Monday, September 1, 2014

Catching Up, Part I: Meeting with Former Research Students at ASM in Boston in May.

You know, I keep meaning to post more often.  Then, as John Lennon famously observed, "Life is what happens when you are busy making plans."  So I am trying to post in a more regular fashion. Lots and lots to do, as is true for most of us; life is a juggling act. 

I have two courses this Fall semester:  one is my normal and much beloved Microbiology course (which I continue to want to call "Microbial Diversity," since I only get the one chance to promote Microbial Supremacy™ to students) for juniors and seniors, and a freshman "writing seminar" on Symbiosis and Parasitism (yes, the latter is part of the conceptual Venn diagram of the former, but many students don't yet know that).  So I expect to write quite a bit about these two courses as they unfold with the awesomosity I expect from our students here in Tacoma!

In the meantime, here is a post I meant to write a while back---I have such pride in my former research students, and I enjoy watching them develop their careers and lives.  I shine by their reflected glory!  

Anyway,  I was VERY happy that six of my former undergraduate students had the time to visit with me at the American Society for Microbiology General Meeting in Boston, last May.  I took them all out to dinner in Boston, and it was truly great to put them all at the same table, ranging across a lot of years, to swap stories and successes and challenges.  I have seldom felt prouder of my students, and more humbled by what I do for a living.

Here is the lineup:



From left to right, here are the former students, and what they are currently doing now.

  • Sarah Studer (Class of 2003, Occidental College).
  • Paula Welander (Class of 1998, Occidental College).
  • Desiree Baron (Class of 2001, Occidental College).
  • Andrew Collins (Class of 2007, University of Puget Sound) 
  • Morgan Giese (Class of 2014, University of Puget Sound) 
  • Kim Dill-McFarland (Class of 2011, University of Puget Sound)

Here is what each of them are currently up to:

Sarah is a science policy fellow in DOE's Fuel Cell Technologies Office, in the Office of Energy Efficiency and Renewable Energy (formal title:  EERE Postdoctoral Fellow). She provides expertise for biological hydrogen production projects in her division.  Sarah earned her PhD with my friend and MicrobialHero™ Ned Ruby at the University of Wisconsin Madison.  

Paula is an Assistant Professor of Environmental Earth System Science (and by courtesy, in Biology) at Stanford University. Her research team studies the biosynthesis and function(s) of molecular fossils (biomarkers) in bacteria. Paula earned her PhD with my colleague Bill Metcalf at the University of Illinois at Urbana-Champaign and did postdoctoral work with Dianne Newman at MIT (now back at Caltech).  Here is Paula's laboratory website.

Desiree is a Research Associate for Daryl Bosco at the University of Massachusetts Medical School, studying the interface between cell biology and amyotrophic lateral sclerosis. She earned her PhD with Kent Hill at UCLA, followed by postdoctoral work with Stephen Doxsey.  

Andrew is a fresh new postdoctoral fellow at the Forsyth Institute in Boston.  He will be working with Floyd Dewhirst, Gary Borisy, and Anne Tanner, studying the uncultured and unknown microbiota of the human mouth.  He earned his PhD with my friend Spencer Nyholm at the University of Connecticut Storrs.

Morgan is a fabulous worker looking for a biotech position in the Seattle area at present. Whoever hires her will be lucky indeed. Incidentally, here is a photograph of Morgan at her poster during the General Meeting.  I received some great reports about her professionalism while people chatted with her about her research...and I was not surprised.


Kim is a graduate student at the University of Wisconsin Madison, working on her PhD with Garret Suen.  Kim has worked on the microbiomes of a number of biological systems with Garret, ranging from hibernating squirrels to sloths (I'm told) to dairy cows.  

The dinner was a lot of fun, of course.  I had T-shirts made for my students (and it was hard to fit everyone into the photo, as you will see!), and gave everyone appropriate magnets to commemorate the event.  Here is the magnet.



I think the "Bdello Bdinner" is funny.  Adding "Bdoston" to may be over the top.  Oh, well.

This is the best I could get for a group shot in the T-shirts.  The restaurant was crowded.




Since Kim was left out of that shot, here is another photograph of her in her T-shirt. Please notice the FABULOUS mini-microfuge tube earrings.  They fluoresce under UV light, by the way.  Kim is stylish that way.



Embarassingly, I messed up some of the graduation dates on their T-shirts.  Sigh. Though I am often (as my father would put it) "a day late and a dollar short," my heart is in the right place.  Gulp!

A wonderful evening was had, and I am grateful to each and every one of these scientists for making some time to visit with me and bring me up to date.

By the way, I was delighted beyond words that two of my former undergraduate research students, Kim Dill-McFarland (mentioned above) and Jillian Waters (Class of 2008, University of Puget Sound) were at the most recent International Society for Microbial Ecology meetings in Seoul, Korea later last summer.  Here is the "twitter proof" that they were there together (courtesy of the very kind Kim).



After leaving the University of Puget Sound, Jill Waters earned her PhD at the University of Illinois at Urbana-Champaign (I have sent four undergraduate students there for PhDs so far!) with the late, great, Abigail Salyers (one of my professors at the Woods Hole Microbial Diversity Course, and a true MicrobialHero™ of mine), and is currently working on a postdoc with the quite fabulous Ruth Ley at Cornell.  Jill always wanted to be (her words) a "poop scientist."  

She is living the dream!

Anyway, there are lots and lots of days where I feel overwhelmed, buried, unsuccessful...fill in the negative blank.  But then I look at these great success stories.  While I think each and every one of them has earned every bit of their accomplishments through their brilliance and hard work, I like to think I had a bit of influence here and there.  Their reflected glory feels pretty nice.

It makes my workdays feel worthwhile, I must tell you.

Next year's ASM General Meeting is in New Orleans.  Perhaps there will be another Bdello Bdinner there, as well.  I certainly hope so!

I'm proud of you all!

Wednesday, July 30, 2014

Summer Research and Lab Themed Desserts!

I have long been super, super interested in bacterial predators like Bdellovibrio, which attacks and consumes a wide variety of Gram negative prey bacteria.  My first microbiology course at UCLA was taught by the late, great Syd Rittenberg, who was then one of THE authorities on the predator.  It's no wonder that the microbe always fascinated me.

Sadly, due to my own struggles in academia, and my position in the Trophic Web of Science at a small undergraduate institution (and without grants at present), I cannot make very big contributions to the field.  There are some true giants in "Bdellovibriology," like Liz Sockett, Edouard Jurkevitch, John Tudor, Henry Williams, Daniel Kadouri, and Eckhardt Strauch.  There are few others, though some friends of mine are starting in the field!

Bdellovibrio is not easy to work with on a daily basis, nor to unravel genetically, but I adore the wee beast.  I wrote a paper long ago about predatory microbes, and my lovely and brilliant bride Jennifer Quinn drew me the life cycle of the ravening microbe.



Many other more detailed or less stylistic depictions exist, but I like Jenny's.  There has always been, and remains, a great deal of mystery about Bdellovibrio's activities, which lead a former classroom student of mine at Occidental College to draw this great "Borg" view of the tiny predator!  Prey cells WILL be assimilated, after all.



When I took the life-changingt Marine Biological Laboratory's "Microbial Diversity" course at Woods Hole in 1996, the great microscopist Tom Pitta took some marvelous photomicrographs for me of Bdellovibrio attacking E. coli, seen here:



And a feeding frenzy by Bdellovibrio against E. coli here (cue the theme to "Jaws," please).




While I was in Los Angeles, I did some fascinating work with a fine scientist, Megan Nunez, who took some truly awesome atomic force micrographs of Bdellovibrio attacking a biofilm here.



And here at Puget Sound, an undergraduate student named Rob Chamberlain took this great electron micrograph of Bdellovibrio attacking Shewanella




Which brings us to today's festivities!  The Summer Research Program here at the University of Puget Sound is a great experience for our undergraduates.  They get a chance to really work hard on a research problem, without those pesky classes to get in the way. But research students need to blow off some steam from time to time.  One way is by fun events---in this case, our famous, delicious,  and totally fabulous "Lab Themed Dessert" competition.

And make no mistake, the competition is intense!  Students struggle to create tasty desserts reflecting their research projects or lab topics.  I have been fortunate in having Madison Cox in my laboratory, who is a great student, hard worker, and a fabulous baker.  Last summer, while she was working (as she does this summer) on the cloacal microbiota of the Striped Plateau Lizard (we have found some interesting aspects of these microbiota/communities, as seen here), Madison entered the Lab Themed Dessert competition for the first time.  

Madison won "Best Tasting" and "Most Aesthetically Pleasing" awards last summer for this masterpiece (note the swabs, inoculating loops, microbes and, um, back end of the lizard---as a cake).



This year, Madison decided to honor Bdellovibrio, by depicting the predator attacking and invading hapless E. coli!




A view to the front shows Madison's attention to anthropomorphic detail.



I got a kick out of watching Bdellovibrio invade the periplasm of the prey cell, as seen below.  The prey cell does not seen unhappy about this unfortunate process, I note. Note also the invading cell visible through the outer membrane of E. coli.



One of my other research students, Katie Frye, wrote up a nice summary of the inspiration for Madison's cakey creation. Collaboration abounds!



Madison did have an interesting approach to depicting the petite predator cells!  No, Bdellovibrio does not possess eyes nor teeth, but it is undeniably cute.



And here is my summer lab crew.  Clockwise from far left: Katie, Young Tia (our high school volunteer), Madison, Austin, and Cheyenne.



Since Tia doesn't like her photograph taken, we forced the issue with great enthusiasm, as you can see.  Never let your labcrew know your weaknesses.  Ever.  


Madison was very proud of her creation as she deftly dissected it for the crowd of ravenous summer research students.



It's well known that Bdellovibrio does not attack human cells.  But Madison seems not so sure.




Katie shares Madison's concerns.



Here is Madison receiving her "Most Creative" award from Dr. Leslie Saucedo in my department (in charge of the Summer Research Program).



Aaaannnddd...Madison coming right back up to receive her award for "Most Aesthetically Pleasing."  Well, Madison did kind of bodyslam the competition into submission with her entry.  Not that I'm prejudiced in favor Madison's artwork.  

Not at all.



Madison barely contains her glee at winning two of three awards, for the second year in a row.  She has skillz, friends.  Mad skillz.



And in the aftermath, three progeny Bdellovibrio cells surround a clay representation of the life cycle of Bdellovibrio created as a gift several years ago by a former student, Kat Schmidt.




And finally, Madison explains both Bdellovibrio and her culinary creation, in this YouTube video.  Thanks to Katie Frye for writing up the summary.



It was a great day for Madison.  For Bdellovibrio.  For Martin's Microbial Menagerie.  The winning entry was ambitious, delicious and predilicious!

Thanks for sharing with me a good day during Summer Research at the University of Puget Sound!

Friday, July 25, 2014

A Nice Surprise from a Former Student!

There are many things I enjoy about teaching and doing research with undergraduates (and yes, there are challenges, too) here in the Biology Department at the University of Puget Sound.  

From time to time---always a pleasant surprise---a student will send me a "thank you" note after graduation.  Such notes are very nice to receive, and to hold in reserve for those difficult times all academics face periodically. Maybe as a deposit to our virtual "I'm okay at my job" emotional bank account, for those days when we have doubts.

By the way, isn't it interesting how we as a culture have no trouble sounding off when things are not to our liking...but seem to have problems telling others when they have done something well, or have had some kind of positive impact on our lives?  Why is that?

Anyway, meet a young lady named Ariana, a transfer student to the University of Puget Sound.  She was assigned to my advisee caseload, and we worked together for a bit over two years.  Ariana was always quiet and a little nervous.  It was great to see her gain confidence over the next two years.  She even did some research with a colleague of mine, so I was able to work with Ariana a bit in the lab last summer.  Ariana graduated in May, and is off to a library science M.S. program in Chicago (she always did love libraries!).

Ariana came to visit the lab this morning, and look at what she made me!  It was a nice surprise, to say the least. Ariana poses with her knit bacteriophage here.


Also, the bacteriophage was happy to consume a donut at morning lab meeting.  And yes, Ariana stitched my first name onto the knit face of that icosahedral head (which made some of my current students snicker that Ariana was implying that I am a virus).

But heck, to misquote the Bard of Avon, "...all the world's a phage...," right?


Here is a nice photo of the impressive knitting project, with a hand for scale.


I don't know exactly what pattern Ariana used.  This is a possibility.  I'm currently thinking about use thick wire to stiffen the phage legs and body, so that I can find a place to hang up the item in my lab or office.

This is why I have a job that is nearly perfect for me, right here. The surprises that let me know what I do and say matter to people mean more than I can easily express. 

Such a nice surprise!  Thank you, Ariana.  It was a pleasure working with you while you were a student at the University of Puget Sound.  I really appreciate the gift, and the kind words. Good luck in Chicago!


Wednesday, July 16, 2014

Fame versus Impact

Just a quick post, and kind of a somber one. Hopefully, it will have a bit of impact as the new academic year approaches, and get educators like myself thinking.

Imagine a classroom of 100 freshmen students.  Some eager, some nervous, some world-weary and cynical, and some half-asleep.  In other words, a slice of the college age, university attending, population.

Ask them if they know the name "Norman Borlaug."

Then ask them if they know the name "Kim Kardashian."

I think you can tell where I am going with this post. You haven't done it yet as I have, yet you can---each and every one of you---predict the responses. 

Kim Kardashian is an inexplicably well-known media celebrity. Come to think of it, she first reached the public eye in a somewhat tacky fashion (though she is far from the only celebrity to use that route to notoriety).  She grabbed at her fame and has monetized it heavily, leveraging a career of sorts.  Can you blame her?  It's all about getting noticed.

By the way, feel free to insert the name of any male celebrity if you wish.

But Norman Borlaug is a name everyone should know.  I don't want to go over his accomplishments.  What I want is anyone reading this post who doesn't know about Borlaug's life and work to read the first link I posted.  Then watch Penn and Teller talk about Borlaug here.  Read this.  Then go on to read this.  Or even watch the whole documentary on Borlaug here

I don't know many people who spearheaded efforts to save a billion human beings from starvation, successfully.

But he didn't get his own reality show, did he?

Perhaps you want something more media-savvy and hip about Norman Borlaug.  How about this?




Isn't that a fantastic way to publicize what Borlaug did?

Did you know all that about Norman Borlaug?  The only reason I did was from debating on scarce world resources in high school, and my plant science professors at UCLA.  

Tell your friends.  And use Borlaug's great comment: 


I'm not one to sit idly by...I'm going to play that card, and play it hard.

Indeed.

I sent a friend of mine this "Scientist Rock Star" poster celebrating Borlaug recently.  



I recommend you order a Borlaug poster from Megan Lee, and post it in your office or lab or classroom.  Do the same with other scientists who need the PR.  For example, this is something I have posted on my office door, not that it surprises anyone.



We need to have a world where we recognize people for their accomplishments.

By the way, don't think that a Microbial Supremacist™ like me is going all plant-centric on you!  Read this American Academy of Microbiology 2013 report, titled "How Microbes Can Feed the World," available here.  The Small Masters are always in my thoughts.  And brain, apparently.

All of this discussion of media popularity versus significance reminds me of the quote by Oscar Wilde:  "I would rather be infamous than not famous at all."  That is how most of our celebrity culture works.  But should it?

We need to find ways to make things better, not "sit idly by" as Norman Borlaug put it.  And when we find it, we need to "play that card, and play it hard."

I'm with Penn Jillette in considering Norman Borlaug one of the greatest human beings in history---and saddened how few folks know his name.  Penn puts it this way, here:
"Norman is the greatest human being in history, and you probably never heard of him."
Tell a friend today about Norman Borlaug, and other real heroes, rather than what's in the National Enquirer.  Honor the people who labor anonymously to make things better for all of us.

Play that card, readers, and play it hard.




Friday, July 4, 2014

Have a Happy and Bioluminescent 4th of July!

You know, I keep meaning to post more often to this blog.  But, as John Lennon famously observed, "Life is what happens to you while you're busy making other plans."  So I will try to do better.  I have several interesting posts cooking, to keep readers up to date.  Hard to say how often people read these posts, but they have some value for me at least (in getting my thoughts down and events remembered).  Thus, onward and upward...

But today is the 4th of July, a mixture of holiday and history.  Many Americans celebrate with fellowship, food, and fireworks.  With the help of some of my summer research students, we created our own "fireworks" of a more biological nature, using our favorite bioluminescent bacterium, Photobacterium leignothi.  Since I recently dropped and damaged my "regular" camera (a Canon G12), I am doing my best with my wife's camera.  The more I think about the relationship between science and art, and how much I enjoy thinking about images (microbiological or otherwise), the more I think I need to upgrade my camera.  

Yes, yes, after I hit the lottery...

Anyway, this is the best I could do this morning using the great plates my students "painted" with a bacterial culture yesterday afternoon.


 Have a happy, safe, and restful 4th of July, everyone!  That goes for your microbiota as well as your eukaryotic cells.  

After all, we each and every one of us are "anthology" organisms, made up of a vast and various community of living things.  But I hope that "all of you individually" agree with me that microbial supremacy is both wonderful and here to stay!

Saturday, May 10, 2014

Freshman Biology and Creativity!

Teaching is often its own reward, but also has its compensatory challenges.  The two main courses I teach (introduction to cell and molecular biology for freshman biology majors, and microbiology for junior and senior biology majors) have different audiences, different challenges, and different joys.

I know that helping students to engage the topics in class through "different eyes" and different strategies can help improve retention and outcomes (meaning exams, on one level).  One method to accomplish that is to encourage students to approach concepts from class based on their interests, using their own skill sets.  I find that most students have impressive talents and special interests that we just don't find out about within the context of a crowded introductory course.  

Nothing motivates students quite like points (he said, cynically), so I often offer "extra credit" for "creative" projects in some of my classes.  This has created some wonderful products in the past, as can be seen in my freshman course last Spring here, and my microbiology course last Fall here.

This Spring, I offered my freshman biology students the same "deal."  They had to talk about their project with me first, to get verbal approval.  Then I needed them to write a one page proposal, to lay out the basic parameters and concept of the project.  I did both of these things to keep students from doing something overwhelmingly last minute (which is in my opinion non-optimal in two ways:  last minute efforts are generally underwhelming, and I also worry that the project might take away from their studies in general).  

The results in the past have been gratifying (as seen in the prior links), and this Spring was no different.  Here are some examples of what these students can do, when they are in the "driver's seat" of their studying and preparations for final exams.  Also note that, for every project, the act of putting these projects together helps students with concepts central to my introductory course. This approach helps the students in an enjoyable and positive manner.

It works.

First, a "piratical" approach to a dihybrid cross that would make Mendel smile.  I hope.



I also had two students who were interested in what I had presented about endosymbiosis, and followed up with Elysia, the chloroplast harvesting sea slug.  In their hands, this topic became a children's book, as you can see from the following two sample pages.




Several students became fascinated by mitosis and meiosis (and well they should!).  One student "cross-stitched" her version of mitosis (very "crafty" as my late mother would have said) as can be seen here. 


Another created a flip book (I am still trying to create a YouTube video to demonstrate, but cannot get the angle quite correct) showing meiosis in action.



Another student created a fun "mini-comic book" about Mendel as her project.  The student pointed out to me, correctly, that the founder of genetics was born "Johann" and only took "Gregor" as a friar in his religious order. 



There was a great deal of creative writing that appeared in this year's "creative projects" offering. Here is a poem about "mitochondrial love" and central metabolism.


  
Another student created an ode to a phospholipid that I think emphasizes some important points.



One student came up with a charming idea I had not anticipated. She told me that she loved the idea of "visual puns" involving biology.  This student created a series of cartoons that mix humor and first year biology pretty well. 

For example, a "Barr Body" takes on a whole new meaning in this student's artistic vision:




 And don't get me started about cell phones in class:



Another student had a more traditional artistic bent, and created this lovely piece of art on canvas that I will hang in my office or laboratory:



I'm not usually surprised by student choices with this kind of assignment, but one student created a "bingo" game that one can use to create a dihybrid Punnett Square.  That is certainly one approach to creating a random selection of alleles during gamete formation!  She included lots of apparatus and instructions.  I can't wait to try it out! 



Another rather shy student wrote a fun poem about the ribosome, that emphases the basic structure and function.



One student asked to do something more "short story"-"creative writing" for her project.  In particular, she wanted to write about Rosalind Franklin.  What the student produced is a ghost story with a slapstick edge.  Here is an excerpt:



Another student had quite an interest in 1930s Gothic literature, such as that of H.P. Lovecraft.  For her project the student produced an analysis---1930s style---of some rather odd families in the H.P. Lovecraft universe, complete with pedigree analysis.  

Ph'nglui mglw'nafh Cthulhu R'lyeh wgah-nagl fhtagn  




Which brings us to some more...theatrical...extra credit productions.  First, three of my students decide to rap a bit about mitosis:
  

Here is their lyric sheet, exactly as they presented it to me.



Another student tried her hand at also being raptastic about mitosis, as you can hear in this audio file:



I don't know how to add an overall cover image, so this is the only way I could determine to upload audio to this blog!  Apologies for the kludge-y approach.  Here are the lyrics to the rap, anyway:



And finally, two students with traditional musical talents put together a pretty fun parody, and do their best to emote for the camera...about mitosis.



Well, I hope that the "creative extra credit" project had some positive aspects for the students.  I know that I was impressed by skills and interests among the students, aspects of them about which I was unaware! And if this kind of project helps the students prepare for their final exam next week, all the better.

I will leave the students with a microbial "good luck" wish, as you can see:



And I recorded this on the last day of class.  I like to think they were clapping because they enjoyed some of the class, not simply that it was over!



I hope you enjoyed this post, as well.  I'll keep trying to merge their creative sides with their studious sides in my classes, never fear!  Give it a try in your classrooms, educators---the students always surprise and impress me!