Biotechnology has advanced so much these days that a new field is rising. It’s called synthetic biology, and scientists in this field create special molecular machines for different purposes. These genetically engineered machines have varied applications, such as sensing biological molecules (biosensors).
For students looking to take advanced biology degrees, synthetic biology is one field they can specialize in. But students learning about genetically engineered machines for the first time might find the lessons daunting. Thankfully, there are many ways to make it more engaging and approachable. Read on to find out how.
First, let’s look at why students find it challenging to learn about genetically engineered machines. Here are the top three reasons experienced by both students and teachers.
Plasmids, genes, restriction enzymes, and even completed molecular machines themselves cannot be seen with the naked eye. Students may find it hard to appreciate the complexity of genetically engineered machines that are “invisible” to their unaided eyes.
Moreover, the processes facilitated by these tiny molecules are equally intricate. Principles explained, in theory, may be hard to translate into actual practice for students.
The entire process of creating a fully-functional genetically engineered machine is complicated. It’s a bit like creating an electronic circuit by assembling each individual part on a circuit board. The process is delicate, requiring high levels of precision at every step.
Unlike electronic circuits, unlike electronic circuits, genetically engineered machines make it more challenging to make because students cannot see the individual components.
Vector design, transformation, and other techniques in molecular cloning take a lot of time to perform. Lab work in creating a genetically engineered machine requires a lot of patience as well as precision. If students are not well-versed in lab techniques, many procedures may have to be repeated, wasting valuable resources and time.
Based on the difficulties students have when studying genetically engineered machines, here are five tips for educators to make the topic more interesting. Each piece of advice addresses a particular challenge that students face.
It’s helpful to introduce students to iGEM, or the International Genetically Engineered Machine (iGEM) Foundation. It is an independent, non-profit organization dedicated to the advancement of synthetic biology, the development of an open community, and collaboration between members of the iGEM community.
iGEM runs three main programs:
iGEM Competition: an international competition for students interested in the field of synthetic biology
Labs Program: a program for academic labs to use the same resources as the competition teams
Registry of Standard Biological Parts: a growing collection of genetic parts use for building biological devices and systems
Pictures, diagrams, illustrations, and videos are helpful in making students appreciate and understand genetically engineered machines. Moreover, students can better understand this topic and related concepts when their learning is aided by graphics, animations, and videos.
Videos, in particular, can make teaching practical concepts easier. Students can replay video demonstrations as many times as they need until they have a good grasp of what they need to know before they work in the lab. They can study vector design, molecular cloning, PCR, and other relevant lab techniques in genetic engineering. By the time they work on a real lab bench, they already have a good idea what they need to do.
Interactive simulations are even better. They let students manipulate lab instruments and reagents virtually, so it’s as if they’re doing the real thing. If they make mistakes, there is no risk to themselves or others. Once they master the technique in the virtual world, they will be more confident as they perform actual experiments in the real lab. The image below is from Labster’s simulation entitled Genetically Engineered Machine.
Students must first grasp fundamental ideas, such as molecular cloning and molecular genetics, to understand how genetically engineered machines work. Here are some of the basics that students need for this topic.
Gene
A gene is a section of DNA. It is the basic unit of heredity in living organisms.
Genes encode information to construct functional proteins. This code is "read" through the process of transcription, which creates a complementary mRNA strand of the gene. mRNA then undergoes "translation" in a cell's ribosomes. The code is used to build a string of amino acids, ultimately constructing a protein.
All the genes combined make up the genome, which can be thought of as the construction plan of the organism. Usually, genes are encoded as DNA, an exception being RNA viruses which contain an RNA genome.
Plasmid Vector
Plasmids, which are circular strands of DNA, are the most commonly used vectors. Plasmids usually occur in prokaryotes, where they encode additional genes that confer traits like antibiotic resistance. The position of functional DNA sequences, which includes origin of replication (ORI), antibiotic resistance (e.g. ampR), promoter, and terminator, on a plasmid are depicted in vector maps. To proliferate a plasmid inside a host cell it needs to contain an origin of replication (ORI) that is specific to the host cell.
Transformation
Transformation is the incorporation of foreign DNA into a host cell. To take up naked DNA a cell needs to be competent. Competency and transformation occur naturally in bacteria when they are stressed.
Transformation is an important technique for molecular cloning. There are several different methods to transform cells; the most common ones are electroporation and heat shock.
Plasmid miniprep
There are several different methods to purify plasmid DNA from bacterial cells. Miniprep is a rapid, small-scale isolation method, which relies on alkaline lysis of the cells, followed by silica column purification of the DNA.
PCR
PCR (short for Polymerase Chain Reaction) is a method used to prepare billions of copies of specific DNA sequences, i.e, to amplify a DNA sample. It is often necessary to have a larger number of copies of a specific DNA sequence for molecular cloning procedures to be successful.
The PCR reaction is highly specific, meaning that it will only produce copies of a desired sequence from the template (sample) DNA. This specificity is ensured by the primers, which are designed to be complementary and anneal to specific regions on each side of the DNA region of interest (target region).
Restriction enzymes
Restriction enzymes cleave the sugar-phosphate backbone of double-stranded DNA. They recognize a specific site of double-stranded DNA and cleave it within, or adjacent to, their recognition site. Restriction enzymes are a very important tool in molecular biology. They allow DNA strands to be cut in a highly predictable manner.
The resulting ends are divided into:
Sticky ends: One strand is longer than the other, resulting in either a 3' or 5' overhang.
Blunt ends: Both strands are cut at the same base pair, resulting in an end without an overhang.
Students who have not experienced using the tools of molecular cloning and synthetic biology may find those tools intimidating at first. For this reason, it’s important to use the firsthand experience to build students’ confidence in using standard lab equipment. Common techniques like pipetting, proper handling of reagents, and the like should be taught in a practical manner.
Once students get the hang of the basic lab techniques, subsequent lab work will become easier for them. They will have developed muscle memory for routine lab methods.
If actual lab exercises cannot be done, video demos and interactive simulations prove useful. Simulations like those found in Labster can help students have the necessary skills before starting actual lab work.
Virtual lab simulations are excellent tools for teaching control of microbial growth. Labster is determined to deliver fully interactive advanced laboratory simulations using gamification elements like storytelling and scoring systems while exposing students to an immersive, realistic, 3D environment.
Check out this simulation called Genetically Engineered Machine at Labster. This virtual lab allows students to perform decontamination and antibiotic selection in a safe, computer-generated environment. With this, students will gain the confidence to eventually perform the procedure on their own in an actual lab.
The image below is an example of what students can explore in the simulation.
Please take a moment to check out Labster’s Virtual Lab called Genetically Engineered Machine or get in touch to find out how you can start using virtual labs with your students.
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