How advancements in molecular biology impact education and training

ABSTRACT

Molecular biology, broadly defined as the investigation of complex biomolecules in the laboratory, is a rapidly advancing field and as such the technologies available to investigators are constantly evolving. This constant advancement has obvious advantages because it allows students and researchers to perform more complex experiments in shorter periods of time. One challenge with such a rapidly advancing field is that techniques that had been vital for students to learn how to perform are now not essential for a laboratory scientist. For example, while cloning a gene in the past could have led to a publication and form the bulk of a PhD thesis project, technology has now made this process only a step toward one of these larger goals and can, in many cases, be performed by a company or core facility. As teachers and mentors, it is imperative that we understand that the technologies we teach in the lab and classroom must also evolve to match these advancements. In this perspective, we discuss how the rapid advances in gene synthesis technologies are affecting curriculum and how our classrooms should evolve to ensure our lessons prepare students for the world in which they will do science.

INTRODUCTION

Molecular biology research has changed significantly over the past decades (1, 2). The pioneers of these disciplines did not have access to the information or reagents that we take for granted in the lab today. As such, investigations often involved not only researching a biological problem but also generating the reagents and materials necessary to do so. Enzymes and other biological components had to be purified (3, 4) and genes had to be sequenced and cloned (5, 6) before a hypothesis-driven investigation into function could begin in earnest. It was this lack of tools, in part, that led to the development of many of the technologies that we now use routinely in the lab and classroom (7).

From these initial forays into molecular biology, the entrepreneurial spirit led to the development of industries that leveraged both this need for reagents by academic labs but also sought to solve important problems facing humanity (8). These companies supply common reagents at a cost that made buying them a practical decision for students when deciding on a course of investigation. In many cases, students have gone from buying individual reagents to purchasing kits that combine several reagents. These kits are used to perform an assay or purify a particular biomolecule and save valuable time during the course of investigation. This process is ever evolving, as every year more reagents and combinations of reagents meant to save time, money, and increase standardization across experimental processes are developed. A comparison of miniprep kits is provided here as an example (9); however, we as authors are not promoting a particular product or reagent.

DNA manipulation is critical for many molecular biology experiments, and there have been many reagents developed that enable investigators to change DNA accurately and efficiently as required for a particular experiment. Teaching students to leverage reagents that cut (10), amplify (11), link (12), and modify DNA (13, 14) have been critical to student training for decades. Such manipulation has advanced significantly over the past decades as the technology to determine the DNA sequences of organisms advanced (5) and more and more efficient reagents to cut and link pieces of DNA together were developed. As such, investigators have become less and less limited by the practical aspects of DNA construct generation. Relatively recent advances in CRISPR-mediated gene editing technology (15) in combination with gene synthesis (16, 17) have only accelerated the pace of this progress and now allow scientists to manipulate DNA in vivo at a scale that was previously impractical.

Many technologies in the biological sciences are developed at cutting-edge research laboratories, and these technologies then spread as they become more user friendly, less costly, and more broadly available. Indeed, gene synthesis has been used to design chromosomes and even entire genomes (18–20). These projects were/are being done by investigators with decades of experience in molecular biology, and these projects had the beneficial complementary effect of lowering the barriers such as cost and availability of gene synthesis for other investigators (16, 17). Indeed, it is now practical for undergraduate students to have constructs synthesized for in class projects (16). As such, synthesis eliminates what can be a significant bottle neck in the research experience. As trainers and investigators, we must consider how this paradigm shift should and could affect our training environments.

At the undergraduate level, molecular biology techniques are principally learned in one of two environments: (i) laboratory classes/CURES and (ii) undergraduate research projects (21). The continued evolution and development of cheap and reliable gene synthesis technologies have the potential to and in many ways already has drastically changed the way we must approach molecular biology education (17). Purchasing DNA constructs as opposed to cloning them yourself can be cheaper and more convenient, but what effects do these protocol shifts have on student understanding of the underlying science? One could argue it is no longer necessary for students to learn to clone in the laboratory in vitro. Adding nucleotides, enzymes, buffer, and template DNA to a tube to generate a construct could be considered an inefficient skill to teach in class or make part of an independent research project. The process of cloning a DNA construct or plasmid, especially those that require multiple steps, can often be done more simply through gene synthesis.

From an educational perspective, this leads to an interesting challenge. To design a DNA construct that will be made by gene synthesis, the designer must understand the experiment they would like to perform and the underlying tenants of the central dogma of molecular biology (22, 23). The incorrect placement of a stop codon or a shift in reading frame can have devastating effects on construct function, and thus, it is imperative that students understand the principles that underly the constructs they are designing. One of the best ways for students to learn these concepts is to spend time cloning a construct (24). The potential for failure can sharpen the mind and make students appreciate why and how they were generating a construct. Furthermore, while cloning in the lab can require multiple steps to all go correctly, the process is often separated into multiple smaller steps many with a high likelihood of success. Successfully performing restriction digestion or PCR can be important for a student, as it helps them gain confidence even if this is only a small part of a larger goal (25). Gene synthesis technologies can eliminate some of these smaller achievements and require students to design a construct potentially without ever having performed the underlying molecular biology experiments necessary to generate such a construct. It is in essence asking someone to design a part for a car after having read the owner’s manual, but without ever having seen or driven a car before, not impossible but potentially confusing.

CALL TO ACTION

As gene synthesis technologies are now more readily available, how should an undergraduate training environment in the classroom look like to prepare students so they will thrive in a workplace leveraging these technologies. One could continue to train students by having them clone by hand, at least initially, so they might more fully understand the rationale behind the design of their constructs. One drawback of this is the obvious time and expense required. In addition, the technology being taught could be considered outdated, and this may not be in the student’s best interest moving forward (Fig. 1). In addition, student-driven cloning projects, especially in undergraduate classes, can be challenging to organize depending upon how often a class meets and the number of students in the class. However, the process of successfully performing an experiment in a lab class can be a powerful motivator and having to physically perform a cloning project can require students to engage in some higher-order thinking skills.

Fig 1.

Pros and cons for different modes of molecular biology training.

A second possibility is shifting classroom activities away from traditional wet lab cloning projects and towards more in silico cloning projects. In these types of exercises, students can design constructs that could be later used in activities in a faculty member’s research lab or classroom experiments. Depending upon the student’s experience level, they could be taught how to design a variety of constructs of varying complexity. This would benefit students by providing the opportunity to participate in more robust construct design than could practically be done in a wet lab. For instance, codon optimization (26), using alternative genetic codes (27), generation of constructs with dozens of fragments are impractical for students to physically do in the lab without gene synthesis. However, many programs used to design such constructs are available for free to academics, and as such the cost of designing such constructs is generally not prohibitive even for undergraduate classes (28, 29). Design of more complex constructs would require students to engage in distinct sets of thinking skills from traditional in vitro experiments, and the skills learned from these exercises may suit the students better in their future careers (Fig. 1).

A third potential possibility, and what might be the most beneficial for students given the current environment, is some combination of in vitro and in silico experimentation. In vitro cloning experiments supplemented with in silico exercises that complement the in vitro exercises to provide a broad learning experience for students. One challenging aspect of teaching molecular biology in the classroom is that physical exercises often have incubations and breaks when students can work on other activities. During this time, students would have the opportunity to complete in silico assignments that complement or supplement the in vitro exercises being performed (Fig. 2). In supplementing a wet lab experience with robust in silico construct design students will gain an appreciation for generating a construct at the bench but also have the opportunity to learn how to design more complex constructs (Fig. 2). Furthermore, because in silico experiments require limited capital expense, the designs students and instructors could work on are limited only by the imagination of the group.

Fig 2.

Potential timeline for incorporation of in vitro and in silico experiences in class. The timeline is based on an in-person lab class that meets for 1.5–2 h per class period. Lecture time can be incorporated into the plan as needed based upon student needs and prior experiences. In silico experiences are recommended to be carried out during in vitro downtime such as incubation periods.

For instance, in our upper-level molecular biology class at an R2 research institution that caters to seniors and graduate students, we find cloning short segments of DNA into a vector provides students with opportunities to practice a variety of core skills including pipetting, dilution, and DNA concentration determination that will serve them well regardless of their interests. Building DNA constructs is also an important concept to understand as it is core to many aspects of assay development. This practice though, can take multiple class periods/weeks, does not always lead to successful generation of plasmid on the initial try, and can lead to class periods with incubation steps or “orphan steps” such as setting up an overnight culture that while required do not have a logical companion lab activity to fill the rest of the class period. This unused time provides students with the opportunity to engage in alternative types of lab learning. During these steps, we initially have students design in silico the construct that they are designing in vitro. While this is a straightforward exercise, it requires the students to understand base pairing, restriction digestion, and DNA polarity key concepts of molecular biology. This can be done before in vitro cloning begins as well. Once these constructs have been designed, one could order them from a vendor so that they arrive before the end of the semester. The number of constructs ordered depends on budget, but it is not necessary to order a different construct for every student, even if in silico they are all cloning a different construct. Once these constructs are ordered, we move on to more complex in silico cloning projects such as, building de novo a construct to express and target a protein to a certain portion of a cell in a particular organism that the students perform while they attempt the simpler in vitro project in class. An example of a potential classroom flow chart for this is provided in Fig. 2.

The description we provide above is an example of how we have adjusted a single class to recent advancements in gene synthesis technology. However, classes do not exist in vacuums and instead are parts of intentional curriculum allowing students to build skill sets and a knowledge base over several semesters. Multi-year/semester approaches should be considered when developing exercises, making sure to provide suitable progression and review as students move through a curriculum. For instance, hands on cloning techniques could be introduced in introductory courses and more in silico methods could be applied in the advanced courses if this is deemed practical for an institution. The size of the class and student experience will all play roles in the determination of what is appropriate. In addition, it is critical that we appreciate that student career goals are not all the same, and thus their needs in training can vary. A student who wishes to go to medical school, for instance, may have different motivations than one that wishes to enter the work force after graduation or proceed to graduate school. Variation in exercise type and better understanding of the student’s career goals can help guide exercise development. In summary, the widespread adoption of gene synthesis techniques in professional settings should fundamentally change the way we approach molecular biology training. It is critical as educators; we are mindful of such advancements and adapt our classrooms to keep pace. Both classroom instruction and personal mentorship of junior scientists by senior personnel play critical roles in laboratory skill development. The extensive adoption of gene synthesis technology will continue to change the nature of this instruction, and such evolution is critical if we are to best prepare students for the workforce they will enter.