Introduction

This year, the Michigan Synthetic Biology Team has chosen to design an educational module that includes some of the basic science concepts used as a part of our iGEM project. We have included videos, word searches, and other entertaining activities along with our written educational material because we felt that this would gamify learning, thus encouraging students to engage more with the content. For example, including a word search at the end of this activity encourages students to read the passage we have written about antibiotic resistance and recombinant DNA technology so that they are able to properly complete the word search. This strategy was employed to optimally engage our target audience of middle school students in STEM-preparatory programs.

We have made this educational activity accessible to a wide audience of young students interested in science and engineering by posting the worksheet on our Wiki page and our team’s public Instagram page. We also have plans to distribute the worksheet to middle schools in the school district surrounding our university by contacting principals and educators as well as utilizing the connections of these schools’ alumni who are members of MSBT. The 4 middle schools we plan to send our materials to for preliminary use include Slauson Middle School, Clague Middle School, Tappan Middle School, and Scarlett Middle School in the Ann Arbor area. We will include a Google Form to collect feedback from these middle schoolers and educators in order to gauge if there are improvements that should be made before further promoting our materials. We are excited to distribute this resource to our local community and see how we are able to increase youth awareness of the intersection of biology and engineering.

Education

What is Synthetic Biology?

This worksheet is intended to introduce you to some basic concepts in synthetic biology. What is synthetic biology? It is the development of new technologies and biological parts using biology. It combines engineering and science to make new things that can be used to help people medically, protect the environment, and so much more! Keep reading to learn more about how synthetic biology can be used to help fight bacteria that make people sick.

Antibiotic Resistance

Antibiotics are a common form of medication used to treat bacterial infections of all severities, from something as simple as strep throat or an ear infection to more severe illness such as a bloodstream infection. If you have ever had pink medicine from the doctor when you were sick, it is possible you were taking an antibiotic! In many cases, antibiotics are improperly prescribed, which can lead to antibiotic resistance. Antibiotic resistance is when certain bacteria in a population contain a mutation that allows them to survive in the presence of an antibiotic that would normally kill them.

When antibiotics are overused, the likelihood that mutated bacteria survive increases and they become hard to treat. As antibiotics are used more and more, especially when unnecessary, the prevalence of the antibiotic resistant mutation in the bacteria population increases. Eventually, this can create an entirely new and resistant strain of bacteria that will not respond to a particular antibiotic. A common example you may have heard of is methicillin-resistant staph aureus, or MRSA. The antibiotic methicillin is unable to kill this strain of staph aureus.

As antibiotic resistance increases to multiple antibiotics, healthcare systems will run out of effective treatments for bacterially caused disease, which could increase the risk of illness and disease in our communities. This poses a major global problem that needs to be addressed.

E. coli bacteria

AMPs

Antimicrobial peptides (AMPs) are naturally occurring proteins, produced by many organisms including insects, reptiles, mammals, and other bacteria, all around the world. These proteins exhibit the behavior of killing bacteria. For this reason, they are being considered as potential alternatives to common small molecule antibiotics like amoxicillin and azithromycin, which bacteria are becoming resistant to. These proteins have a variety of structures and functions which make them effective in killing a range of bacterial species. One example of how they kill bacterial cells is by making them pop open in a process called apoptosis.

One challenge of using AMPs as antibiotics is that they are expensive to make. A common way to make a large quantity of a protein is by making changes to bacteria that cause them to make a lot of the protein. However, if AMPs kill bacteria, it would be hard to produce them in bacteria because the AMPs would just kill them. If effective production methods for AMPs are established we could potentially use AMPs as new antibiotics, helping to treat sick people with bacterial infections.

Encapsulins

The discovery of a new type of bacterial compartment called encapsulin nanocompartments spells an exciting future in the fields of synthetic bioengineering and drug delivery mechanism development. Encapsulins are proteins that can surround another protein, like an AMP, within a cell. This shelters the cell from the protein that is inside the encapsulin. Specifically, encapsulins are protein nanocompartments that are composed of many identical portions of smaller subunits that come together in a cage-like structure to form the larger encapsulin. This can be thought of like the patches that join to form a soccer ball. Each encapsulin subunit is like a patch on a soccer ball, and the patches can assemble around something that we want to carry in the encapsulin.

Encapsulins are of special interest because they are able to sequester, or contain various proteins inside their cage-like structure. For example, if we put an AMP in an encapsulin, the AMP would be blocked from going into a bacteria cell and killing it.

Plasmids

If we want to study a protein, like an AMP or an encapsulin, how would we do that? Plasmids are circular pieces of double-stranded DNA naturally found in bacteria. They are separate from the main chromosomal DNA of the bacteria. They can easily be uptaken from the environment into bacteria or transferred from one bacterium to another.

Plasmids are a valuable tool to scientists. In research, they are commonly used to insert and express certain genes in the target cell or organism. The genes do not have to come from bacteria, they can come from people or other organisms. This means that we can make bacteria produce a wide range of proteins that we do not usually make. For example, a plasmid containing DNA that encodes a protein for insulin can be used to make bacteria produce large quantities of insulin. The insulin can then be purified out of the bacteria and given to diabetic patients whose bodies cannot make their own insulin. This allows diabetic people to live a healthy life. Due to the structure of plasmids, it is very easy to cut and insert different pieces of DNA into the original plasmid. For this reason, there are near-endless possibilities of functions plasmids can serve in scientific settings!

Transformation

Once a researcher has designed a plasmid, how do they put it into bacteria so they can begin making a protein? The answer is transformation! Transformation is a basic experiment run in a lab in order to prompt a bacterial population to uptake a bacterial plasmid from its environment. The plasmid contains a DNA sequence that is being targeted for testing. A key component of a transformation involves heating bacteria to a high temperature, usually 42°C (ouch, that’s hot!), which enables the membrane of the bacteria to uptake the foreign plasmid. We have to be very careful not to overheat and kill the bacteria though! Transformation is an important step in cloning. Cloning is the process by which DNA is recombined in a bacteria so that the bacteria can make many copies of the plasmid DNA that is put into it. One reason that we would want many copies of a sequence of DNA is to sequence the DNA. Sequencing is used to find the genetic code of a specific region, which requires high quantities of the plasmid.

Lab Safety

Lab safety is one of the most crucial components to research and lab work. Across the world, standard procedures and precautions are in place to ensure that scientists remain healthy and unhurt in their work. Included in these precautions are the use of gloves, safety goggles, lab coats, and closed-toed shoes. It is also important to wear clothes under lab coats which cover most of the body. Procedural safety measures include the employment of specialized techniques for certain lab tasks, especially those including the use of live cells and harmful chemicals, and proper disposal techniques. Disposal techniques are differentiated depending on the nature of the waste – whether it is corrosive, biohazardous, or sharp, for example. These rules and regulations can be difficult to follow, but not only is their implementation vital to the wellbeing of scientists – they are one of many things that unite the entire scientific community around the globe!

Activities

We also put together several activities in the realm of synthetic biology, including a crossword, word search, and word unscrambler! Try all of the activities below to test your knowledge.

Crossword Puzzle

A crossword puzzle on lab safety can be completed at the following link: lab safety crossword

An image of the crossword along with solutions are shown below:

Word Search

All of the words listed below can be found in the letters below. Try looking up and down, backwards, and diagonally!