Thursday, December 24, 2015

Happy Luxmas 2015!

Well, as most people know, I am something of a #MicrobialSupremacist™.  That is just how I roll, microbially speaking.

So my holidays are required to revolve around microbiology.  And this is a good thing, not a "yuck" thing.

For example, I love teaching my micronauts that bacteria can make ice form.  Yes!  Pseudomonas syringae makes a protein on its surface called (rather uncreatively) the ice nucleation protein.  Ice nucleation protein, as its name suggests, catalyzes ice crystal formation in a chain reaction.  I have written about this before, with many informative references.

This video (from my Fall 2015 Microbiology course at the University of Puget Sound) shows supercooled deionized water. One drop of Pseudomonas syringae and...well, see for yourself.

This protein is used in snowmaking machines, by the way, and is commercially called Snowmax.  So yes:  you are skiing the microbial slopes, friends!

I also enjoy using reporter gene fusions in E. coli to create colorful displays.  I used GFP and RFP to draw this festive bit of Petri dish art.

Now, again, anyone who knows me understands I have a mania for bioluminescence.  So I naturally have created some Luxmas™ (lux for light production) displays on Petri dishes, using Photobacterium leignothi as "living paint."

Finally, my brilliant and artistic mathematician wife Dr. Jennifer J. Quinn (that's right:  I am married to "Dr. Quinn, Mathematics Woman") is SO tolerant of my microbiological mania.  She allowed me to put up a microbial Luxmas tree year round.  Here it is tonight.  It is festooned with a blazing Shewanella from the Mudwatt people, has various GiantMicrobes on it, and features beautiful Petri dish ornaments from the fabulous artist Michele Banks.

And here is my Luxmas Tree with bioluminescent ornaments.

Finally, Dr. Quinn helped me to create this wonderful time-lapse video a few years ago.  I adore it.

Thus, I wish each and every one of you a wonderful Luxmas, with much microbiological merriment.  I salute you and your microbiota!

Wednesday, December 23, 2015

Microbiology and Creative Extra Credit

Once again, the semester has gotten away from me!  I have many things to post over Winter Break about the past frantic yet rewarding semester, but let me start with this tradition of mine.

During the past few years, I have been encouraging students in my freshman level "Introduction to Cell and Molecular Biology" and junior/senior level "Microbial Diversity" courses to explore course material via creative approaches.  I have posted about these efforts in previous blog posts, such as this or this.  

I do this via an extra credit "creative" assignment.  I scaffold it as follows:  (i) the student must get verbal approval from me about their idea, (ii) the student must turn in a one page description of their project for review, and (iii) turn in their project!  The scaffolding serves several purposes.  First, I am able to ensure that the idea sortofkindof matches course material. Often I discuss the approaches and directions of the proposed project.  More importantly, I am able to work with the student to make sure that the proposed project doesn't eat into their study time (I don't know about you, but when I was a student, I would do nearly anything but study as finals approached:  clean my room, write fiction, fight with loved ones...).

This year's microbiology class has produced some interesting creative approaches to the field I would like to share with you, ranging from the very serious to the whimsical.  I'm proud of my micronauts, as usual.

First, Macaulie decided to make microbially themed cupcakes, as can be seen here.

Strangely, the STD ones were the last to be chosen.  Hmmm.  At the same time, I was pleased to see basic course concepts reinforced multiple times.  And tastily, too.

One of the things I ask my micronauts to think about is how microbes are portrayed in the media---versus the MicrobialTruth I preach in my class.  This led Cheyenne and Taylor to create these microbially relevant magazine covers.

I did spend quite a bit of time chatting about antibiotic resistance, so this makes sense.

I take no responsibility for the beer references, but we did a lab exercise with lactic acid bacteria.

Well, of course.

I guess that the lab exercise isolating Sporosarcina from areas that dogs, well, watered has stuck with them.

Brian has had some interesting results in lab brushing his beard onto Petri plates with various media this semester.  Here is just one example.

Um. Microbial diversity reigns.

So his "beard-ome" artwork was expected...and fabulous.

Mariko loves Disney movies, and decided to share a "Whole New (Microbial) World" with the class.

A student from my class who does not wish to be named created something quite lovely here---a different view of microbial bullying and antibiotic resistance.  I was VERY impressed with the approach, creativity, and sentiment!  The student should be very proud.

One of my favorite historical figures from microbial genetics is Jacques Monod.  He famously once opined that "What is true for E. coli is true for elephants," making clear the centrality of biology. So Kailee created this is honor of that MicrobialTruism™.

One of the things that has long bothered me about MattersMicrobial is the constant drumbeat of negative PR in the popular (and sometimes scientific) press.  There are so many #SwabStories where folks swab a particular area and find it---surprise, surprise---covered in microbes.  It's a microbial world, and my micronauts and I just shake our heads at the headlines and false-scary pronouncements. Here are two video approaches to that problem.

First, Hailey became a #MicrobialMythBuster.
Next, Reilly and Madison created #ClubMicro.

Best way to keep microbes away from clubs?  No people!

Olivia created a story based on "Cinderella" that she called "Bacterella."  Here are some images from her informative and amusing creative project.

What is interesting here, again, is how many concepts from class appear in this microbiologically themed fairy tale.  There are many ways to learn, indeed.

Emily and Emma had a plan for this particular assignment. But they would not tell me the nature of their plan, assuring me that I would "like it very much."  I told them that they still needed to hand in their one page summary of the project.  So they did.

Um.  I didn't ask if they had relatives in the NSA.  Seems likely.

Anyway, what Emily and Emma brought was interesting.  Each person in class got a Petri dish.  There were several choices.  Here was mine.

Inside the Petri dish was a booklet.

The booklet had good information.

Did I mention the stickers?

So I did indeed like it very much.  Don't you?

Last, but certainly not least, was a fun video by Olivia and Ruth, about bacterial bioluminescence and lovely, lovely quorum sensing. Notice the symbiotic aspect!

Some folks deride these kinds of projects.  I don't.  The reason? Again, there are many ways to learn.  We honor diversity in education; why not diversity in approaches to learning?  This is but another arrow in the quiver of our pedagogical strategies, I think.

I have found that people learn best when they have "ownership" in the process.  And having a carefully chosen "extra credit" creative project can genuinely reinforce concepts from a course in a way that will be long lasting and memorable (instead of filling in a blank on an exam).

I am proud of the efforts of my micronauts, and I hope you are as well.

Saturday, October 31, 2015

Time for a #MicrobialHalloween and a #ParasiticHalloween

Now, anyone who knows me knows that I simply adore Hallowe'en. I always have.

Yes, I spread bioluminescent bacteria on Petri dishes, and then inserted them into a pumpkin.  A #MicrobialJackOLantern.
So it should not be a surprise that I like to incorporate this special holiday into my classes, and have a long history of doing so. Today, Saturday, is Hallowe'en.  But even so, my Microbiology students on Thursday, and my Symbiosis and Parasitism freshmen writing students on Friday, participated.  I would like to share their creativity and humor with you.  Learning can take many forms, I have found.  Plus it is fun!

First, one of my #Bio350 students shared their own #MicrobialJackOLantern with me.

Nothing wrong with some streptococcus and a microscope on a rainy Hallowe'en.  Am I right?  Here are some close ups.  I think that these were made by Brian in my class.

First, a Streptococcus-O-Lantern:

Then, a MicroscopicPOV-O-Lantern:

And another student in my #Bio350 course,  Ruth,  just made an interesting pumpkin---a #BacteriophagePumpkin?  A #PhageOLantern?

Now, I generally don't dress up for Hallowe'en any more.  This year was an exception, as you will see a bit later.  But I encouraged my #Bio350 micronauts to let their OMG™ (overwhelming microbial greatness) show itself this holiday.  And some of them did precisely that!

Here are some of my micronauts in #MicrobiallyThemed costumes.

Then, a video.

Let's view what we are seeing here.  

Madison would love to be a "genomic islander."

Kailee and I agree that calling a tool for spreading microbes on a Petri dish a "hockey stick" does a disservice to the sport.  So she expressed that well, and in competitive spirit.

Olivia decided to show her bacterial side in her outfit.  Yes, the blue flagella say it all.

Here is a close up.  I adore seeing transcription and translation taking place as a creative exercise!

Macauley decided for a more minmalist approach, depicting Serratia's lovely prodigiosin, and inexplicably carrying sriracha sauce.  The color?  Maybe the antimicrobial effects?

Hailey tried out a "Two Face" approach to microbiology, as you can see.  She even burned herself with a hot glue gun to promote her craft.

Brian honored his commitment to sterile procedure by depicting that goal via costume.  I don't know about the white hair.

Emily and Emma were inspired by a recent discussion of riboswitches in class, and became "ribos-Witches."  Very creative!

Finally, Cheyenne and Taylor created a two part costume showing the medieval view of plague, and a plague victim.  The makeup was impressive.  And fits in, I think, with some of our zombie interests in popular media these days.

Very nice!  But what about me?

Another one of my obsessions these days is the small but mighty tardigrade.  My long suffering wife Jennifer Quinn has allowed me this obsession, as she does with my microbial tattoos.  After all, they are much cheaper than red sports cars.

I have enjoyed watching them under the microscope.

Unsurprisingly, I tend to collect tardigrade toys of the plush variety.

And even of the 3D variety.

My wife in fact built me a tardigrade table for my birthday this year.

And even commissioned the great Brian Mock to create a tardigrade sculpture for me.

Yes, I seem to have a problem.

So it should not be a surprise that when I decided to dress up for Hallowe'en for my classes, I would choose a tardigrade...and its associated microbiota.  Here is an explainer.

And a close up of the truly fabulous mask Jennifer Quinn made for me.

I also received a nice surprise from one of my #Bio350 micronauts on Friday:  my very own #MicrobialJackOLantern with artwork of the logo for this year's microbiology course.  

As you can guess, I was very touched by this particular #MicrobialHalloween!

My other course this Fall is my freshman writing seminar revolving around symbiosis and parasitism.  So a #ParasiticHalloween sounds grand.  Several of my students dressed up (and I did, too, as my Disco Tardigrade).

In class on Friday, we watched "The Host," an old episode from "The X-Files," about a mutant giant fluke parasite (very appropriate given the course topic).  I also brought gummi worms for the full effect.


Theo is quite interested in parasites in the fossil record, so I shouldn't be surprised at his costume.

Cotton, on the other hand, has an deep fascination with sharks. This appears to be a "cookie cutter shark."

Carmen and Genevieve had a costume that, while not related to symbiotic associations, represents one of my favorite movies.  Can you guess what it is?

Braith did a pretty awesome job depicting a banana slug.

And I have to admit, Mary had perhaps the most horrifying costume of all.

Get it?  Sigh.  This one is less pointed than in earlier years, at least.

But when it comes to humor, I think that JT and Lauren got the greatest laughs with a highly appropriate costume that cost next to nothing.  Such creativity!  Here is the video.

You see, they are depicting the Schistosomiasis parasite, seen here.  The larger male has a channel in which the female attaches.

You can read more about these seemingly "loyal" parasites, and the serious diseases they cause, here.

So in all, it was QUITE the Hallowe'en.  I hope yours was as frightening fun as my own!