The trip to the City of Houston water treatment facility was truly an incredible experience! There were so many things to learn from at the learning center, and I found myself jotting down what felt like hundreds of interesting facts to share with my students later. Our guides were very knowledgeable and they shared with us multiple interesting activities that we could bring back to our classrooms.

One set of items in particular that caught my eye in the learning center was a collection of WANTED posters detailing water-borne pathogens that have wreaked havoc around the world (pictures below). I absolutely loved the creativity of these posters. They were simultaneously engaging, informative, and even made me laugh at some of their creative phrasing. At first, I thought about how much I would love to have these exact posters in my classroom, but after thinking a bit more I came upon an even better idea.

The past two years, I have used project-based learning for our virus and bacteria unit. Previously, I’ve had my students create booklets that could be used to inform patients on the differences between viral & bacterial diseases and their treatments. How fun would it be to somehow incorporate a WANTED poster component? They could be modeled directly after the posters that we saw in the center, providing the same type of information about how they make you sick and their method of transmission and reproduction. As I was thinking about this and looking at the posters, I realized they were a bit out of date. It looks like the last time they were updated was 10 years ago, so many of the “last known location” dates and places are now incorrect. That gave me another idea. How amazing would it be if we could actually team up with the learning center and have students design posters/exhibit components that could actually be implemented in the learning center? I have now made a new commitment to myself to see if there is a way that we could make this happen so that my students can engage in a project that will challenge them to build a final product that will ultimately have an influence that reaches beyond the confines of our classroom.

First, thank you everyone who took the time to read my last blog post about the activity I designed for my biology class. I really appreciate all of the support and feedback! While last week, I focused on how to get my students into the engineering process, this week I will talk about how I got a taste of the engineering process through my research. Attend the tale of the mysterious vanishing bacteria.

Once upon a time, there was a lab at Rice university using viruses to eliminate harmful bacteria. Every day they would work to test how well these viruses could eliminate bacteria, but never had they imagined they would have to figure out how to grow more bacteria. That is, until the week of June 25th, 2018 when a mystery struck the lab. Dun dun dun! *cue lightning and spooky sound effects*

Normally, when we plate bacteria and our phages in order to count the colonies, we mix planktonic bacteria (meaning, bacteria growing in liquid medium) with the phages and soft agar and then pour it on the plates. In doing so, we get a nice bacterial lawn with a few clear plaques forming where the viruses infect and lyse the bacteria. However, for about the past week and a half this was not going as planned. Rather than forming a bacterial lawn, the bacteria was growing in skinny swirls at best and at worst, it was not growing at all! What could possibly be happening to our bacteria? Well, turning to our handy dandy engineering and design method helped us figure it out.

Each day, we would try adjusting our procedure slightly to see if it would help the bacteria grow.
Define the problem: Bacteria are not growing
Brainstorm Solutions: Maybe we are putting too high of a concentration of viruses, so the bacteria are unable to grow a lawn due to high rates of infection?
Test Our Solution: Adjust the procedure by diluting our viruses 100x
Evaluate Our Solution: Hmm…bacteria still aren’t growing….
Iterate: Let’s try diluting the viruses 1000x and 10000x
Test Our Solution: Still no bacteria…
Brainstorm Solutions: Maybe it’s the temperature of the agar when we pour the bacteria in? If it’s too hot, that would kill the bacteria.
Iterate: Wait longer for the soft agar liquid to cool before adding the bacteria (and fail at this a couple times due to waiting too long and the agar hardening in the tube, sigh.)
Test Our Solution: Still no bacteria… (cries inwardly)
Brainstorm Solutions: Maybe it’s not the temperature of the agar, but the nutrients in the agar? The bacteria is growing just fine in the liquid media, why don’t we try adding some of that media to our agar?
Test Our Solution (crossing our fingers): SUCCESS!! The agar needed more nutrients (see images below). We will have to be sure to add the liquid media any time we are plating this type of bacteria.

Communicate Our Solution: Be sure to label all bottles of soft agar appropriately and only use the ones with media added. Tell labmates that this is the new procedure so that they don’t fall into the same mistake.

Case closed! The mystery of the missing bacteria has been solved all with the help of some engineering.

While going through the engineering process again, and again, and again can feel a bit frustrating sometimes, at the end of the day, figuring out what went wrong and how to fix it was incredibly rewarding. Sometimes in science we forget how much engineering we actually do. Even if it’s not building a device to use, we design and redesign our methods constantly using the engineering design process. I feel even more confident than ever in guiding my students through the engineering process and all of the frustrations and successes that come with it.

Hello everyone! Last week I briefly mentioned an activity that I had in mind for part of my maker challenge lesson plan. I promised that I would go more in depth the next week , so I have dedicated this post to explaining my natural selection of viruses activity. I have included the background and outline of the activity so that you can have an overview before looking at the activity itself.

Background

Imagine jumping into the perfect pool on a hot summer’s day. The water is cool, crisp and clear thanks to a filter that helps to keep it clean. Now, imagine jumping into the worst pool. It’s probably green, grimey, and gross. That grimey gunk that lines the sides of the pool is known as a biofilm. Biofilms are layers of bacteria or algae that grow on surfaces, and they form in lots of places: pools, shower tiles, and even your teeth! Biofilms also tend to form on water filters, so if you don’t replace the filters regularly, bacteria can leak into your pool or even the water you drink! But, what if we could remove this biofilm without needing to replace the filter or releasing toxic chemicals into the water? Scientists have found a seemingly unlikely hero in viruses. Just like there are viruses that infect us and make us sick, there are some viruses that specifically infect bacteria. These viruses have specific structures on their surface that help them attach to the bacteria. Some even have special abilities to kill bacteria even faster using special enzymes. The problem is that there is more than one type of bacteria in these biofilms, and viruses are usually very specific to one type of bacteria. Scientists need a way to engineer viruses so that they can infect and kill as many different bacteria as possible. That’s when you come in!

In this activity, students will experience how some scientists are using the principles of natural selection to engineer viruses that infect multiple bacterial hosts. By sequentially changing the environment through switching out the type of bacteria, over the course of a few generations, scientists are left with viruses that can infect all of the different bacterial hosts. This model will help students visualize natural selection as well as the process of viral infection.

Materials

• At least 4 styrofoam balls/blocks (“viruses”)
• At least 20 sets of velcro circles (“surface proteins” and “bacteria”)
• Double Sided (or single sided, folded) tape (“surface proteins”)
• At least 10 small fuzzy pom poms (“bacteria”)
• At least 10 small squares of paper (“bacteria”)
• 1 container

Setup

First, you will need to attach the surface proteins to the viruses as outlined below:

• Virus A: soft velcro surface proteins
• Virus B: spikey velcro surface proteins
• Virus C: soft & spikey velcro surface proteins
• Virus D: double sided tape surface proteins (or single sided, folded as pictured)
• Virus E: soft velcro, spikey velcro, and tape proteins

For this demonstration you will be walking your students through the process of introducing your viruses to different bacterial environments. An outline of these different environments and the expected outcomes is shown below:

Challenges/Future Directions

• The tape was actually somewhat sticking to the fuzzy pom pom bacteria. Perhaps a different type of surface protein or bacteria will need to be used? Any advice is appreciated.
• It could be interesting to ask students which method they think would work better, sequentially exposing them to the bacteria or exposing them to all of the different bacteria at the same time (Figure 7).
• Merits/detriments of actually showing the viruses reproducing. Should they add one more of each of the viruses that attached? This could take extra time to prepare and explain but it could also be more accurate in showing natural selection.

Thank you for taking the time to read my lesson idea! Any and all comments/advice is much appreciated!

I began my research experience in the Alvarez lab last week, and I have already learned so many amazing things about research, nanotechnology, and the future of medicine. In the Alvarez lab, we are conducting research to develop bacteriophages that can effectively disrupt the biofilms that form on membranes in water treatment plants. This research is positively fascinating to me, especially since it has the potential to have broad-reaching applications far beyond the original intent of improving water treatment. While I have certainly learned a lot about the scientific content relating to my research, my biggest takeaways this past week were that I gained:

1. Confidence in my laboratory skills
2. Creative ideas for a maker activity for my biology class
3. Connections for my students & new considerations for my future

Confidence in my laboratory skills

On my second day in lab, my mentor introduced me to a multi-step protocol for measuring the effectiveness of the adsorption of viruses to their bacterial hosts. In reading the protocol on my own first, I felt a bit confused about a few parts but for the most part I felt excited to try something new. My mentor walked me through the procedure completely, and I was sure to take notes the whole time I was shadowing him. Once we reached the end, he turned to me and said, “Now that you know how to do it, why don’t you go teach your labmate so that he can know how to do it?” I felt my heart stop for a split second, uncertainty filling my brain. Then I chuckled to myself because I thought maybe he was kidding. Nope. He brings over my labmate and tells him that I will teach him how to do the protocol. The smile left over from my chuckle disappeared and I’m sure I looked white as a ghost. About one-hundred “what ifs” flooded my brain. What if I mess everything up? What if I ruin the experiment? What if I teach him incorrectly and then all of his subsequent experiments will be wasted? But all of the “what ifs” ended once I said to myself, “What if this means that he truly trusts you and believes in your ability to do it?” I held on to this thought, that my mentor must believe in me to give me this task, and I guided my labmate through the process. Were there still times that I needed to go over to my mentor to ask for clarification? Yes. Were there still times I felt uncertain? Of course. But I pushed through it and ultimately the experiment came out as a success. This experience truly helped me grow in my confidence in ways that wouldn’t have been possible had I not been given this chance. Anytime I feel uncertain or down on myself in the future, I know I can look back on this and think, “Laurel, if you could teach a lab protocol on your second day in lab, then you can do this.”

Creative Ideas for My Classroom

Since my blog post is already growing a bit long, I will save the details of my ideas for a future post; however, what I will say here is that I have loved reading the scientific literature from my lab and have already developed a few ideas for how I can use the concepts in my biology class. Since I am working with bacteria and viruses, there are clear applications to the viruses and bacteria unit. We can discuss how viruses infect cells using surface proteins that attach to cell receptors, and my mentor mentioned how I can use this as an opportunity to mention helpful viruses whenever we are discussing helpful vs harmful bacteria. Yet, the ideas that I am most excited about are the ones that model natural selection. In my lab, there are a couple clear instances of this. First, when preparing the magnetic nanoparticles, they isolate the most magnetic ones by exposing the solution to a magnet and removing all of the particles that stay suspended in solution rather than moving towards the magnet. After a couple rounds of washing the particles in this way, you will be left with only the most magnetic of the particles. Second, and perhaps most interesting in my opinion, my lab isolates polyvalent phages (viruses that can infect multiple strains of bacteria) through a process similar to natural selection. By sequentially exposing the phages to different hosts, you are ultimately left with only the phages that have the ability to infect all of the hosts. I will go into more detail about how I will model this in a future post.

Connections & New Considerations

My mentor has been truly amazing in helping me learn more about this research, and one of the ways he has helped me was by inviting me to a symposium on Friday. This symposium was not about water, but about combatting antibiotic resistant organisms in the gut, specifically C. diff bacteria. I am a huge nerd, so I absolutely love museums and conferences and symposiums of any kind, and this one was especially important to me as my grandfather passed away following complications with a C. diff bacterial infection. All of the talks were fascinating and exposed me to a wide variety of perspectives on the topic from pharmaceuticals in development to the biochemistry of antibiotic resistance to bioinformatics being used to predict how an individual’s gut microbiome may respond to certain antibiotics. While at this conference, I had the pleasure of meeting many fascinating and intelligent people whom I learned from. A couple of these people even offered to look into the possibility of visiting my school or having some of my students conduct research with them. I am really excited to see where these connections lead for my students. Additionally, this experience as a whole has made me consider perhaps earning a masters in biology sometime in the future. I had truly forgotten how much I love learning about science and conducting scientific research myself. I am looking forward to continuing to learn more this summer, and I will be sure to update you more on my lesson plan in the next post.

Thank you for reading!