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Two years of using the online discussion board Piazza

A couple of years ago I stumbled across the free online discussion board Piazza.  I had just starting relying more heavily on my University’s learning management system, Angel, but was not happy at all with its built in discussion board.  I forget exactly how I found Piazza, but the features and look intrigued me and I started to play around with it.  After using it sparingly in two classes last year I took the plunge and made Piazza the primary discussion platform for my first all-online course last summer: Bio 100 Human Biology.  This past Fall semester I used Piazza in the largest class I have taught, a 48-student introduction to cellular and molecular biology, and again this past semester for my Marine Biology course (check out the screenshot below).  It’s a great platform: easy to use, bug-free with good tech support when you need it and the ability to post pictures and videos.

Piazza screenshot

In my all-online class I relied on Piazza as the primary platform for discussions.  I required students to post at least three times each week and provided a rubric explaining how I would grade their contributions.  To earn the points for online discussion students had to post something substantive.  This could be a class related news item they found, comments on course material or reflections on each other’s posts.  While I saw a range of quality in student posts, many took the online discussions seriously and made solid, substantive contributions.  One popular use of the board was to ask questions about course activities, quizzes and exams.  I encouraged students to answer each other’s questions, and would wait to post my own response to give students a chance to do so.  There are several great features in Piazza, such as the ability to endorse students’ answers, pin any post to the top of the page and set up a list of tags that can be used to organize posts.  And while setting up two discussion boards for my online courses this summer I found the ability to clone a previous course, which imports all of your past settings, including your custom tags.  Piazza’s search functions also make it easy to find posts on a certain topic, or list all of a single student’s posts when it is time to grade their activity.

I have been asking students on course evaluations what they think of using Piazza.  I have found a consistent pattern that some students love the platform, finding it easy to use and helpful, while others can’t stand it.  A minority mention that it is hard to use while others don’t like having another webpage to log into for class (Piazza can integrate into LMS platforms, but my University’s IT department has not been able to pull that off with our Angel system).  Some of these more negative comments make me rethink using Piazza in my classes, but I really believe that the platform has opened up a whole new dimension of student interaction outside of the physical classroom.  This is of course required for online courses, but has also been a great addition for face-to-face courses.  For the past few years I have wanted to have students help crowd-source topics for my classes, and Piazza seems to be a great mechanism for doing so.  That was clearly the case in my spring marine bio course, where my students often raised topics that I had not planned, and that led to great discussions in class.  So why do some students not like it?  My sense is these are the students resistant to putting in the energy required for quality interactions outside of class.  But I will keep monitoring those evals.

Have you tried Piazza or another good online discussion board?  I’d love to hear about it.

Back from hiatus

Tree Nage Head woods reducedI can’t stand blog posts that begin “it’s been ages since I wrote”, but here I am almost one year from my last post, and what else is there to say?  The lack of posts does not reflect a boring year.  The past 12 months have been action packed, which may actually be the problem.  Every time I think about getting back here I am not sure where to start.  So I figured it was best to just take the plunge.

I plan to spend the summer months getting you all caught up on a number of exciting happenings:

  • I taught my first all online course last summer, and am repeating it starting next month
  • My National Institutes of Health research grant ended this past January, but the renewal proposal is in the works
  • Former lab members are doing exciting things
  • We had two research papers published this past year
  • I taught my first semi-flipped intro biology course
  • Fun with some new teaching tech tools

You can see why I have been a bit intimidated to post, especially while contributing heavily to my University’s Science News blog and staying active on Twitter.  But here goes.  And in the meantime enjoy the image above from my Marine Biology class’ recent trip to the Outer Banks of North Carolina.  We spotted a rare Outer Banks bald eagle from this beach in Nags Heads woods.  More about the trip soon.

Lab alumnus entering dental school at Case Western Reserve University

Zack Haley

Long-time lab member Zack Haley recently graduated from Ashland University and will be entering the Case Western Reserve University School of Dental Medicine this Fall.  Zack started working in our lab during his sophomore year and took the lead on our current project characterizing how mammals and zebrafish regulate the expression of alpha crystallins, proteins involved in protecting cells from damage during physiological stress.

During his time in our lab Zack presented his research at a meeting of the Ohio Academy of Sciences and at two undergraduate research symposia at Ashland.  He was a co-author on a poster I presented at last month’s Seattle meeting of the Association for Research in Vision and Ophthalmology.  Check back soon for some news about the trip to Seattle.  In the meantime, the zebrafish embryo below is data from our poster showing green fluorescent protein expressed under the control of a promoter for mouse alpha B-crystallin.  This result shows that zebrafish cells are able to “read” this mouse DNA sequence and direct the expression of the gene under its control.

GFP protein expression driven in the zebrafish notochord by a mouse alpha B-crystallin promoter

GFP protein expression driven in the zebrafish notochord by a mouse alpha B-crystallin promoter.

Lab member heading to Michigan State for summer internship in plant genomics

AllmanOne of my undergraduate research students, Josh Allman, was recently accepted into a summer research program at Michigan State University in plant genomics funded by the National Science Foundation.  Josh is doing his independent research in my lab on the regulation of alpha crystallin expression in zebrafish.  Last summer he worked with me to genotype populations of the grass Phragmites to distinguish between native and invasive population.  This work was part of a recent publication in the Journal of Chemical Ecology.  

Josh will be returning to AU for his senior year with plans to enter graduate school in molecular biology or bioengineering.




Look what washed up on the beach

The storms last week along the Outer Banks of the North Carolina Coast brought flooding in Kitty Hawk and again washed out route 12 through Pea Island.  But the rough surf also brought some interesting marine animals onto the beach.  Sunny, warm weather on Friday provided a good chance to check them out.  In the photo below of the white baby ears you can see them still attached to their large muscular feet.  Click on each image to see a larger version.

Assorted purse crabs and sea stars washed up from recent March storms

Assorted purse crabs and sea stars washed up from recent March storms

Purse crabs, Persephona punctata. Arranged with males on the left and females on the right.

Purse crabs, Persephona punctata. Arranged with males on the left and females on the right.

White baby ears, Sinum perspectivum, arranged to show their muscular foot.

White baby ears, Sinum perspectivum, arranged to show their muscular foot.

Lab’s new paper challenges hypothesis on mechanism behind Phragmites invasiveness

Phragmites stand in Duck, NC

Phragmites stand in Duck, NC

Our lab had the opportunity to contribute to a new paper in the Journal of Chemical Ecology that shows the release of toxic gallic acid by the common reed Phragmites australis is not the key to its successful invasion of freshwater and brackish habitats in North America.  A series of previous publications suggested that release of gallic acid might explain the reed’s ability to produce large stands and exclude native plants.  However, work by our collaborators in the Ashland University Department of Chemistry with four Phragmites populations from Ohio and North Carolina found only trace amounts of gallic acid in the plant and none in surrounding soils.

Josh Allman, a junior conducting research in my lab, performed an analysis of a genomic region that differs between North American native Phragmites populations and the invasive strain.  Josh’s restriction length polymorphism analysis showed that all four populations in our study were invasive and, according to past work, should contain gallic acid.  The lack of gallic acid in these populations suggests that at a minimum gallic acid release is not a general explanation for the invasive success of Phragmites.

Students in Ashland University's Marine Biology course collecting Phragmites samples in Nags Head, NC

Students in Ashland University’s Marine Biology course collecting Phragmites samples in Nags Head, NC

Students in my spring 2012 marine biology course took part in the collection of samples from North Carolina during a 4-day field trip to the Outer Banks.  Another student in my lab, Kelly Sullivan, is following up on this work by developing methods to study whether chemicals produced by Phragmites repel the snail herbivores in their habitat.  Hopefully I can report back on that work soon.

Lab paper gets coverage in JEB

A recent issue of the Journal of Experimental Biology included a summary of our PLoS One paper on thermal adaptation in the small heat shock protein alpha A crystallin.  Our study identified single amino acids that affect alpha A crystallin’s ability to protect other proteins from stress by comparing the structure and function of this protein from six fish species living at different temperatures.  We used this information to genetically engineer a zebrafish alpha A crystallin with the enhanced protective abilities found in the Antarctic toothfish.

Thanks to JEB and the author of the summary, Hans Merzendorfer of the University of Osnabruek, for a great explanation of our work.

Lab alumna starts practicing veterinary medicine

Congratulations to former lab member Carrie LaCava who recently graduated from The Ohio State College of Veterinary Medicine and will begin practicing in southern Illinois.  Carrie will be working in a practice with five other doctors conducting appointments and surgeries with both large and small animals, including farm visits.

While an undergraduate at Ashland University Carrie worked in my lab to produce the first proteomic map of the adult zebrafish lens using two-dimensional gel electrophoresis.  Another student and I are now writing up a follow up study examining how the protein content of zebrafish lenses changes during the development of the lens.  These studies will allow us to better understand the protein damage that causes lens cataracts, as well as provide foundational information on the roles that lens proteins called crystallins play in the development of the lens.

Our lab’s newest paper published in PLoS One

I’m excited to announce that our latest paper has been published in PLoS One.  OK, this news is a little old since the paper came out March 29th, but with the end of the academic year, a trip to the ARVO eye meetings in Florida and the start of summer research with three undergraduate students in lab it has taken me some time to write this post.

Antarctic toothfish alpha A crystallin has evolved more flexibility to function at low temperatures

My lab studies the function of a family of small heat shock proteins called alpha crystallins, which plays a role in keeping the lens of the eye transparent and focusing light on the retina.  These proteins are also found in other tissues like brain and muscle where they protect cells during physiological stress.  Alpha crystallins keep other proteins from sticking to each other during this stress, which could otherwise cause a wide range of diseases such as Alzheimer’s and Parkinson’s.  Recent research also shows that more alpha crystallin is made during many types of cancer, perhaps as a protective response by cells.  We would like to better understand how alpha crystallins, and small heat shock proteins in general, protect other proteins and prevent disease.  Understanding this function might allow us to design altered alpha crystallins with greater protective abilities.  Our approach to studying alpha crystallin function is a bit unique as we examine these proteins in fishes.  Why fishes?  We use them as a model to dissect how natural selection has altered these proteins to function in different environmental settings.  In particular, we looked at alpha crystallin function in fish species with different body temperatures to see how evolution has molded this protein to protect other proteins in bodies as different as the Antarctic toothfish (-2 degrees C) and the zebrafish (27 degrees C).  This type of study is not possible in mammalian models like mice and rabbits whose body temperatures are all similar.

Structure of alpha A crystallin showing position of three amino acids that affect protective function

We hypothesized that the protective abilities of alpha A-crystallin, one of three alpha crystallins found in fishes, had evolved to function at the specific body temperature of the six fishes in our study.  We found just that.  When all six fish alpha A-crystallins were compared side by side at the same temperature, those from the cooler bodied fishes (like the Antarctic toothfish) were more flexible to compensate for the stabilizing effects of cold temperature.  This greater flexibility allowed them to protect other proteins more readily than the comparatively stiffer alpha crystallins from the warmer species.  By comparing the structure of all six proteins we identified three amino acid building blocks that differed between the cold and warm fishes that could cause this increase in protective function.

The most exciting part of our study was that when we took a zebrafish alpha A-crystallin and genetically engineered it to look like the Antarctic toothfish at the three amino acids, two of the changes increased its protective function.  By comparing alpha crystallins from these six fish species we were able to identify specific parts of the protein that may be evolving to fine-tune protective ability to different body temperatures, and then showed experimentally that those changes are functionally significant.  Because alpha A-crystallin is so well conserved between fishes and mammals we now want to see if similar changes will increase protection in the human version of this protein.  While it may seem unusual to study a protein that causes human disease in a bunch of fish, our new study shows that this comparative approach can be quite effective.  Stay tuned for updates.

Live tweeting a class field trip to the Outer Banks

Kayaking out of Manteo harbor with the Queen Elizabeth II in the background

This Thursday morning my marine biology class at Ashland University will be piling into two vans and trekking for 13 hours to the Oregon Inlet Campground on the outer banks of North Carolina for three days in the field.  This is the fourth time I have taken this class to the Outer Banks for an end of semester trip, after previous expeditions to the much colder Assateague Island, Maryland.  On past trips I have posted photos to this blog and shot video in the hopes of editing it together into a summary of our trips.  But that editing never happened after the last trip as I succumbed to summer research and administrative duties.

Plans for this year are a bit different.  Instead of relying primarily on this blog, I will be tweeting from the trip and am encouraging my students to do the same.  They are required to keep field notes from the sites we visit, but I have offered them the option to keep those notes via Twitter.  With 12 students and three faculty on the trip I hope to have a solid crowdsourced record of the trip.  You can follow these tweets at #aubio412.

Once we get back I plan to turn the tweets, YouTube video and any other material into a story on Storify.  Wish us luck.