Grant Awarded to study the mechanisms of sensitization maintenance and decay

Woot! The Slug Lab has just been awarded a 3-year R15 grant from NIH to study the transcriptional mechanisms of sensitization memory and decay. What does that mean? It means that Irina and I will continue to be working our a**’ off trying to understand what genes are activated as an animal stores a long term memory, and even more importantly, as a long-term memory is forgotten.

Here’s the screen grab from ERA commons:

Big thanks to our dedicated and amazing students, and to the incredibly supportive colleagues and administrators we have here at Dominican University. We’re looking forward to crushing it with this project.

*Technically, that’s not the actual notice of the award, but of our priority score from a peer review of our grant proposal by a panel of esteemed scientists in the field. We got the award letter via email last week.

What’s the best way to teach methods and statistics?

No easy answer, but I’m co-author on a new paper that has some hints (10.1177/0098628315573139). Well, actually, it’s just a summary of some assessment data my department has been collecting to help evaluate an integrated and inquiry-based approach to teaching methods and stats. We provide lots of opportunities for apprenticeship, with student completing independent correlational and experimental projects across a 2-semester sequence. Currently, we’re using Nolan & Heinzen as a stats text, but I’m hoping that we’ll be using Cumming & Calin-Jageman by 2017.

Pliske, R. M., Caldwell, T. L., Calin-jageman, R. J., & Taylor-ritzler, T. (2015). Demonstrating the Effectiveness of an Integrated and Intensive Research Methods and Statistics Course Sequence. doi:10.1177/0098628315573139


New Publication on ERIN, Educational Resources in Neuroscience

Just after I started at Dominican in 2007 I had the good fortune to team up with Richard Olivo to help in the development of ERIN, an online curated database of educational resources for neuroscience. It was a long process, but ERIN has now been online for the past three years serving up great resources to faculty prepping their activities for neuroscience courses. You can take a spin for yourself at

To cap off our efforts with ERIN, Richard took the leading in writing up an article for JUNE, the Journal of Neuroscience Education. You can find it online here: (26240519).


Qualtrics Tips – A HTML5 and JavaScript Word-Search Task

Here’s a second experimental task I wrote for use with online social psychology experiments. This one is a word search. Again, the code is a series of kludges cobbled together from examples I could findwith Google. But it works out pretty well as a task you can embed in a Qualtrics survey. You can define the grid and the word list as you’d like, and you can have Qualtrics pass parameters that specify which grid and words list to use for a specific participant. It looks nice, and I’ve had good success using this online.

This particular grid is a control grid is a sample I adopted from a book of word searches. It’s a really tough one due to the size of the grid. If you want to see what finding a word looks like without, you know, actually finding a word: “Tradition” starts in the 8th letter of the bottom row.

I have a couple of papers I’m working on that use this task. When either goes to press, I’ll post the reference here for citation. The first one is finally in press, (10.1371/journal.pone.0140806) with three student co-authors:

Cusack, M., Vezenkova, N., Gottschalk, C., & Calin-Jageman, R. J. (2015). Direct and Conceptual Replications of Burgmer & Englich (2012): Power May Have Little to No Effect on Motor Performance. PLOS ONE, 10(11), e0140806. doi:10.1371/journal.pone.0140806,

Email me if you’d like the source code, or scrape it directly from this page. The code is a hot mess, but it should be enough to get you started.


Qualtrics Tips – A HTML5 and JavaScript Mirror-Tracing Task

Social relationships can confer power on some to control the fates of others. There is a large and growing body of social-psychology research examining the psychological effects of power, with findings documenting profound changes in cognition, motivation, moral reasoning, and more.

One intriguing finding is that having social power can actually improve motor skills. Specifically, Bugmer & Englich (2012) have shown that manipulating power substantially improves power at mini-golf and darts (10.1177/1948550612452014).

I’ve been working over the past two years to replicate this finding. While it was easy enough to replicate mini-golf with real, live participants, I wanted to test the study online, with a much larger and more diverse pool of participants. But how to measure motor skill online? My solution was to develop an online version of the classic mirror-tracing task, using HTML 5 and Javascript.

A paper describing the results is finally in published (10.1371/journal.pone.0140806) with three student co-authors:

Cusack, M., Vezenkova, N., Gottschalk, C., & Calin-Jageman, R. J. (2015). Direct and Conceptual Replications of Burgmer & Englich (2012): Power May Have Little to No Effect on Motor Performance. PLOS ONE, 10(11), e0140806. doi:10.1371/journal.pone.0140806,

Below you can see a sample in action. The top box is the mirror–the bottom box is the drawing pad. Move the mouse into the green target in the drawing pad–this starts the trial. From this point on, you mouse will leave a mirrored trail in the mirror-box. Try to trace to the red target while staying in the line of the figure in the mirror. When you are within the line, the trail will be red–go outside the line and the trail is blue. You’ll see your score as a % of time within the line just below the drawing pad. The trial ends automatically when you reach the green target. Note that this WordPress theme uses a bunch of white-space—you may need to increase or decrease the zoom on your browser to get both boxes to show within your screen without scrolling

I kludged this task together even though I’ve never previously written javascript before. I relied heavily on examples found via Google. The final produce works, but could really use a code review both a) to clean up all the horrible on-the-fly decisions I made in getting this to work, and b) to credit the sources I used in taping this together.  Still, there are some cool features to this task:

  • The final drawing is saved back to a server as an image, complete with score–this allows you to visually inspect performance to get a feel for how different participants are scoring.
  • The scoring is fully automated.
  • The script runs fine within a Qualtrics survey, and Qualtrics can read the scores back from the script.
  • As expected, I found a consistent negative correlation between performance and age–this indicates the validity of the task and provides a useful covariate for reducing within-subjects noise.
  • As expected, performance improves from first to second-trial.
  • With this task, one can analyze overall performance and performance change across trials (though fatigue seems to set in within a few closely-spaced trials for most participants)
  • Difficulty can be varied by changing line thickness.
  • Any arbitrary line tracing can be uploaded–I matched all mine for number of turns and total line length.
  • It’s a fun task!

If you’d like to adopt this for your own studies, please shoot me an email and I’ll be happy to send you the code and some instructions for how to use it (or you could probably just rip it off directly from this page).  When (if) I get the paper using this task published, I’ll post the reference for citation.

Mirror Tracing Demo


2014×3 – Transcriptional correlates of long-term habituation

Third paper of the year for the lab (gasp!) is now out in Learning and Memory (10.1101/lm.036970.114).

The focus of the project is habituation, considered the simplest and most ancient form of memory. Long-term habituation requires changes in gene expression, but to date there is almost nothing known about what specific changes are required to encode and store a long-term habituation memory.

We’re not the first to try to tackle this issue, but it turns out to be a very difficult topic for study. Habituation is typically very site specific, occurring only at the site of training. This implies a relatively discrete set of neurons encode the memory, and that presents a real problem for qPCR and microarray analysis, because the signal from memory-encoding neurons could easily be washed out from signal from non-encoding neurons, glia, etc.

Our strategy was to develop a new, automated protocol for inducing long-term habituation over the entire body of an Aplysia. With the help of a tinker-toy set, a windshield-wiper motor, a relay box, an old computer with a parallel port, and some qBASIC programming (blast from the bast), we developed a slug car wash–an apparatus we could place over the tanks to repeatedly (though gently) brush Aplysia without any need for human intervention during training. We made a video to show off the system, which you can see here.

The slug car wash turns out to work great. We tracked the development of habituation over repeated rounds of training and saw a classic pattern of behavior–robust decreases in behavior at the end of each round of training, substantial overnight recovery (forgetting), but a progressive development of a persistently decreased response within 3 days of training. Importantly, we could observe habituated responding when stimulating the animal at the head, the siphon, or the tail. Moreover, the effect sizes were huge. So it was pretty clear that the slug car wash was producing the high impact we were looking for. In addition, we found that pattern of training really does matter–when training has breaks between sessions and is spaced out over 3 days it is extremely effective; massing all the same stimulation together into a single one-day session (at a slightly higher rate to squeeze it all in) produced neither long-term nor short-term habituation. This is a useful finding because it gave us an additional no-memory control, one which could ensure any molecular correlates identified are specific to memory formation, not just to the activity induced by brushing.

So what’s changing transcriptionally? We decided to focus on the pleural ganglia containing the VC nociceptors. These are relatively high-threshold neurons, and are probably not carrying the bulk of the activity induced by the brush. Unfortunately, though, no one yet knows *where* in the Aplysia nervous system to find the cell bodies of the low-threshold neurons that mediate light touch (probably in the periphery). Not to worry, though–we did record from the VCs in reduced preps and found that they do actually get some activation from the brush: about 1/4 fired APs, and most of the rest got lots of IPSPs from off-center stimulation.

To track transcriptional changes, we used the custom-designed microarray we recently developed in the lab (25117657). Some quick words about methods: We again used a large-ish sample size (n=8/group; can you believe that n=3/group is still common in microarray!?). We also used very high statistical standards by adopting the ‘treat’ function in limma which allows you to specify a reasonable null hypothesis (e.g. at least 10% regulation in either direction, rather than the standard practice of testing against a null of no regulation). Adopting a more reasonable null enables you to test for statistical and practical significance at the same time, and we’ve found that transcripts which pass such a rigorous test generalize very well to new samples. We’ve been finding R and limma surprisingly easy to use, which is pretty fantastic for free software.

Anyways, back to the data. The microarray results were a bit of a bummer. Out of over 20,000 transcripts tested, only *one* came up as strongly regulated. Bummer. Another 20 transcripts came up as regulated if you use a standard null hypothesis, but, as expected, none of these validated.

Although the microarray results were not what we hoped, we did further explore the one regulated transcript, and it turns out to be quite interesting. From sequence alignment, it seems to be an Aplysia homolog of cornichon, an auxiliary subunit for AMPA receptors. In invertebrates, cornichon seems to limit trafficking to AMPA receptors to the membrane and therefore reduces glugatmate-induced currents(24094107). Note that this is precisely the type of effect that could produce behavioral habituation. Moreover, one of the few known molecular correlates of long-term habituation is a decrease in surface expression of glutamate receptors (14573539). Fits perfectly!

To ensure that cornichon is truly regulated in our paradigm, we did some additional follow-ups. First, we used qPCR to check cornichon levels not only in the microarray samples but in an additional, independent set of samples. Sure enough, we confirmed up-regulation of cornichon in the pleural ganglia 1 day after training. In addition, we checked levels in massed animals, who display no memory after training. In this case, cornichon was actually slightly down, and was significantly different than in the regularly trained animals. So, cornichon is quite specifically and consistently up-regulated after long-term habituation training. As far as we know, this is the first specific transcriptional correlate of long-term habituation to be identified.

Needless to say, we’re quite proud of this work. It wouldn’t have been possible without two of the most talented undergrads we’ve had in the lab: Geraldine Holmes and Samantha (Sami) Herdegen. Geraldine was the most diligent slug trainer in the history of the lab. For this paper alone she ran over 48 animals, testing each 8 times a day for 3-5 days–that’s a whole lot of behavior to monitor! Sami, of course, has been the qPCR wizard in the lab, testing lots and lots and lots and lots of transcripts for regulation. It’s no surprise that both are on to bigger and better things, Geraldine is now in a PhD program in Canada and Sami is soon to start pharmacy school. We also had contributions from John Schuon (when he could fight his way in for some qPCR; now off to medical school), Ashly Cyriac (who helped start the project before heading off to pharmacy school), Jamie Lass and Catherine Conte. Congrats!

As has now become the norm for the lab, all the raw data from this study been posted online at the Open Science Framework:


Sluglab Strikes Again – New paper tracing dynamics of learning-induced changes in transcription

A nice way to wrap up 2014–we have a new paper out (25486125) where we trace learning-induced changes in transcription over time and over different location in the CNS. We think it’s a nice follow-up to the microarray paper, because:

  • We show that some transcriptional changes are likely occuring in interneurons and motor neurons, not just in the VC nociceptive sensory neurons.
  • We found some transcripts which, like Egr, are rapidly *and* persistently up-regulated by sensitization training (GlyT2, VPS36, and an uncharacterized protein known for now as LOC101862095). We’re interested in such transcripts because they could be related to memory maintenance
  • We were able to better test the notion that CREB supports memory maintenance. So far, our evidence continues to go against this hypothesis, with no long-lasting changes detected in the VC sensory neurons nor in the pedal ganglia.
  • As a methodological point, we found that microdissecting out the VC cluster really really improves signal:noise for identifying transcriptional changes induced by learning. This is exciting–most work on the molecular mechanisms of memory uses tissue samples representing homogenous cell types. Zooming in on a single cell type of known relevance for storing the memory really enhances the power of the analysis.
  • We re-rested the four novel transcripts identified in our microarray paper from earlier this year (25117657). All four validated again! Moreover, all 4 were specifically up-regulated in the VC nociceptors (and some elsewhere as well). Another good indication that we’re on the right track with our microarray approach.
  • Another 3 student co-authors on this paper! We’re especially proud of Sami, Catherine, and Saman.
  • The paper is free on PLOSE ONE: Also, you can download our raw data to examine for yourself at the Open Science Framework:


    New Publication – Microarray analysis of sensitization

    We’ve got a new paper out (25117657) with the first of what we hope will be a series of studies using microarray to track the transcriptional changes following long-term sensitization training. This paper looks at the changes that occur immediately (1 hour) after training. It provides lots of details and data to validate the microarray design we developed, but also identifies a set of 81 transcripts that are strongly regulated after learning. Best of all, for a microarray paper, we use a large sample size (n = 8) and show using a subset of transcripts that most generalize to a completely independent sample. Among the changes we fully validated are up-regulation of a c/ebp-gamma (what the what!?), a glycine transporter, and a subunit of ESCRTII. The rest of the gene list that we’re working on has some exciting possibilities, too.

    Another thing to be proud of, is our three student co-authors on the paper.

    The paper is free for the next 50 days via this link, then it goes behind a paywall for 305 days, then it will be in PubMedCentral for free again (strange, right?). All the raw data is available on the Open Science Framework:


    Registered Replication In Social Psychology – Our contribution and amazing special issue

    Tracy Caldwell and I have a new paper out which we’re very proud of (10.1027/1864-9335/a000190)–a registered replication of a previous finding that superstition can cause a substantial improvement in skilled performance (10.1177/0956797610372631).

    We conducted 2 high-power and extremely precise replication attempts of this finding, pre-registered our design, sample targets, and analysis in advance. What we found was disappointing–performance did not strongly improve in the superstition conditions despite successful manipulation of feelings of luck. But the overall approach of conducting registered replications–well, that was a real treat.

    We’re especially proud that the paper is in a special issue dedicated just to registered replications of social psychology. We will also be presenting the paper at a Social Psych conference in Amsterdam this summer!