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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.

Midwest Regional 3D Symposium K12 Poster Session

An example of what a student poster session

Exciting New Opportunity for K12 Students – The Midwest Regional 3D Symposium has a call out for K12 students and their instructors to submit abstracts for projects that they have completed using 3D technologies! This is the 3rd year for the symposium and first time they’ve had this opportunity for a student poster session. The symposium is being held at Children’s Mercy Park the home of Sporting KC on Friday, June 7. The deadline for abstract submission is this Friday, May 10 at 11:59 pm CST.

You or your students need to be committed to having posters hung between 8-10:00 am and your students would need to be present for presenting their work to judges between 11:50 am and 1:30 pm. There are prizes to be won!

See the following pdf documents for more information on the symposium and the poster session and submission guidelines.

Material Science and Ecological Impact Using 3D Printing Materials

I haven’t exactly been subtle about how sweet 3D print can be…

The various options I’ve seen and imagined have usually focused on the engineering aspects of making. In biology classrooms, I can do a better job of building maker experiences with rich biological connections. Some community conversations have led me to sharing this idea for a project that marries 3D printing and biology is an interesting way.

h/t Drew, Jessica, and Shannon. Also, Topeka Public Schools STEM teachers for a great conversation while I was considering this article – your work impacted this post.

Context

This project could hit lots of standards, but these are the few I had in mind when I wrote this:

Our driving question is important, and is going to mean different things to different people:

“What plastic should we use when 3D printing?”

I would ask the students to begin operationalizing what that question means to them. There are probably going to be two themes in the answers:

  1. What printing materials create the best print products – probably defined by strength.
  2. What printing materials have the fewest negative impacts – probably defined by plastic waste consequences.

I will proceed assuming the first question is the initial focus. If that’s the case, I wouldn’t force any consideration of the second question… it will give us a fun payoff later.

Phase 1: Best Print Products

Students can be given time to create a procedure for stress testing parts printed with different plastics.

What’s important throughout this whole testing process is that you ensure students save every print they make. Broken parts, failed prints, unused replicates… everything they print, they keep!

Phase 2: Matter Cycling

After students complete their analysis of strength, they can return to their driving question. Do they have an answer? If they say ‘strongest is best’, then we can let the conversation move on… to clean-up. What do we do with all this PLA and ABS plastic?

If a particular plastic is best, then we can ask them to think about scale. What happens when everyone starts using it? A big draw for PLA is that it’s not petroleum-based (which is good). The issue still remains of disposal. PLA is compostable, and ABS is recyclable… right?

Students can then read this article from engineering.com – “What They Don’t Tell You About 3D Printing PLA”. Despite the title, it lays out a good description of what PLA production and disposal looks like. What does it mean for PLA to only be compostable in “industrial settings”? This article from 3D Printing Industry “Is Recycling PLA Really Better Than Composting” describes the various disposal methods of PLA.

This leads into an opportunity for students to learn about matter cycling and home composting. Ideally, they’d create their own compost piles. They can measure moisture and temperature… lots of great science in a compost project.

Phase 3: Solve a Problem

Now that students have some experience with composting and 3D printing plastic, it’s time for them to solve a problem they themselves have made (all their leftover prints)! The students can design their own methods for adding their PLA printed parts to their compost piles. Here are some resources to help:

  • Students can compare the impact of the PLA/PCL blending methods on their originally considered model properties with this peer-reviewed paper

Students could implement a method for adding their plastic to the compost piles, and then collect data for the next month or so. Class could shift focus to other topics while students continue monitoring their projects. The extended time frame could provide the students an opportunity to present the results of a major project around the end of a semester.

These are just some rough ideas I had when I came across the first article. There are basically three steps, and you could approach each in lots of different ways:

  1. Print.
  2. Compost.
  3. Design.

What do you think? Anyone want to try it? I’d love to help/consult with someone who wants to give it a shot.

In My Classroom: POOP LAB! (AKA Fecal Floats/intestinal parasite lab)

A lab favorite in my classroom is the Poop Lab. I teach a Veterinary Medicine course for high school juniors and seniors (life science credit). Parasitology is one of the class foci (is it because I LOVE the gross factor? Probably). If you cover parasites, zoology or even zoonotic diseases, this lab is a must do! YOU DO NOT NEED A CENTRIFUGE to do this lab. Alternative instructions are written on the student lab.

Goal of the lab:  
Perform a fecal float analysis with sample from a  family pet.  Determine if that pet has possible intestinal parasites.

Rationale: Determining if the students’ own pet has a parasite is extremely  engaging (or the neighbor’s pet).  Plus, it’s a darn good microscopy 
exercise on identifying what is significant or not (hair or air bubble).

Homework the night before: I send students home with a disposable fecal collection chamber (1). If you don’t have those, a Ziploc or other small disposable container will suffice (the thicker the better stink barrier it will be). I also give them the option of grabbing a set of exam gloves in case they are horrified by the thought of poo grazing their hand. Students are instructed to collect 2-5 cc of FRESH ANIMAL poo from their pet at home (or ask a neighbor for use of their yard/litter box/etc.). No human poo accepted. ANY pet will work. Iguana, dog, chicken, horse, cat, goat, hamster, chinchilla, etc.

Such a memorable lab…

I’ve usually emailed home to give the parents a heads up that bringing an ANIMAL poop sample to school is legit (no worries about stuffing it someone else’s locker as a prank). FRESH IS BEST so collection morning of the lab preferred, but most animals don’t poop on command. If they have an evening pooping animal, it’s OK to collect the night before, but should be refrigerated overnight (um, this is again where a parental heads up comes in handy – probably won’t want container of poop in the family fridge). If poop is banned from the kitchen, a lunch box with freezy pack. If they use ice to keep it cool, make sure the water doesn’t leak into the poo container. That is a lunch box sludge that is best avoided.

Lab Day: If this is not your students’ first time using a microscope, this lab can be completed in a 45 minute session, including cleanup. This is possible because I prefer to maximize the use of disposable items. After the first student spills a test tube of sugared poo slurry and you see how difficult it is to clean up the sticky mess, you’ll thank me for that little tidbit of wisdom. Try asking your local Sonic, etc. for a donation of a box of smoothie straws (AKA disposable scoopulas) to mentally scar students’ future enjoyment of smoothies following this lab.

Here’s the one-page handout of instructions that I give each student:

Who wouldn’t be all smiles after retrieving the poo slurry from the centrifuge?

I built tips into the instructions, so give it a good read before trying with students. You will need a comparison chart [(2) or extension activity described below BEFORE this lab] so that if students find something that looks like a parasitic egg (4), they can try to identify which parasite might be infesting Fluffy’s intestines.
You will need to order or mix up a sugar solution ahead of time (3). Wards has a “Fecal Slide Analysis Activity” which boils down to this same lab. I wouldn’t spend the money on it (although I did the first year), unless you like the handy dandy teacher manual (which does have some interesting fun facts – but that’s all I like about it).

How it works:  The parasite eggs (4)  are less dense than the solution.  After centrifuging (or allowing to sit  for a length of time), the eggs float to the top of the tube.  They bind to  the coverslip, allowing us to see the eggs on the scope.  The parasitic  infection can be determined based on the shape/appearance of the eggs on the slide.

IF there is anything suspect, use an identification chart (2) or a scientific based website to try to match the microscope image with known parasite pictures. See additional activity ideas below. Check out this website:
http://www.pet-informed-veterinary-advice-online.com/fecal-float.html I like that towards the bottom, they also identify other items which might be seen on the slides and are no cause for alarm (normal bacterial flora, hairs, air bubbles).

My students have seen green blobs that look like stacked bricks. It’s a hoot for them to try to guess what network type of parasite that might be, only to finally draw the connection between plant cells from Bio I and, “oh yeah, my dog ate grass.”

Strongyles from horse. Image from my class, fall 2018. Note that this slide sat on the scope a little too long so the sugar solution is starting to get sticky under the coverslip. Too much longer and it would have been crystalized.



Three swine whipworm eggs can be seen, approximately diagonal from upper right to lower left. Image from my class, fall 2016. This was considered a low parasitic load and we did not treat the pig sounder at that time.

Note about livestock: It is actually considered normal for a livestock animal to have some parasitic load. This keeps the immune system fighting the parasites instead of treating again and again to the point they become resistant. Instead of a fecal float (like this lab) for diagnosis, a count is performed after isolating possible eggs. A cell count slide is used (sounds like a hemocytometer to me). If 1 cc of fecal matter yields over a certain threshold for that parasite in that animal, then treatment is administered. Don’t ask me the threshold – if you come across any more info about this, please add to the comment section below. Fall 2018, my students found Strongyles (a horse nemotode) in the poo I brought in from one of my horses. I showed the picture to my veterinarian. Although we didn’t quantify, she felt it was probably a low parastitic load and would naturally be kept at bay. I rotate through a different dewormer for my horses every spring and fall. Horse strongyles can’t be passed to my happily horse poop eating hound dogs, so they continue to be clear every time my class looks at their poop.

What to do if evidence of parasite IS found in a pet:
Instruct the student not to panic. Have the student take a photo of the microscope image. It is recommended that he/she share the information with the parent to possibility be passed along to the family veterinarian. The vet while likely ask for a fecal sample or to bring the pet to the clinic for a fresh sample to be taken (via tiny spoon inserted into the anus – very fresh). Some veterinarians might do a version of an ELISA to confirm various parasites. After doing this 10 semesters in our suburban school setting, I have only had one pet fecal sample come out positive (Coccidia). That was a sample collected the morning of class from an abandoned poo pile in the student’s yard. Honestly, the HUNT for parasitic evidence is fun – you really don’t want a positive result. That means the pet *likely* has a parasite.

Coaxing 2-5 cc of horse fecal matter into the collection tube.

Extensions / additional activities pre or post lab:

References to above

If you want the “real thing,” these are two types of fecal collection chambers on the market.

(1) – Ordering info for collection chambers – the “official” fecal collection chambers aren’t needed. A disposable conical lab tube (with lid) would be fine. However, if you want the “real thing,”

(2) – Identification chart: You might be able to obtain some charts through your local veterinarian OR make your students create a chart as a pre-lab (described in extension activities). I have found that Pinterest has several charts, found through a quick Google search (make sure you’re looking at companion animals, not just goat parasites):
https://www.google.com/search?q=veterinary+parasite+identification+chart&safe=active&sa=X&rlz=1C1GCEA_enUS762US762&biw=1242&bih=568&tbm=isch&source=iu&ictx=1&fir=0UCOnjmsSngtCM%253A%252CiMdeL3n_rdcDwM%252C_&vet=1&usg=AI4_-kT8I1O40h9HcKINDu9L7M-xel3U9Q&ved=2ahUKEwiugub5osbhAhXLs54KHQJrCwsQ9QEwAHoECAkQBA&scrlybrkr=11de4934#imgrc=3ShBbbz1RdtkaM:&vet=1

(3) – Ordering info for Sheather’s Fecal Float (sugar) Solution – you can mix this up yourself with sucrose and dWater. The exact specific gravity should be 1.27. The solution is described in Dr. Dryden’s article below (Magnesium Sulfate solution can be used instead of sugar, also described in the article). Alternatively, you can order the solution pre-made.

  • Dryden MW, Payne PA, Ridley R, et al. Comparison of common fecal flotation techniques for the recovery of parasite eggs and oocysts. Vet Ther2005;6(1):15-28.

4) – “Eggs” are used generally in this article. Depending on the parasite, students may actually be looking at/for the actual protozoa (Giardia trophozoite), the egg (tapeworm or hookworm oocyte) or cyst (Giardia cyst – tenacious temperature tolerant oocyte manifestation).

(5) – Possible companion animal parasites include: Alaria (intestional flke), Spirometra (taepworm), Paragonimus kellicotti (lung fluke), Platynosomum fastosum (liver fluke), Dipylidium canium (flea tapeworm), Taenia species (tapeworm), Capillaria aerophila (lungworm), Trichuris vulpis (whipworm), Uncinaria stenocephala (hookworm), Ancylostomas species (hookworm), Physaloptera species (stomach worm), Toxascaris lonina (round worm), Toxocara cati (roundworm), Toxocara canis (round worm), Baylisascaris species (racoon roundworm), Strongyloides larvae (threadworm), Giardia trohphozoite, Giardia cyst, Isospara species (Coccidia), or Toxoplasma gondii.

Additional resources:

3D Printing Authentic Fossil Samples

I had some biology students developing a guest lesson on fossils, and we got to thinking about how we could put real fossil examples in the hands of students. Here are our standards:

Sure we can find some fossil examples on Thingiverse, but what we can find are somewhat hard to predict, their organization does not have a scientific basis, and their origin is not always clear (not to mention concerns about the company practices of the owners of the platform). I wanted to look elsewhere for better models provided by organizations more aligned with my professional values.

I found GB3D Type Fossils. Here is who they are and what they do (from their own website):

“The GB3D Type Fossils Online project, funded by JISC, aims to develop a single database of the type specimens, held in British collections, of macrofossil species and subspecies found in the UK, including links to photographs (including ‘anaglyph’ stereo pairs) and a selection of 3D digital models.”

You can search at their home page using appropriate scientific names for the samples you want to find. Check it out:

From the search results you can find actual research samples, linked to their papers and researchers. It comes with high-res photos and 3D scans of the sample.

3D scans are still pretty finicky, so you’ll want to groom the model before you go to print it. We’re going to bounce back and forth between a couple programs to get this bryozoan ready to print:

  • Meshmixer – Processing software from Autodesk, for fixing model errors and generating supports.
    • Free, but not open source.
  • Slic3r – Slicing software for converting models to 3D printer instructions.
    • Free and open source

Step 1: Make the scan a “solid” – Meshmixer

This will take the crazy scans you get from researchers and forcibly make it something slicing software can interpret.

  • “Import” the .obj that you download from GB3D and extract from the ZIP file.
  • “Transform” the model and drag it up and over so it’s positioned in the middle of your build plate.
  • “Make Solid” and let the computer fix this nonsense.
  • “Export” the model as an .stl

Step 2: Orient the model – Slic3r

This will take your (probably wonky) model and orient it for printing. You might be able to skip this step, if you don’t need to rotate your model. This example needs it, because the flat bottom is not actually aligned with the build plate.

  • “Add” your recently exported .stl of the fossil.
  • Select the fossil model, and click “Rotate to Face” (see below)
  • Click on something that should be the bottom.
    • Even apparently flat surfaces are probably not truly flat. We need to fix this, so don’t be fooled.
  • “Export STL” and you can overwrite your previous .stl with this new file.

Step 3: Perfect the bottom – Meshmixer

This will smooth the rough bottom surface, so our print will actually adhere to the build plate.

  • “Import” the recently updated .stl file of the fossil from Slic3r.
  • Use “Plane Cut” to chop off the very bottom surface (see below)
  • OPTIONAL – If your fossil requires supports, now is the time to add them.
    • Find Meshmixer supports under “Analyze” → “Overhangs”
  • “Export” the finalized model as an .stl

Step 4: Print – Slic3r (or whatever)

The model is done and you can now print using whatever your preferred printing workflow may be. Slic3r does a good job creating Gcode, and a simple extension can convert it to .x3g if your printer requires that.

Don’t forget OctoPrint – an awesome Raspberry pi printing option


From here you can go give your students fossils to analyze! I imagine asking them to paint the samples to highlight what they think they are seeing could be cool. They could also color-code homologies across multiple fossil types.

How else could you use fossils in class? Share your ideas and photos of your awesome prints!

In My Classroom: Trying to make Cellular Respiration & Photosynthesis suck less.

Hey all! While having coffee with KABT President Rhodes on this lovely Presidents’ Day, she suggested I share this activity that I did with my AP Bio students recently.

If you know me at all, then you probably know I don’t particularly care for teaching photosynthesis and cellular respiration. Yes, they are important topics, but I find them to be incredibly dull. And it shows in my classroom. This year, I started my energy unit in AP Bio by saying “This will suck, and I’m sorry, but we just gotta do it”. Bad teaching, I know.

HOWEVER, there was some exciting research that came out recently from Paul South at the U.S. Department of Agriculture. His team found a way to streamline photorespiration in tobacco plants, which increased plant growth by 40%. If I could get excited about this topic, then I figured my students might as well. I also saw the perfect opportunity to introduce scientific articles into my class and to let my students struggle with understanding primary literature.

I started by giving my students the article from Science (You can read it here: http://science.sciencemag.org/content/363/6422/eaat9077)

I used this guide from Rice to help my students understand the research and to break it down into manageable chunks. http://www.owlnet.rice.edu/~cainproj/courses/HowToReadSciArticle.pdf

After we dissected the article, we had a Socratic Seminar in class to discuss the research. It was cool to hear my students speak about statistics, evolution, GMOs, and, yes, cellular respiration/photosynthesis in a meaningful, authentic way. Socratic Seminars are new to me and they’re a tool I’m hoping to use more often. My students seem to learn a lot from each other and are engaged in the discussion. To help facilitate the discussion, I gave my students a handful of open-ended questions to discuss, such as “Why do you think Rubisco uses O2 in place of CO2 about 20% of the time? What does this suggest about the plant’s evolutionary history”, and “Why does increasing plant biomass matter to humans?”.

Anyway, that’s it! Socratic Seminars! Yay! Reading primary literature! Yay!