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2019 Summer PD – Ecosystems Across Kansas (Konza Prairie)

Several universities across this great state have partnered together on a massive interdisciplinary project (MAPS – Microbiomes of Aquatic, Plant and Soil Systems). As part of this project, they are holding annual Summer Institutes for teachers interested in these fields. This summer is the second edition, being held 17-21 June 2019 at the Konza Prairie Biological Station. Participants are given travel allowances and a stipend, and anyone with a commute >1 hour driving time from Konza will be provided with lodging.

If you are interested in applying, click here.

If you have any questions, contact one of the project leaders, Dr. Peggy Schultz (pschultz@ku.edu). KABT Members Drew Ising, Michael Ralph, Marylee Ramsay, Andrew Davis and Bill Welch were participants or organizers for the first summer institute and can also help.

Sickle Cell Anemia Investigation: Day 8/9

This was a day where we did gel electrophoresis. I got my Sickle Cell test kits from Minione. This is the same supplier that we got our gel electrophoresis units from. I ran a kit which wasn’t anything too spectacular or creative here. The gels can be microwaved, loaded, and cool into tiny forms in 15 minutes at the beginning of class. This left students with about 60 minutes to load their DNA in wells and turn on their electrophoresis kits. I had every student group run their DNA all the way through. Running the DNA only took 22 minutes. During the time that it took to run the DNA I had the students complete an assignment made by mini PCR to check their understanding of gel electrophoresis.

I quickly realized that I needed the students to help me aliquot the DNA samples into numbered microcentrifuge vials that corresponded to particular patients. This added several minutes at the beginning of classes but it saved me over a hour of prep time.

My students were pretty focused on this day. I was too so I don’t have many photos. It turns out if you treat students like scientists they act like scientists. One student literally even student “I feel like a real scientist”. AAAAHHH it still gives me all those tingly teacher feelies. 🙂

The next day we talked about the activity one more time. I used a time lapse video that one of the students took.

Many students got really similar results.

After this time I showed HHMI’s video on Sickle Cell Anemia to answer the guiding question, “Why does sickle cell disease only occur in some locations around the globe.”

Educational GOLD!!!
We used this video to discuss how the malaria parasite hijacks blood cells.

Finally, I went through the way that Hb A and Hb S alleles would behave in a zone of low malaria and a zone with high malaria. I made them predict at their table what would happen and explain why. I actually had to be very aggressive to get them to argue. Often we talk about argumentation as an important skill. My students were simply saying things, yet, I knew that they had all the skills necessary to make good predictions based on logic.

Once the students saw what would happen in low malaria zones I made each table develop an argument for what would happen in areas with high malaria. They had to simply support their hypothesis with logic, but they hated this. I’m still mad about their unwillingness to apply what they had learned to a prediction.

In areas with high incidence of malaria the two alleles stabilize producing a high percent of the population that is heterozygote and thus advantaged.

I loved this whole experience, and I thought it was a great story for students to remember how a system can work from a change in DNA all the way to a population being changed. They will remember this information for much longer than a traditional presentation of the material, because it was presented as a story and humans are primed for narrative not a jumble of incoherent facts and events. I can imagine a suite of biological stories that move from DNA science to evolution. This would serve to create a coherent sense of how biology works rather than a patchwork of biological units that the student never ties together.

Narrative gives biology meaning just as it gives our lives meaning. We should use narrative to weave the large concepts of biology together for a view of life with a little more grandeur.

Sickle Cell Anemia Investigation: Day 7

Today we practiced using a micropipet and loading fluid into the wells of gels. I used several resources from miniPCR to do this.

First of all, this is an amazing video resource to help teach your students how to micropipet. I paused it several times and had the students pass around micropipets to practice with.

Next, I had them compete against one another to pipet their solutions as accurate as possible onto micropipetting practice cards.

This activity requires the students to get the correct amount of fluid to fill the tiny circle on the card.
Water and food coloring and glycerin at 10% were used to make a solution that students could work with.
Student groups of two competed with students across the table to have more accurate pipetting skills.
This silicone gel requires no work on my part so I feel I am wasting less time. The students can’t gum it up and jam into it the way they normally do when they are practicing loading gels.
Next, I had students load their gels into the Electrophoresis machines and then submerge them in water. They filled the wells in their silicone practice gel to get the hang of loading a gel.

This was a very successful day and I am glad I spent the time preparing the students on how to do the practice. I also spent much of this day explaining what is actually occurring when a gel is running.

Sickle Cell Investigation: Day 6

Today we had to retreat back to notes just to get clarity on what was going on. I simply had the students answer the first guiding question with notes.

“How does the gene for sickle cell anemia cause such dramatic changes in people’s health?

This brought students through the following:

DNA-> Mutation-> mRNA-> Amino Acid leading to unusual folding of protein -> Clumping of Protein -> Change in cell shape -> Change in cell function -> symptoms of disease


I actually got a new activity that I wanted to try here to teach the students about how the proteins clump. However, I felt that I didn’t have time. I will try new things next year, but sometimes you simply have to pitch the ball right across the plate.

Finally, I went through a powerpoint that was created by miniPCR to explain how gel electrophoresis works.

In my classroom: Mathematical modeling of Influenza spread (and comparison to Coronavirus COVID-19)

Every biology classroom is likely teeming with discussions about COVID-19. This offers a unique opportunity to share real-time data and situations with students. Each day brings new developments in this world public health crisis. How are the epidemiologists working to temper the spread?

This week, I adapted a lesson plan which I co-developed for high school students as part of the CDC.gov Science Fellowship program in 2014 (1). The plan is “Have You Herd” and is available for free, in its entirety, on the CDC website. Here is the pdf link: https://www.cdc.gov/careerpaths/scienceambassador/documents/hs-have-you-herd-modeling-influenza-2014.pdf which is also listed in references below (2). The lesson has links to NGSS standards on page 14 of the pdf (page 11 if printed hardcopy of lesson).

SEMANTICS NOTE: The novel coronavirus, which is central to the current outbreak, is notated as SARS-CoV2. This virus causes coronavirus disease, identified in 2019, which is notated COVID-19 (3).

Time estimate: 90 minutes-ish, depending on length of discussion and if you assign the pre-lab the night before or have students complete in class.

Why use an influenza lesson to teach about COVID-19? From the CDC website: “the newly emerged coronavirus disease 2019 (COVID-19) is a respiratory disease that seems to be spreading much like flu. Guidance and tools developed for pandemic influenza planning and preparedness can serve as appropriate resources for health departments in the event the current COVID-19 outbreak triggers a pandemic” (4).

Learning Objectives:

After completing this lesson, students should be able to (coronavirus addendums are in parentheses):
• employ mathematical models for influenza (SARS-CoV2) outbreak scenarios to calculate measures of disease spread and intervention effectiveness.
• synthesize effects of physical (e.g., social distancing or non-pharmaceutical interventions) and medical (e.g., vaccines) countermeasures for influenza outbreak scenarios. What are COVID-19 physical countermeasures which can be employed (especially since a vaccine is currently unavailable)?
• identify public health countermeasures that restrict the spread of an influenza (SARS-CoV2) outbreak.
• IF PART 2 OF LESSON IS USED: explain the importance of vaccinations and monitoring cases of infectious diseases. Since there is currently no vaccine is available for COVID-19, this part of the lesson really only works if using only influenza as written. You can discuss that there is a race to create a vaccine to SARS-CoV2.

Overview: I taught the lesson plan as it was written, but added the following components:

  • Opening: Make it clear to students that this lab is about influenza, however when appropriate, COVID-19 data will be discussed as a comparison.
  • Prelab: Assigned students to make a chart to compare flu to COVID-19. I did this ad hoc, but you could take the basic chart from Appendix 1A and have the students make a second column for COVID-19. I especially like the “misconceptions” line – they could list anything they heard early on about COVID-19. Note that at this time, seasonality of SARS-CoV2 is unknown, so that part of the chart students would leave blank. Another column of “cause” would be helpful to distinguish the difference between COVID-19 to SARS-CoV2 (as noted in the semantics note/paragraph 3, above) versus. influenza to influenza virus A, B or C.
  • Worksheet 1: Note that there are three different demographic scenarios to this activity, A-C. One-third of your class should each be given their corresponding version of Worksheet 1. For reference, A = urban/dense population; B = suburban/moderate population density; C= rural/low population density. Wetlab opening – Perform as written in lesson. Point out that the wetlab simulation of rapid influenza test is a nasopharyngeal swab (long Q-tip thing which makes you gag – they will relate). The CDC SARS-CoV2 test kit uses a similar collection method, plus may also collect sputum (6). Tests are described on the CDC website (6). Discussion questions & R0 calculations – Calculate as written. I like to work through this worksheet as a whole class but allowing each group (A-C) to work together to perform their calculations and double check each other. Then we discuss questions as a class. Helpful R0 information is listed in references below (7). Something which struck me as this lesson was developed was that although small towns have less people, therefore less opportunity for interactions with an infected person, the folks an infected person encounters is more likely to be someone they know (closer contact). It is more likely they will hug, shake hands, hug, etc. if they know the person. Thus, your students will see that the scenario C is not too far off from R0 of scenario A. As you conclude the calculations (discussion questions 1-9), compare the various R0 for your three different populations to the R0 value for COVID-19. One source that I found reported R0 for COVID-19 to be anywhere from 1.4 to 4.08 (8). I’ve seen the number in various places and, situationally, it varies, which makes sense. Examples to discuss are a cruise ship vs. various providences in China. Check out the description in that source (8) with a nice comparison of R0 for different diseases. If you are not familiar with R0 and are Googling around, note that it is different than RE (effective reproduction number). RE is addressed in Worksheet 2.
  • Worksheet 2: Although optional for the purpose of COVID-19 knowledge (because there currently isn’t a vaccine), I went ahead and had the students work through Worksheet 2 where they calculate herd immunity threshold (Ic) and the critical vaccination level (Vc). We discussed the effective reproduction number (RE) of influenza and who is appearing to be susceptible to COVID-19. CDC has a rapidly changing risk assessment description available on their website (9).
  • Assessment (Appendix 4A): I love the figure of genetic evolution of influenza virus H7N9. It really shows how genetic shift occurred in a possible bird/poultry market to generate a novel virus which affected humans in 2013 China. Relate this to the source and spread of SARS-CoV2 (10). Make sure your students know what zoonotic diseases/zoonoses are! Merck Manual online (source 3) is my go-to for animal related information (I teach a veterinary medicine course). Search “zoonotic diseases” on Merck Manual or any credible source.

Extensions:

  • Worksheet 1, before question 3, have actress Kate Winslet from 2011 movie, Contagion, introduce the concept of R0 in about 10 seconds: https://www.youtube.com/watch?v=VrATMF_FB9M
  • Do some epidemiological studies. There is a great module on the CDC website, complete with slides for teacher use (11).
  • Have students choose a section to research from the JAMA article, Characteristics of and Important Lessons from the Coronavirus Disease 2019 (COVID-19) Outbreak in China (12). Then, report back to the whole class in jigsaw style.
  • Deconstruct the epidemic curve (“epi curve”) of that same article (12).
  • Show some video clips about herd immunity (13 & 14), especially if you had the students complete Worksheet 2.
  • Have students compare COVID-19 to MERS and SARS. Compare and contrast. Ask them to look into the zoonotic origin. What are zoonoses/zoonotic diseases (15 and 3)?
  • Some more fabulous resources to share with your students in references (16 & 17). Check in back in with those resources periodically as a class.

REFERENCES

  1. CDC.gov Science Fellowship program: https://www.cdc.gov/careerpaths/scienceambassador/index.html
  2. “Have You Herd” lesson plan: https://www.cdc.gov/careerpaths/scienceambassador/documents/hs-have-you-herd-modeling-influenza-2014.pdf
  3. COVID-19 vs. SARS-CoV2, and description of coronaviruses: https://www.merckmanuals.com/professional/infectious-diseases/respiratory-viruses/coronaviruses-and-acute-respiratory-syndromes-covid-19,-mers,-and-sars
  4. Why use an influenza lesson to teach about COVID-19? How is the United States preparing for a pandemic? https://www.cdc.gov/coronavirus/2019-ncov/php/pandemic-preparedness-resources.html
  5. Nasopharengeal samples for COVID-19 testing, described in “Specimen Type and Priority” section at https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html
  6. Tests for COVID-19 described at https://www.cdc.gov/coronavirus/2019-ncov/about/testing.html
  7. R0 information – 9:00 min video for the teacher if you’ve never calculated “R-naught” AKA “basic reproductive number”: https://www.youtube.com/watch?v=jKUGZvW99os
  8. R0 for COVID-19: https://sph.umich.edu/pursuit/2020posts/how-scientists-quantify-outbreaks.html
  9. COVID-19 CDC Risk Assessment: https://www.cdc.gov/coronavirus/2019-nCoV/summary.html#risk-assessment
  10. Source and spread of SARS-CoV2: https://www.cdc.gov/coronavirus/2019-nCoV/summary.html#source-spread
  11. Introduction to Epidemiology: https://www.cdc.gov/publichealth101/epidemiology.html#anchor_topics
  12. JAMA Network article synthesizing CDC data: https://jamanetwork.com/journals/jama/fullarticle/2762130?guestAccessKey=bdcca6fa-a48c-4028-8406-7f3d04a3e932&utm_source=For_The_Media&utm_medium=referral&utm_campaign=ftm_links&utm_content=tfl&utm_term=022420
  13. Herd immunity –  3:31 min video:  https://kcpt.pbslearningmedia.org/resource/nvvs-sci-herdimmune/herd-immunity/
  14. Herd immunity – 2:17 min video: https://www.youtube.com/watch?v=oAJDoLbrNRE
  15. Zoonotic Diseases/Zoonoses – why are they so deadly? https://bionexuskc.org/coronavirus-outbreak-raises-questions-why-are-bat-viruses-so-deadly/
  16. Current situation report, compiled by the World Health Organization: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports
  17. Rolling updates on Coronavirus from World Health Organization: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/events-as-they-happen

Sickle Cell Anemia Investigation: Day 5

Today did not go too well. I must remind myself that it is quite a lot for students to jump from DNA to mRNA to Protein Shape & Function to Cell Shape to bodily function. Still, I think today should have worked much better than it did.

We started with a video by BioVisions at Harvard titled Cellular Visions. It shows how many different types of proteins function in a cell.

It also includes a scene of actin polymerizing which I could pause and discuss. Because It would play into our class discussion.

Then we reviewed that cells shape helps them to perform their function and that their shape is determined by a sequence of amino acids. I told several other protein ‘stories’. I then ended with a visual from Utah Genetics that shows cell size and scale so that I could compare a red blood cell and a hemoglobin protein. I still have many students who cannot interpret that cells are much larger than proteins.


Next, I tried to do a hands on activity with the students that I got from HHMI titled How Do Fibers Form. I think the lesson should work but I couldn’t get it to click. I had lots of blinking and phone issues instead of engaged hands and minds.

Essentially, students take cut out paper models of hemoglobin and they try to piece them in a cell to see how the proteins interact and determine the shape of the cell.

Normal Hemoglobin is “closed” when it is carrying an oxygen molecule. That is, it has no open pocket to accept DNA. So the proteins simply bounce off one another .

I pulled up David Goodsell’s Molecule of the month blog to show the students the behavior of this hemoglobin molecule.

I physically move my body to imitate the hemoglobin in a closed configuration. By pretending to catch oxygen.

On the other hand when an oxygen is not bound to the heme group of hemoglobin it enters an “open” configuration.

This molecule is ready to accept an Oxygen. Thus, it is ‘open’ I slink my body around the room like a catcher with his mitt open and ready to receive a ball. *don’t you wish you had a picture of that 🙂

We can model this with a piece of paper that has a hole punch to show that it is open.

I ask the students to show how these proteins might interact if they were bouncing around a cell. None of my students got this at all…There were literally crickets chirping in my Leopard Gecko cage folks… pppsssssssth 🙁

One or two students suggested that they may clump together.

Next, I had them manipulate models of hemoglobin that had been mutated.

Actually, several of the students started stringing them together… but none (literally 0/111) of them put together that this growing chain of proteins could actually push on the cell membrane to change the shape.

some students got this idea that the proteins would clump together
No students had the notion that the proteins would change the shape of the cell.
None of my students got this far.

I actually did a clearer example with better models that I had printed off.

These ‘normal’ hemoglobins wouldn’t clump
This mutated protein has a pocket for binding to occur in.
Here they could really see how the proteins would stack up to form a polymer fiber that pushes out the cell.

By the last hour I simply just showed them how this could work with my overhead projector. Then we went outside with the last 10 minutes of class and played hacky sack.

I am going to try again on Monday.