Biotech Virtual Learning – Agarose Gel Electrophoresis

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Taking lab courses that are only VIRTUAL requires some creativity on the part of the student if you really want to prepare yourself for a job. To review agarose gel electrophoresis, I used a FREE VIRTUAL SIMULATION.

Praxilabs.com simuation guides you through the steps of separating DNA fragments by size via electrophoresis.

You begin with preparing the agarose gel by combining the gel powder with TAE buffer, heating and cooling it, and then adding a dye. I like that the activity includes setting up the electrophoresis device along with having to enter the voltage before running the experiment.

These simulations do have their challenges – absolultely no moving forward until you properly cap the bottles and discard your used pipette tips! Once you figure this out, the simulations run a lot more smoothly.

Once the device is set up, you prep the DNA samples and pipette them into the wells of the gel tray. I got stuck for a bit with the requirement to put a dark object underneath the gel to make it more visible so I had to go to the YouTube video to figure out what to do there.

The simulation ends with you using a UV Transilluminator to see the separated DNA fragments. However, the lab ends rather abruptly with only brief glimpse of the stained fragments. That was disappointing! But otherwise, I highly recommend checking it out for yourself.

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Learning Biotech in a Pandemic!

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Trying to change careers into biotechnology during a pandemic has its challenges – the biggest that my in-person lab courses are completely virtual! I found that it was really necessary for me to supplement my coursework with my own investigations into the basic laboratory techniques that I would otherwise be performing in-person if the college would allow it. I am sharing how I organized my own learning as it may be helpful to others in my situation, so I’m posting the resources I am using for each technique.

Virtual Learning about Protein Electrophoresis (SDS-PAGE)

There are a lot of videos on YouTube that probably do a great job of explaining protein electrophoresis, but I can’t watch them all and so I had to just choose (eeny-meeny-miny-moe style). I ended up using the videos of two sources for most of my lab education: YouTube channel “Biomedical and Biological Sciences” and “Bio-Rad Laboratories”. I find the videos to be well-made, completely on-topic and not too long for my attention span!

Videos:

1. The principle of SDS PAGE-a full and clear explanation of the technique and how does it work – – explains how this type of electrophoresis separates proteins by molecular weight. Explains separating and stacking gels, how to prepare the protein samples with denaturation buffers, the key role of SDS detergent and the other components of the buffer.

2. SDS-PAGE of Fish Muscle by Bio-Rad – shows all the steps for setting up the electrophoresis device and removing the gel and moving it to a staining tray.

Virtual Simulation:

Praxilabs.com – Protein Electrophoresis (Polyacrylamide Gel Electrophoresis – PAGE). This simulation is NOT free, but I purchased a one-month subscription for only $9.99 so I could do 8 different simulations.

Simulation Details: This simulation has me prepare the polyacrylamide separating and stacking gels, load the gels, fill the device with electrophoresis buffer, add loading buffer to each sample and then fill the wells with the protein standard and the four samples.

It begins with prepping the glass plates, and includes using vortex mixers and water baths, along with the electrophoresis tank and power supply.

OPTIONS:  You can see what the simulations are like in two ways: 

1. Video versions of many of their simulations are on YouTube. These are really helpful in case you get stuck on a step. I could not find one for this exact simulation, but there is one for Agarose Gel Electrophoresis.

2. The simulation for this technique is also FREE at praxilabs.com so try it out there too!

Share the NASA/SpaceX Crew Dragon flight and Artemis mission with your students

I made this Google Slides presentation to make sure my middle school students know about the historic May 30 flight of American astronauts on the first commercial flight to space. Also, many people are not aware of NASA’s Artemis program – the new mission to put people on the moon in 2024 with the purpose of eventually sending people to Mars!

Our students today are the Artemis Generation, but they don’t know it yet! Educate your students about it with this free presentation…

Click on the Image to go to the slide show.

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I’m loving this… Virtual Circuit Builder!

With DISTANCE LEARNING I wasn’t able to do the hands-on electrical circuits lab with my wonderful 8th graders so I had to come up with another way for them to learn the basics. A web search brought me to this really cool VIRTUAL circuit builder that does NOT use Flash – which is awesome because Flash is no longer supported by Chrome.

Here’s a brief video of how this Phet interactive works.

Pros:

  • easy to learn how to use
  • can build series and parallel circuits
  • there are a few different components to experiment with such as the light bulb, resistor and switch
  • can experiment with how adding and subtracting components affects resistance.
  • multiples of all of the components can be added, such as adding two batteries to increase voltage
  • the anmeter is fun to play with!
  • you can view the parts of the circuits in symbols to practice with engineering pictograms

Cons:

  • There are no particular directions so if you want to be sure your students really learn what you want you’ll need to come up directions for them.

Don’t have time to design an activity? No sweat – use mine!

Internet Activity:  Build Circuits Virtually!

My worksheet guides students in
constructing series and parallel
circuits using the Phet interactive.
No prep required – just have
students watch the video above so
they know how to attach/detach
components.

Unit Confusion SOLVED!

Many of my students struggle with solving basic physics formula, and most of all, in understanding which units go with the answer to the question being asked.

Is this familiar to you… The question ask for “HOW LONG does it take for the skateboarder to roll 25 meters while moving at 2 m/s?”, and the student answers 12.5 m/s!!!

Students MIGHT use the right equation (time = speed/distance) , but the answer nearly NEVER has the right units – the question is about time or distance and no matter what the student puts “m/s” as part of the answer! Mind boggling to one degree, but this is all new for them and it’s normal to have trouble applying old skills to new problems.

PROBLEM (nearly) SOLVED!

speed square

The first formula is use in my 8th grade physics class is the equation for speed (or velocity). I have found that by guiding my students through the process of choosing the formula, writing the formula, and forcing them to pay attention to the units involved through this graphic organizer, greatly improves their success!

See MORE about SPEED SQUARES here.

speed squares cover

I also have created DENSITY SQUARES and I’m working on making resources for all of the formulas I use in my science classes.

3D Cell Models – Go beyond basic plant and animal

I wanted my 7th graders to make cell models this school year, but I didn’t want everyone just making the same thing so I searched the internet for a variety of labeled pictures so that the students could make a variety of cell types.

Bone Cell
Amoeba Cell
Euglena – single-celled Protist (with both plant and animal characteristics)
Plasmodium Cells – protists that cause Malaria
Fat cells
Paramecium – single-cell protist
Budding Yeast Cell
Plant Cell
Nerve Cell

Send me an email at generationscience3@gmail.com if you’d like more information about how I did this activity, including a rubric.

Mineral Lab for a Tight Budget

If you don’t have any supplies for studying minerals, my experience suggests that the following mineral specimens and supplies provides you with the least amount of materials you need for hands-on activities.

Mineral Samples

I chose these three because you get a variety of mineral properties for low cost. Talc is a cheap replacement for graphite and fluorite can work in place of hematite for a middle level hardness, although its luster and streak are the same as quartz.

MineralHardnessStreakLuster
graphite1.5-2blacksubmetallic
red hematite5-6red-brownearthy
quartz7whiteglassy

Additional Supplies

  • white streak plates (Unglazed porcelain tiles) – sets are about 10 bucks
  • pennies
  • nails
  • steel butter knives (if allowed)

With these supplies your students can make observations and practice testing minerals for streak and hardness.

Need a Lab Worksheet?

Level Up Your Ecology Lessons with Real-World Food Webs

Bats are birds. Snakes eat grass. Insects aren’t animals. Nature knowledge seems to be at an all time low among my own students.

In response, I designed two food web activities to simulate connections between a diverse set of organisms that actually interact in nature.

Eastern U.S. Woodland and Field Food Web

The 12 cards look like these below – sun, 4 plants and 6 animals

food web cards

The cards can be used for many activities, such as constructing this food web:forest food web cover page 2

Both activities includes directions and worksheets for students to..

  1. Construct a food web
  2. Construct a food pyramid
  3. Classify by type of food source (heterotrophs, carnivores, etc.
  4. Classify by type of organism

North American Atlantic Coast

ocean food web
ocean food web COVER PAGE 5
woodland food web cover pageocean food web COVER PAGE 1

 Follow up with a food web research project.

Students construct their own using a great online resource that provides predator/prey information for a variety of forest (Eastern, mid-Atlantic) organisms.

Are students off-task and unruly during labs and activities?

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Hands-on learning is an important part of science education, but it can be miserable for you and for many of the students if your class lacks lab behavioral expectations that are taught and enforced.

At the beginning of the school year I take the time to explicitly teach and model behavioral expectations for working in a group and/or lab activity. Why this is essential:

  • students begin the year with an expectation of an orderly and safe classroom
  • students begin the year thinking that my class might be better than what they usually experience
  • students cannot claim that they do not know what I expect when they are unruly and off-task
  • I will be much happier and more motivated to engage students in hands-on learning

Better Science Teaching Task 1: Teach My Expectations

  1. No interrupting members of other groups – no talking to or bothering anyone in a different group. This disrupts the lab and gets lots of people off task quickly.
  2.  Stay on topic – fooling around and talking about other things results in delays in work being accomplished and diminishes the learning opportunity for everyone involved.
  3.  Use lab supplies appropriately only – any lab supply, including the Slinkies and toy cars, are for scientific use as allowed in the lab. Students will not respect the science supplies if this expectation is not fully expressed and enforced!
  4.  Stay at your station unless otherwise directed. Students cannot just wander around at their leisure. Doing so leads to misbehavior so be clear about this and enforce it!
  5.  Follow clean up procedures (as directed). As we often do in life, I had to learn the hard way about this important procedure. Students need clear instructions on what they are expected to do for clean up.

Teach, demonstrate and practice lab rules and procedures. Believe in their power to promote learning (they do NOT diminish fun, they stop chaos!). Rules are meaningless without (emotion-free) enforcement.

Better Science Teaching Task 2: Enforce My Expectations

There are two parts to me enforcing lab behavioral expectations:

  1. All rules are enforced for all students at all times. The is the only system that is fair and that is effective. Much of my success with lab/classroom management comes from the wonderful work of smartclassroommanagement.com. Check them out if you have a hard time believing in the educational power of enforcing your rules.

  2. Students earn a Lab Performance grade for any substantial group activities that promotes following rules and collaboration.

My Lab Performance Rubric

  • each student begins with 10 points – 2 points per category

  • categories are:rubric cover image
    • Disrupt – lose points for disrupting other groups
    • Teamwork – lose points for poor collaboration
    • Supplies – lose points for misuse
    • Effort/focus – lose points for being off-task
    • Completion – lose points if did not complete the activity as expected

Save yourself time and make labs more productive and fun (for everyone). You can purchase this editable rubric for only 99 cents!

Students are told that they are being graded and each category is explained. They understand that they begin with 10 points and lose a point (or sometimes 1/2 a point) when they break a lab rule or are showing lack of effort and teamwork.

Should I give a warning first? My recommendation is to not give a warning before taking off a point. I have found that the best way for students to take me seriously regarding my expectations is to for me to be serious about my behavior rubric. As soon as I see an off-task behavior I quickly (but respectfully) point it out and take away a point. This usually results in the particular student staying on-task the rest of the time and everyone else getting the message.

So, my recommendation for Better Science Teaching – Set Expectations – Teach Expectations – Enforce Expectations