New preprint on the very long-lasting transcriptional response to learning

The sluglab has a new preprint out, currently under review at the Neurobiology of Learning and Memory.  We shows that both transcription and savings can persist for as long as 2 weeks after the induction of long-term sensitization, way beyond the decay of recall.  Interestingly, all the long-lasting transcriptional changes start within 1 day of training.  Lots of student co-authors on this one; it was a *lot* of work.  Looking forward to the reviews.

Slug Lab Triumph! First place in the cSFN undergraduate poster competition for Leticia Perez and Ushma Patel

So pleased and proud to announce that Leticia Perez and Ushma Patel have won first place in the Chicago Society for Neuroscience undergraduate poster competition.   Congrats Leticia and Ushma on a great presentation on the work you’ve been doing in the slug lab on the transcriptional correlates of forgetting and savings memory.

Leticia and Ushma are following up their spectacular win with exciting post-graduation plans.  Leticia is enrolling at the University of Illinois School of Vetrinary Medicine (and had her choice of programs!).  Ushma is enrolling at UIC’s prestigious medical illustration MA program (and also had her choice of programs!).  Congrats to both on all the hard work they put into collecting data, analyzing results, and presenting their exciting research.

Want to know more about the research Leticia and Ushma presented?  See their paper in Learning and Memory here: (Perez, Patel, Rivota, Calin-Jageman, & Calin-Jageman, 2017)

Not to brag, but this is the 3rd time a DU student has placed in this competition in the past 10 years (Kristine Bonnic had a 3rd place win and Tim Lazicki had a first place win).  That means DU neuroscience students have earned 1/3 of all the awards given out for undergraduate research by the Chicago Society for Neuroscience–an organization that includes Northwestern, Loyola, University of Chicago, DePaul, Midwestern, Roosevelt, North Central, and more…. relative to our student body we’re punching way above our weight!

Perez, L., Patel, U., Rivota, M., Calin-Jageman, I., & Calin-Jageman, R. (2017). Savings memory is accompanied by transcriptional changes that persist beyond the decay of recall. Learning & Memory (Cold Spring Harbor, N.Y.), 25(1), 45–48. [PubMed]

Memories fade..but something remains

Most long-term memories are ‘forgotten’–meaning that it becomes harder and harder to recall the memory.  Psychologists have long known, though, that forgetting is complex, and that fragments of a memory can remain.  For example, even after a memory seems forgotten it can be easier to re-learn the same material, something called ‘savings memory’.  That suggests that there is at least some fragment of a memory that persists in the brain even after it seems forgotten…but what?

Today our lab has published a paper shedding a bit of light on this long-standing mystery (Perez, Patel, Rivota, Calin-Jageman, & Calin-Jageman, 2017).  We tracked a sensitization memory in our beloved sea slugs.  As expected, memories faded–within a week animals had no recall of the prior sensitization.  Even more exciting, we found similar fragments of memory at the molecular level–there was a small set of genes very strongly regulated by the original training even though recall had fully decayed.

Why?  Do these persistent transcriptional changes help keep a remnant of the memory going?  Or are they actually doing the work of fully erasing the memory?  Or do they serve some other function entirely (or no function at all)?  These are some of the exciting questions we now get to investigate.  But for now, we have these fascinating foothold into exploring what, exactly, forgetting is all about in the brain.

As usual, we are enormously proud of the undergraduate students who helped make this research possible: Leticia Perez, Ushma Patel, and Marissa Rivota. Ushma, who wants to do science illustration, is making an incredible piece of artwork representing these findings.  A draft is shown above.  She submitted it for the cover of the journal, but sadly they journal selected a different image (boo!).  Still, a very exciting and proud day for the slug lab!

Perez, L., Patel, U., Rivota, M., Calin-Jageman, I. E., & Calin-Jageman, R. J. (2017). Savings memory is accompanied by transcriptional changes that persist beyond the decay of recall. Learning & Memory, 25(1), 45–48. doi: 10.1101/lm.046250117

Workshop at the Society for Neuroscience Meeting

This year was a big year for our lab at the Society for Neuroscience conference.  Leticia Perez, who has been in the lab for the past two summers, gave an amazing talk on our work on forgetting.  In addition, I (Bob) helped organize a Professional Development Workshop on doing better neuroscience.

It was a huge honor to get to lead this workshop.  I gave a presentation on sample-size planning (which is sooo vital to doing good science).  David Mellor at the Open Science Framework spoke about pre-registration.  And Richard Ball, who co-directs project Tier, spoke about reproducible data analysis.  Like the good Open Scientists we are, we used the Open Science Framework to post all our slides and resources: https://osf.io/5awp4/.  SFN also made a video, which should be posted soon.

SFN staff told us it was the best attended workshop for the meeting.  Hooray!  Hope all our attendees will go forth to spread the good word about these small tweaks that can have such a big impact on scientific quality.

Here’s what it looked like from my perspective:

The New Statistics for Neuroscience Education.

This summer I (Bob) was asked to write a series of perspective pieces on statistical issues for the Journal of Undergraduate Neuroscience.

My first effort has just been published–it is a call for neuroscience education to shift away from p values, and an explanation of the basic principles of the New Statistics with an example drawn from neuroscience.

It turns out that the paper was published just before the annual meeting of the Society for Neuroscience, which I am currently attending.  It’s been very gratifying to see the paper is already sparking some discussion.

Here’s the key figure from the paper comparing/contrasting the NHST approach with the New Statistics approach with data from a paper in Nature Neuroscience.

Getting Started with the New Statistics – A talk at Indiana University

This fall I (Bob) was invited to give a talk at Indiana University as part of a series on good science and statistical practice organized by the university’s Social Science Research Commons (which is like a core facility for getting advice on statistics and experimental design…what a cool thing for a university to have!).

I really enjoyed my visit (thanks Emily, Cami, and Patricia)–good conversation with fascinating people in a beautiful setting.  The series has a video archive, so my talk is now posted online as a video and as a powerpoint. Here’s the link–take a look if you want to know more about how to get started using Open Science practices and the New Statistics:  https://media.dlib.indiana.edu/media_objects/gt54kp23k

Maintaining Memories, Changing Transcription

Under the right circumstances, a memory can last a lifetime.  Yet at the molecular level the brain is constantly in flux: the typical protein has a half-life of only a few hours to days; for mRNA a half-life of 2 days is considered extraordinarily long.   If the important biological molecules in the brain are constantly undergoing decay and renewal, how can memories persist?

The Slug Lab has a bit of new light to shed on this issue today.  We’ve just published the next in our series of studies elucidating the transcriptional changes that accompany long-term memory for sensitization in Aplysia.  In a previous paper, we looked at transcription 1 hour after a memory was induced, a point at which the nervous system is first encoding the memory.  We found that there is rapid up-regulation of about 80 transcripts, many of which function as transcription factors (Herdegen, Holmes, Cyriac, Calin-Jageman, & Calin-Jageman, 2014).

For the latest paper (Conte et al., 2017), we examined changes 1 day after training, a point when the memory is now being maintained (and will last for another 5 days or so).  What we found is pretty amazing.  We found that the transcriptional response during maintenance is very complex, involving up-regulation of >700 transcripts and down-regulation of <400 transcripts.  Given that there are currently 21,000 gene models in the draft of the Aplysia genome, this means more than 5% of all genes are affected (probably more due to the likelihood of some false negatives and the fact that our microarray doesn’t cover the entire Aplysia genome).   That’s a lot of upheaval… what exactly is changing?  It was daunting to make sense of such a long list of transcripts, but we noticed some very clear patterns.  First, there is regulation influencing growth: an overall up-regulation of transcripts related to producing, packaging, and transporting proteins and a down-regulation of transcripts related to catabolism.  Second, we observed lots of changes which could be related to meta-plasticity.  Specifically, we observed down regulation in isoforms of PKA, in some serotonin receptors, and in a phosphodiesterase.  All of these changes might be expected to limit the ability to induce sensitization, which would be consistent with the BCM rule (once synapses are facilitated, raise the threshold for further facilitation).  (Bienenstock, Cooper, & Munro, 1982).

One of the very intriguing findings to come out of this study is that the transcriptional changes occuring during encoding are very distinct from those occuring during maintenance.  We found only about 20 transcripts regulated during both time points.  We think those transcripts might be especially important, as they could play a key regulatory/organizing role that spans from induction through maintenance.  One of these transcripts encoded a peptide transmitter called FMRF-amide.  This is an inhibitory transmitter, which raises the possibility that as the memory is encoded, inhibitory processes are simultaneously working to limit or even erode the expression of the memory (a form of active forgetting).

There are lots of exciting pathways for us to explore from this intriguing data set.  We feel confident heading down these paths because a) we used a reasonable sample size for the microarray, and b) we found incredibly strong convergent validity in an independent set of samples using qPCR.

This is a big day for the Slug Lab, and a wonderful moment of celebration for the many students who helped bring this project to fruition: Catherine Conte (applying to PT schools), Samantha Herdegen (in pharmacy school), Saman Kamal (in medical school), Jency Patel (about to graduate), Ushma Patel (about to graduate), Leticia Perez (about to graduate), and Marissa Rivota (just graduated).  We’re so proud of these students and so fortunate to work with such a talented and fun group.

Bienenstock, E., Cooper, L., & Munro, P. (1982). Theory for the development of neuron selectivity: orientation specificity and binocular interaction in visual cortex. The Journal of Neuroscience : The Official Journal of the Society for Neuroscience, 2(1), 32–48. [PubMed]
Conte, C., Herdegen, S., Kamal, S., Patel, J., Patel, U., Perez, L., … Calin-Jageman, I. E. (2017). Transcriptional correlates of memory maintenance following long-term sensitization of Aplysia californica. Learning and Memory, 24, 502–515. doi: 10.1101/lm.045450117 [Source]
Herdegen, S., Holmes, G., Cyriac, A., Calin-Jageman, I. E., & Calin-Jageman, R. J. (2014). Characterization of the rapid transcriptional response to long-term sensitization training in Aplysia californica. Neurobiology of Learning and Memory, 116, 27–35. doi: 10.1016/j.nlm.2014.07009

Red, Romance, and Replication – Cross posted with thenewstatistics.com

I (Bob) have a new replication paper out today, a collaboration with DU student Elle Lehmann (Lehmann & Calin-Jageman, 2017).  The OSF page for the paper with all the materials and data is here: https://osf.io/j3fyq/ (Calin-Jageman & Lehmann, 2015).

The paper replicates a set of previous findings showing that the color red dramatically increases romantic attraction for both women rating men (A. J. Elliot et al., 2010) and men rating women (A. Elliot & Niesta, 2008).  Elle and I conducted two replications: one in-person with a standard psychology participant pool, the other online with MTurk participants.  In each case we planned for an informative sample, used original materials, pre-registered our design and analysis plan, and used extensive exclusion criteria to ensure suitable participants (e.g. testing for color-blindness).  In both cases, we are sad to report that there was little-to-no effect of red on perceived attractiveness or desired sexual behavior.

Example of the types of stimuli used in red-romance studies (not the actual stimuli we used, though)

There were a few weaknesses: 1) for the in-person study we didn’t obtain nearly enough men to make a good test of the hypothesis, 2) for the online study we couldn’t control the exact parameters for the color red.  Still, we found no strong evidence that incidental red influences perceived attractiveness.

Beyond the (disappointing) replication results, there are some really interesting developments to this story:

  • Our replication work drew the attention of science journalist Dalmeet Singh who wrote a cool article summarizing the field and our contribution for Slate.  Dalmeet has made covering negative results a part of his beat–how great is that!
  • There have been some questions about these studies almost from the start.  Greg Francis highlighted the fact that the original study of women rating men by Elliot & Niesta (2008) is just too good to be true–every study was statistically significant despite very low power, something that ought not to regularly happen (Francis, 2013).
  • Although there have been some studies showing red effects (though often in subgroups or only with some DVs), there is a growing number of studies reporting little-to-no effect of red manipulations on attraction: (Hesslinger, Goldbach, & Carbon, 2015)(Peperkoorn, Roberts, & Pollet, 2016)(Seibt, 2015)(Lynn, Giebelhausen, Garcia, Li, & Patumanon, 2013)(Kirsch, 2015) plus a whole raft of student-led precise replications that were part of the CREP project (Grahe et al., 2012): https://osf.io/ictud/
  • To help make sense of the data, Elle and I embarked on conducting a meta-analysis.  It has turned out to be a very big project.  We hope we’re nearly ready for submission.
  • Andrew Elliot, the original investigator, was extremely helpful in assisting with this replication.  Then, as the meta-analysis progressed, he became even more involved and has now joined the project as a co-author.  The project’s still not complete yet, but I’ve really enjoyed working with him, and I’m proud that this will (hopefully) become an example of how collegial and productive replication work can be towards better and more cumulative science.

References

Calin-Jageman, R., & Lehmann, G. (2015). Romantic Red – Registered Replications of effect of Red on Attractiveness (Elliot & Niesta, 2008; Elliot et al. 2010). Open Science Framework. https://doi.org/10.17605/osf.io/j3fyq [Source]
Elliot, A. J., Niesta Kayser, D., Greitemeyer, T., Lichtenfeld, S., Gramzow, R. H., Maier, M. A., & Liu, H. (2010). Red, rank, and romance in women viewing men. Journal of Experimental Psychology: General, 139(3), 399–417. https://doi.org/10.1037/a0019689
Elliot, A., & Niesta, D. (2008). Romantic red: red enhances men’s attraction to women. Journal of Personality and Social Psychology, 95(5), 1150–64. [PubMed]
Francis, G. (2013). Publication bias in “Red, rank, and romance in women viewing men,” by Elliot et al. (2010). Journal of Experimental Psychology. General, 142(1), 292–6. [PubMed]
Grahe, J. E., Reifman, A., Hermann, A. D., Walker, M., Oleson, K. C., Nario-Redmond, M., & Wiebe, R. P. (2012). Harnessing the Undiscovered Resource of Student Research Projects. Perspectives on Psychological Science, 7(6), 605–607. https://doi.org/10.1177/1745691612459057
Hesslinger, V. M., Goldbach, L., & Carbon, C.-C. (2015). Men in red: A reexamination of the red-attractiveness effect. Psychonomic Bulletin & Review, 22(4), 1142–1148. https://doi.org/10.3758/s13423-015-0866-8
Kirsch, F. (2015). Wahrgenommene Attraktivität und sexuelle Orientierung. Springer Fachmedien Wiesbaden. https://doi.org/10.1007/978-3-658-08405-9
Lehmann, G. K., & Calin-Jageman, R. J. (2017). Is Red Really Romantic? Social Psychology, 48(3), 174–183. https://doi.org/10.1027/1864-9335/a000296
Lynn, M., Giebelhausen, M., Garcia, S., Li, Y., & Patumanon, I. (2013). Clothing Color and Tipping. Journal of Hospitality & Tourism Research, 40(4), 516–524. https://doi.org/10.1177/1096348013504001
Peperkoorn, L. S., Roberts, S. C., & Pollet, T. V. (2016). Revisiting the Red Effect on Attractiveness and Sexual Receptivity. Evolutionary Psychology, 14(4), 147470491667384. https://doi.org/10.1177/1474704916673841
Seibt, T. (2015). Romantic Red Effect in the Attractiveness Perception. In Proceedings of The 3rd Human and Social Sciences at the Common Conference. Publishing Society. https://doi.org/10.18638/hassacc.2015.3.1.186

APS Workshop on Involving Undergraduates in Replications

I had the pleasure of presenting with Geoff Cumming, John Grahe, and Fiona Fidler at this year’s APS meeting on the topic of involving students in replication projects (also, our discussant was Rebecca Saxe, who was terrific).

For my presentation I tried to collect together what I’ve learned from supervising student replication efforts. I especially tried to emphasize the benefits of using positive controls in psychology research to help make replication data (or any data for that matter) more interpretable.

In developing the talk it dawned on me that it would be useful to collect materials together to walk students through the process of developing a replication project. So I created a project page on the Open Science Framework where I’ve put together a bunch of resources for selecting projects, developing materials, including positive controls, etc. It’s all available on the OSF here: https://osf.io/jx2td/

APS Presentations

APS was in Chicago this year, so the replicators I have been supervising were out in full force.

Clinton Sanchez presented his replications of a study claiming that analytic thinking promotes religious disbelief. (10.1126/science.1215647). His manuscript is having a rough time, but we’re hoping it will be out soon. Clinton is now in a MA program in Clinical Counseling at DePaul. Data from his project is here: https://osf.io/qc6rh/

Elle Lehmann presented a poster of her replications of a studies showing that red enhances perceived attractiveness of men rating women (10.1037/0022-3514.95.5.1150) and women rating men (10.1037/a0019689) . Elle’s paper is in submission–she found little to no effect for either gender. She’s now working on a meta-anlaysis which has become quite a project, but really interesting. She has graduated and will be applying for a Fullbright in the fall. Data from here project is here: https://osf.io/j3fyq/

Last but not least Eileen Moery presented a poster of her replications of a study which claimed that organic food makes you morally judgemental (10.1177/1948550612447114). Eileen’s studies were recently published (10.1177/1948550616639649). She found little to no effect of organic food exposure on moral judgements. She’s starting an MA program in clinical psych at IIT in the fall!. Data from here project is here: https://osf.io/atkn7/

Photos came out a bit blurry (new phone, but crappy camera!).

Elle and me at her poster.
Elle and me at her poster.
Clinton and Elle at his poster.
Clinton and Elle at his poster.

Bibliography