned it, and reharvested it, you digest it with restriction enzymes. Then, to make sure your plasmid was cut, you then run another gel to confirm it was cut by your restriction enzymes.

Running a gel is also an important step in PCR (short for polymerase chain reaction) quality control. A PCR is a method used to clone a segment of DNA. By running a gel with your PCR product and control, you can figure out how good your primers are, if there was any contamination, and whether your PCR actually worked. But that’s not all. After running a PCR, your product often contains impurities such as primers and DNA polymerases. To purify your product, you can load the crude product into a gel. Only the DNA will move through the gel. Then you can just cut out your band, dissolve the surrounding gel, and obtain a purified DNA product.

So next time you see a gel while reading a paper, take some time to figure it out instead of moving on to the more interesting figures. After all, it’s been the backbone of modern molecular biology since 1950 and will only become more important as gene editing becomes more widespread.


Baking Bad

Disclaimer: The title of this entry is not representative of how pleasant baking and biomedical research are. Rather, it is a poor pun referencing “Breaking Bad” made by the author solely for the sake of the author’s amusement.

Many times before has science been likened to cooking, and protocols to recipes. I personally find biological research procedures to be much more like baking. Firstly, you can’t exactly sautée cells without potentially killing them. If you even attempt to “fry” your nucleic acid samples, consider all your proteins and DNA strands denatured. And if you find your cell cultures to be a perfect golden brown, there are way too many cells clumped together in that tiny space, and they need to be separated between new plates. Also, never steam any of your reagents, as they become utterly useless if not kept on ice.

So why would baking be a better analogy for biotechnological practices? Simple. You put stuff into a bowl (collection tube), mix your ingredients (reagents) all together by whisk (centrifuge machine) and wait for it to bake in the oven (incubator) for a long while. Afterward, your valiant efforts reward you with delicious cake — or rather, satisfactory (sometimes not) results for your research project.

Like baking, laboratory work is a hit or miss. One day you may have made the most heavenly soufflé with the perfect fluffiness to it. In lab, that day would be when your quantitative results show successful amplification of your complementary DNA samples. Another day, you may find that you didn’t add enough yeast to your cupcakes, and they droop down so sadly like the frown on your face upon seeing them. In lab, that day is when you don’t add enough yeast to your bacterial growth media, and you produce very few bacterial cells that possess your engineered gene of interest.

There is a secret to both baking and scientific research, however, that make a recipe become the magnum opus of the baker and the protocol the publication-worthy study of the scientist: improvisation. What does one do when the results aren’t coming out quite right? Add a little more of so-and-so to balance out whatever is the cause of a not-so-pleasant result. Try another method. Spoons were made for tasting, so why not try a smidge of that cookie dough to determine what is still missing?

But for the record, as similar as biomedical research is to baking, I would advise against eating anything in the lab given some poisonous, carcinogenic reagents, bacteria, and viruses you’ll likely be working with.