Learning the Tools of Modern Molecular Biology

How did we get from Sanger sequencing and PCR to Next-Generation Sequencing? I’m about to find out!

It was a short but memorable conversation about life, science, careers, and projects. I was standing with Dr. Charlie Uhl, PhD, an emeritus professor of Plant Biology in what once was the Cornell University laboratory room of Barbara McClintock in the Plant Science Building, which he had inherited. This was a classic 1930s room of cabinets and drawers filled with specimens. Barbara had left the campus well before I was born but we all knew of her Cornell Legacy and her Nobel Prize, and of course her expertise in both plant breeding and botany genetics in maize (corn). Barbara was a role model and pioneer for me and other women in science, especially as she was readily accepted at the already progressive Cornell University. She was interested in cytology, mitosis, meiosis, and ploidy of plants, but was probably best known for her work on the crossover of chromosomes as well as discovering transposable elements, those ‘jumping genes’, which she studied in the colorfully expressed favorite fall crop “Indian Corn”.

My conversation with emeritus professor Dr. Uhl was deep and dealt with scientific projects and theories. We talked about whether a transposon was involved in a phenomenon one of my colleagues was studying (he disagreed) and we honestly chatted on how classically trained scientists could become more than a little frustrated with the next new hot technique for modern science (modern for the early 1990’s that is) that came out.  We also talked about how modern scientists for that time and funding agencies were too preoccupied with molecular phenomenon and losing site of understanding the basic physiology and anatomy mechanisms of plants. It was one of many conversations I had with a few classically trained scientists when I was just starting out. As I was pursuing my doctoral degree, I did find the need to work on “learning the tools” of the modern molecular biology, but I will always remember how important the influence of classical science was and is. We should all be more interested in the “why” than the “how”.

Retooling Molecular Tools

I have been thinking about my conversation with Dr. Uhl a lot lately. More than 25 years into my career after receiving my Ph.D., I once again find myself at an interesting juncture in science and in my own life. I am a “classically trained” molecular biologist and many of the techniques which I learned are now considered old. Some of the tools have been automated and certainly all the chemical reagents that we once made “from scratch” are now easily and affordably purchased at increased purity. Our ability to do experiments has become more streamlined, too.  Yes, I still have my blue recipe box containing lots of experimental set-up solutions, but I don’t really need them now. I used to calibrate and clean pH meters in the late 1980’s as a lab assistant, and now my own lab doesn’t even own a pH meter. My extensive experience in recombinant plasmid cloning is not needed anymore either as we can just simply buy the DNA sequence custom-made for minimal cost. Crazy, amazing, and forcing us to sharpen our tools and our minds to remain “relevant”.

Using molecular biology techniques to characterize materials, we are on a cusp of a major shift in the way we approach the classic question of “what is in my vial?” when ensuring safety, identity, and characterization of client materials. The evolving guidance by government and scientific agencies for testing certain drug substances have included recommendations that affect our work with in vivo as well as in vitro methods, and just within the last few decades we have embraced PCR techniques to look for unknown and known potential contaminants. Newer methods have now become available which include a next-generation sequencing step in an “agnostic” (not knowing what one is looking for) approach to make a deep dive of the potential contaminants. For example, a recombinant antibody for cancer immunotherapies, generated in a ‘CHO-K1’ cell line, may be screened for certain viruses, but now the material may be “deep sequenced” for a gamut of potential contaminants. Other work includes identity testing of materials by experimentally deriving long-reads of sequences which may eventually replace much of the Sanger Sequencing work now performed. I understand and this is OK. I understand because before the “modern” capillary electrophoresis instruments, I also was transitioning in the early 1990’s from radioactive experiments using long acrylamide gels run for hours and prepped for days. I now see transitions again. What took me six months in graduate school now takes a day. Wow, progress!

I myself have taken a leap into extending my own education and embracing working within a company-sponsored four-week sabbatical to learn these NGS techniques. Gaining knowledge of the NGS techniques will be satisfying and yes even fun! Plus, I am well aware of the answers these experiments can generate, and how a valuable a tool it is for our industry, clients, people, and science.  

And yet how does this all relate to those days when I just started on my Ph.D.? What can I bring from my 30 plus years of experience on the lab bench to help the ‘Next Generation’ of scientists? By remembering my ‘deep-dive’ conversation with Dr. Uhl, by understanding the needs of our work and the systems, by remembering to ask the right questions, and to always keep learning.