The Sluglab is back!

- rcalinjageman

Today we received a shipment of Aplysia–the first shipment we’ve had since February of 2020.

It’s been a long, frustrating, and anxiety-ridden time for the animal colony to be empty. It’s not that the lab has been inactive–in fact, we published what I think is our best paper ever just a few months ago​1​ . But it has been a long stretch without being able to provide the our typical level of involvement and excitement for our student researchers in the slug lab.

It feels really good to know that we are getting back on track. In fact, in addition to welcoming new slugs we’ve welcomed 5 new lab members: Lucas Eggers, Cynthia Espino, Daniel Mason, Delaney Mcriley, & Steven Proutsos. They join continuing member Melissa Nguyen to round out the Fall 2021 edition of the Sluglab. Let’s kick some a**! (scientifically)

First batch in a long time: Dr. Bob, Dr. C-J, and new lab member Cynthia Espino, October 2021

Our first project with this batch of animals will be to explore for epigenetic markers accompanying long-term sensitization.

Over the last summer, C-J has worked like crazy on protocols for measuring methylation. We’ve found that it is surprisingly easy to full yourself, to obtain signals due to non-specific binding. What we’ve settled on is a process to check specificity of primer sets exhaustively by using synthetic DNA that we can manually methylate. Using this approach we’re pretty sure a key CPG island in the CREB1 promoter is *not* methylated in either control or trained animals. And our summer results also identified a CPG island in the egr promoter that seems to be default methylated, but with no change after sensitization. Our goal with these new animals is to now survey other methylation sites in the promoters of highly learning-regulated transcripts. Having lab meetings back in person has been fantastic (masks, of course, and DU has a vaccine mandate which has been very well implemented); very excited to see where research involvement takes our latest batch of slug lab members.

  1. 1.
    Rosiles T, Nguyen M, Duron M, et al. Registered Report: Transcriptional Analysis of Savings Memory Suggests Forgetting is Due to Retrieval Failure. eNeuro. Published online September 14, 2020:ENEURO.0313-19.2020. doi:10.1523/eneuro.0313-19.2020

Research lemonade: RRR on the short-term benefits of emotional reappraisal interventions in an online context

- rcalinjageman

When the pandemic hit, all in-person research was shut down at Dominican (of course). This left a real challenge in terms of trying to figure out how our psychology majors could continue to engage in authentic and interesting research.

One solution I (Bob) worked on during the summer of 2020 was to assemble a collection of studies that would be a) socially relevant, and b) feasible to replicate and extend fully online (https://osf.io/xnuap/). This worked out really well for our research methods sequence.

I also worked with colleague TJ Krafnick on another approach: getting DU involved in some RRR projects (registered replication reports). Specifically, TJ and I applied to take part in a massive RRR organized by the psychological science accelerator (https://psysciacc.org/). What was especially exciting about this RRR was that it featured a trio of experiments, each designed to test online interventions to help modify emotional/behavioral responses to the Covid-19 pandemic (https://psysciacc.org/studies/psacr-1-2-3/). TJ and I obtained local IRB approval, and then we worked with our research methods students to collect data at DU. Students in my fall 2020 research and methods course then analyzed the data from our DU and wrote it up for their semester-long term projects. It was a really good experience for the class; we turned lemons into lemonade.

Now the psych science accelerator has assembled the data from all the team sites and published the manuscript for the first project ​(Wang et al., 2021)​. TJ and I are proud to be co-authors in a very long-list of talented collaborators (reading through the Google docs of draft proposals and manuscripts was incredible–at times, the manuscripts were probably more comment than actual text!).

So what was the actual study and what did it find? Participants (N > 23,000!) were randomly assigned to receive either a brief training in an emotional regulation strategy (reappraisal or reconstrual) or to a control condition. Participants were then asked to rate their positive and negative emotions in response to a series of genuinely heartbreaking images related to the Covid-19 pandemic. There were clear and consistent effects of the interventions on self-reported emotions: participants who received the training reported more positive emotions (d = -0.59!) and fewer negative emotions (d = -0.39) in response to the photos. This was true across essentially all study sites regardless of language or culture. That’s pretty amazing! On the other hand, the intervention was short term, and the dependent variable relied entirely on self-reported emotional responses, which might not be very reliable and which could be susceptible to demand effects from the study. Still, an encouraging win for emotional re-appraisal strategies.

  1. Wang, K., Goldenberg, A., Dorison, C., Miller, J., Uusberg, A., Lerner, J., … Moshontz, H. (2021). A multi-country test of brief reappraisal interventions on emotions during the COVID-19 pandemic. Nature Human Behaviour, 5(8), 1089–1110. doi: 10.1038/s41562-021-01173-x

What is forgetting? Slug lab provides some new insights!

- rcalinjageman

Today, the SlugLab can share an exciting new paper, with contributions from Tania Rosiles, Melissa Nguyen, Monica Duron, Annette Garcia, George Garcia, Hannah Gordon, and Lorena Juarez ​(Rosiles et al., 2020)​.

Where to even start?

  • Contributions from 7 student co-authors! It’s been such a long haul; we’re proud of each of you for sticking with it and for all your contributions to this paper.
  • This paper is a registered report: We first proposed the idea and the methods, even writing a complete analysis script. This was then sent to peer review (you know, when you can still do something if the reviewers turn up an issue or problem to consider!) and after some back and forth received an ‘in principle’ acceptance. Then we completed the work and the analysis and submitted it for one more round of review focused solely on the interpretation of the data. This approach to publication lets peer reviewers have a more meaningful impact on the project and it also helps combat publication bias. People tend to think of this model for replication research, but in our case we used a registered report because we wanted to establish a fair and valid test between two competing theories and to ensure that the approach and analysis were pre-specified.
  • This paper is exciting! We were able to test two very different theories of forgetting:
    • decay theory, which says that memories are forgotten because they physically degrade
    • retrieval failure, which says that memories don’t degrade at all, but simply become more difficult to retrieve due to interference

We found clear support for the retrieval failure theory of forgetting, something I (Bob) was completely not expecting.

So, what was the study actually about?

Even memories stored via wiring changes in the brain can be forgotten. In fact, the majority of long-term memories are probably forgotten. What does this really mean? Is the information gone, or just inaccessible?

One clue is from savings memory, the fact you can very quickly re-learn seemingly-forgotten information. Savings memory is sometimes taken to mean the original memory trace persists, but it could also be that it had decayed, and the remnants prime re-learning.

We noticed a testable prediction:

  • If forgetting is decay, savings re-encodes the memory and must involve the transcriptional and wiring changes used to store new information.
  • If forgetting is inaccessibility, savings shouldn’t involve transcriptional/wiring changes

To test this prediction, we tracked transcriptional changes associated with memory storage as a memory was first formed, then forgotten, then re-activated. We did this in the sea slug, Aplysia calinfornica as a registered report (with pre-registered design and analyses).

The memory was for a painful shock—this is expressed as an increase in reflexes (day 1, red line way above baseline). Sensitization is forgotten in about a week (day 7, reflexes back to normal), but then a weak shock produces savings (day 8, reflexes jump back up)

What’s happening in the nervous system? Our key figure shows expression of ~100 transcripts that are sharply up- or down-regulated when the memory is new. At forgetting, these are deactivated (all lines dive towards 0). At savings? No re-activation! (lines stay near 0)

Our results show that savings re-activates a forgotten memory without invoking *any* of the transcriptional changes associated with memory formation. This strongly suggests the memory is not rebuilt, but just re-activated—the information must have been there all along?!

Lots of caveats (see paper), but the results seem compelling (though surprising) to us. In particular, we used an archival data set to show we would have observed re-activation of transcription had it occurred. Transcriptional changes with savings are clearly negligible.

  1. Rosiles, T., Nguyen, M., Duron, M., Garcia, A., Garcia, G., Gordon, H., … Calin-Jageman, R. J. (2020). Registered Report: Transcriptional Analysis of Savings Memory Suggests Forgetting is Due to Retrieval Failure. Society for Neuroscience. doi: 10.1523/eneuro.0313-19.2020

What psychology instructors should know about Open Science and the New Statistics

- rcalinjageman

Beth Morling and I (Bob) have a new commentary out in Teaching of Psychology that provides an overview of the Open Science and New Statistics movements and gives some advice about how psychology instructors can bring these new developments into the traditional psychology curriculum ​(Morling & Calin-Jageman, 2020)​.

Beth is a superstar, on many fronts, but is perhaps best known for her incredible Research Methods in Psychology textbook (https://wwnorton.com/books/9780393536263). Just being asked to work on this commentary was a thrill. Then, working together, I learned a lot from her, especially with her approach to writing, which kept us on task and productive.

The article is open-access, so check it out. Here’s my favorite paragraph:

Introductory coursework is the ideal time to foster estimation thinking. Teachers can use the prompt, “How much?” to help students consider the magnitudes of effects and to seek context. Using the prompt, “How wrong?” can encourage students to embrace uncertainty and to introduce the key idea of sampling variation. Finally, prompting students with, “What else is known?” helps them see science as a cumulative and integrative process rather than as a series of “one-and-done” demonstrations. These three questions instill a nuanced view of science, where any one study is tenuous, and yet the cumulative evidence from a body of research can be compelling. This is a sophisticated epistemic viewpoint that avoids both excessive confidence and undue cynicism.

Morling & Calin-Jageman, 2020, p. 174
  1. Morling, B., & Calin-Jageman, R. J. (2020). What Psychology Teachers Should Know About Open Science and the New Statistics. SAGE Publications. doi: 10.1177/0098628320901372

SFN 2019 for the Slug Lab

- rcalinjageman

We’ve just wrapped up a great Society for Neuroscience conference for the slug lab. This year’s meeting (2019) was held right here in Chicago, which provided lots of opportunities for our talented crop of students.

We presented a poster examining the time course of forgetting and transcriptional changes at the undergraduate session and at the main meeting. Leading the poster presentation were Tania Rosiles and Melissa Nguyen. After warming up in the undergrad session they were bombarded with tough questions at the main meeting–and they handled themselves amazingly well, doing an awesome job presenting the research. Here they, basking in the knowledge that they had completely crushed it:

Tania Rosiles and Melissa Nguyen presenting that the 2019 Society for Neuroscience Meeting.

I guess they made a big splash, because later at the meeting, guess who asked me for a selfie?

Bob, Nobel-Prize Winner Eric Kandel, and Lisa Gabel. Kandel’s the one in the middle.

Ok – maybe it was me asking Kandel for a selfie, but either way it was cool to briefly meet the godfather of sea slug studies at the meeting.

Sluglab 2019 – It will be an unforgettable summer

- rcalinjageman

It’s summer and the slug lab is rocking. We have 8 students working in the lab (!), and a number of really exciting projects.

Here’s the lab photo to start the summer.

From left to right: Kiara Rana, Dr. C-J, Dr.Bob, Tania Rosiles, George Garcia, Annette Garcia, Hannah Gordon, Lorena Juarez, Monica Duron, and Melissa Nguyen

We knew this spring that we had recruited a special group of students in to the lab. So far the work this summer has confirmed our hunch–we’ve already completed two rounds of behavioral testing, students are making progress learning qPCR, and yesterday we had a great start to learning electrophysiology. I’m sure we’ll have our ups and downs, but it seems like we’re poised for a fun and productive summer.

Projects we’ll be working on include: 1) investigating if savings memories are re-formed or re-covered, 2) investigating the role of the peptide transmitter FMRF-amide in forgetting, 3) exploring the role of methylation in memory maintenance, and 4) some exciting pilot testing with a paradigm for sensitization in fruit fly larva, in collaboration with Scott Kreher in biology.

Our work this summer continues to be supported by the NIH (our current R15 expired at the end of May, but looks like it will be renewed starting July 1). Huzzah.

In addition, Dominican has received a generous donation from Joe Moskal to start the Moskal scholars program. Joe is a professor of biomedical engineering at Northwestern, a biotech entrepreneur, a Dominican trustee, and an all-around amazing guy. He generously helped Irina and me develop pilot data for our first grant and provided a sparkling letter of support… so it is no exaggeration to say he has already helped make the slug lab what it is today.

This year, Joe took the next step in his efforts to develop and broaden the biotech pipeline by funding the Moskal scholars program. Over the next five years this program will fund students interested in careers in the life and health sciences to spend a summer engaged in intensive research. The goal is for students to have the space, mentoring, and encouragement to develop their skills and passions in the science, and to launch them forward to great things.

Our first two Moskal scholars are Annette Garcia and Tania Rosiles. Tania will be spending her second summer in the slug lab–she’s already gained tremendous lab skills and helped co-author our recent paper on the long-term transcriptional response to sensitization ​(Patel et al., 2018)​. Annette is new to the lab, but was a star in Dr. C-J’s neurobiology class and has already been making big strides in the lab.

The inaugural Moskal Scholars: Annette Garcia and Tania Rosiles

Neither Irina nor I would be where we are today if we hadn’t been fortunate enough to have amazing summer experiences. For Irina it was a summer working at Loyola Medical School. For me, it was a summer at Carnegie Mellon. In both cases it was generous funding from sponsors that enabled us to forgo our usual summer jobs and spend 3 months in intense and life-altering contemplation and study. We are so excited and proud to pay that forward each summer with a new batch of slug lab recruits, and we’re extremely grateful to Joe Moskal for his generosity and support.

One of our annual summer traditions is having DU photographer Ryan Pagelow come to the lab for a group photo and some science B-roll. As always, he does an amazing job. Here’s this year’s album:

 
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  1. Patel, U., Perez, L., Farrell, S., Steck, D., Jacob, A., Rosiles, T., … Calin-Jageman, I. E. (2018). Transcriptional changes before and after forgetting of a long-term sensitization memory in Aplysia californica. Neurobiology of Learning and Memory, 474–485. doi: 10.1016/j.nlm.2018.09.007

Updated word search and mirror-tracing tasks for Qualtrics

- rcalinjageman

I finally had some spare time to document and post the mirror tracing and word-search tasks I developed for some replication work my students and I completed ​(Cusack, Vezenkova, Gottschalk, & Calin-Jageman, 2015)​.

Each task is (I think) pretty nifty, and I’ve had lots of emails about them over the past couple of years. I’ve finally posted both code bases to github along with working demos in Qualtrics and some rudimentary instructions. The code itself is not pretty–I was learning javascript and wrote most it during a conference I was attending in Amsterdam. Still, it works, and I’m sure it could come in handy.

The mirror-tracing task is just like it sounds–participants trace an image with their mouse or track pad but the mouse movements are mirrored, making it hard to stay in the line. You can vary task difficulty by changing line thickness. There is an expected weak negative correlation with age. The script can even posts the traced images back to your server, which is cool for making figures showing how groups differ with representative data.

The word-search task is also like it sounds. You can use pre-defined grids, or the script can generate a grid for you. I’ve used it to try priming for power (control vs. power-related words hidden in the grid) and to look at frustration (by having a grid that *doesn’t* have all the target letters…mean, I know).

  1. 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, e0140806. doi: 10.1371/journal.pone.0140806

Kids, Neurons, and Robots

- rcalinjageman

At the end of February I (Dr. Bob) visited a local elementary school as part of the Oak Park Educational Foundation’s Science Alliance Program.

I was matched up with Sue Tressalt’s Third Grade Class at Irving Elementary. For an activity, I brought along the neuroscience program’s collection of Finch Robots, a set of laptops, and the Cartoon Network simulator I have been developing (Calin-Jageman, 2017, 2018). I introduced kids to the basic rules of neural communication, and they explored Cartoon Network, learning how to make brains to get the Finch Robots to do what they wanted (e.g. avoid light, sing when touched, etc.). It was a great class, and a ton of fun.

I’m proud of Cartoon Network, and the fact that it can make exploring brain circuitry fun. It’s simple enough that the kids were able to dive right in (with some help), yet complex enough that really interesting behaviors and dynamics can be modelled.

As a kid, my most formative experience in science was learning logo, the programming language developed by Seymour Papert and colleagues at MIT. Logo was fun to use, and it made me need/want key programming concepts. I clearly remember sitting in the classroom writing a program to draw my name and being frustrated at having to re-write the commands to make a B at the end of my name when I had already typed them out for the B at the beginning of my name. The teacher came by and introduced me to functions, and I remember being so happy about the idea of a “to b” function, and I immediately grasped that I could write functions for every letter once and then be able to have the turtle type anything I wanted in no time at all.

Years later I read Mindstorms and it remains, to my mind, one of the most important books on pedagogy, teaching, and technology. Papert applied Piaget’s model of children as scientists (he had trained with Piaget). He believed that if you can make a microworld that is fun to explore, children will naturally need, discover, and understand deep concepts embedded in that world. That’s what I was experiencing back in 2nd grade–I desperately needed functions, and so the idea of them stuck with me in a way that they never would in an artificial “hello world” type of programming exercise. Having been a “logo kid” it was amazing to read Mindstorms and recognize Papert’s intentionality behind the experiences I had learning Logo.

Anyways, bringing Cartoon Network to an elementary school for a day gave me a great feeling of carrying on a tiny piece of Papert’s legacy. The insights kids develop in just an hour of playing with neural networks are amazing–the idea of a recurrent loop made immediate sense to them, and that also sets up the idea that both excitation and inhibition are important. And, like in Logo, the kids were excited to explore–to know that their experience was not dependent on getting the ‘right’ answer but on trying, observing, and trying again.

The day was fun and even better I received a whole stack of thank-you cards this week. Reading through them has kept a smile on my face all week. Here’s a sample.

This kid has some great ideas for the future of AI

“I never knew neurons were a thing at all”–the joy of discovery
“Your job seems awesome and you are the best at it”—please put this kid on my next grant review panel.
  1. Calin-Jageman, R. (2017). Cartoon Network: A tool for open-ended exploration of neural circuits. Journal of Undergraduate Neuroscience Education : JUNE : A Publication of FUN, Faculty for Undergraduate Neuroscience, 16(1), A41–A45. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/29371840
  2. Calin-Jageman, R. (2018). Cartoon Network Update: New Features for Exploring of Neural Circuits. Journal of Undergraduate Neuroscience Education : JUNE : A Publication of FUN, Faculty for Undergraduate Neuroscience, 16(3), A195–A196. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/30254530

SlugLab Alum Derek Stek heading to medical school with a full ride scholarship

- rcalinjageman

Graduates of the sluglab have been moving on to amazing careers. So we were excited to get the news that lab alumni and neuroscience major Derek Stek has just been offered a full scholarship to attend medical school at the School of Medicine and Public Health at the University of Wisconsin. Woo hoo!

The slug lab in summer of 2018. Derek is the tall guy on the left-side of the table; this was just before he shipped out to UCLA.

Derek spent the summer of 2017 working in the lab, and also did summer research programs at the University of Colorado (2016) and UCLA (2018). In the sluglab, Derek learned how to do extract RNA (which does *not* start by vortexing the DNA-ase) and conduct qPCR. He helped track the expression of several transcripts regulated after learning, and was a co-author on the lab’s most recent paper (Patel et al., 2018).

Derek was also a star outside of the classroom, playing a big part on the DU varsity basketball team. This year, as he finishes at DU, Derek has been working with children with autism and learning behavioral therapy.

Congrats, Derek!

  1. Patel, U., Perez, L., Farrell, S., Steck, D., Jacob, A., Rosiles, T., … Calin-Jageman, I. E. (2018). Transcriptional changes before and after forgetting of a long-term sensitization memory in Aplysia californica. Neurobiology of Learning and Memory, 474–485. doi:10.1016/j.nlm.2018.09.007

The remarkably long-lasting fragments of memory

- rcalinjageman

It was a whirlwind 2018. Irina and I are just now catching our breath and finding some time to update the lab website.

One awesome piece of news we forgot to publicize is that our latest paper came out in the August issue of Neurobiology of Learning and Memory (Patel et al., 2018).   This paper continues our work of tracking the molecular fragments of a memory as it is forgotten.  Specifically, we tracked 11 genes we suspected of being regulated *after* forgetting (Perez, Patel, Rivota, Calin-Jageman, & Calin-Jageman, 2017).  Things didn’t work out quite as well as we had expected: of our 11 candidate genes 4 didn’t show much regulation, meaning that our previous results with these genes were probably over-estimating their importance (curse you, sampling error!).  On the other hand, we replicated the results with the other genes and found that some of them are actually regulated for up to 2 weeks after the memory is induced, long after it seems forgotten.

Here are two key figures.  The first is the memory curve for sensitization in our Aplysia -it shows that after memory induction there is strong sensitization recall that decays within a week back to baseline.  Even though the memory seems gone, giving a reminder 2 weeks after learning rekindles a weak re-expression of the memory. That’s a classic “savings” effect.  

The next figure traces the time-course of memory-induced gene expression (levels of mRNA) for 6 specific genes, measured in the pleural ganglia that contains neurons known to be important for storing sensitization memory.  You can see that each of these transcripts is up- or down-regulated within 24 hours of learning, and that in each case this regulation lasts at least a week and sometimes out to 2 weeks.  So, just as the behavioral level of the memory fades but isn’t really completely gone, the some of the transcriptional events that accompany learning also seem to persist for quite some time. 

Why would this occur?  Perhaps these transcripts are part of savings…maybe they set the stage for re-expressing the memory?  Or maybe they are actually part of forgetting, working to remove the memory?  Or maybe both?  For example, one of the transcripts is encodes an inhibitory transmitter named FMRFamide.  It is really up-regulated by learning, which would normally work against the expression of sensitization memory.  So perhaps this helps suppress the memory (forgetting), but in a way that can be easily overcome with sufficient excitation (savings)… that’s an exciting maybe, and it’s the thing we’ll be working this summer to test.

As usual, we’re so proud that this paper was made possible through exceptional hard work from some outstanding DU student researchers: Ushma Patel, Leticia Perez, Steven Farrell, Derek Steck, Athira Jacob, Tania Rosiles, and Melissa Nguyen.  Go slug squad!

Patel, U., Perez, L., Farrell, S., Steck, D., Jacob, A., Rosiles, T., … Calin-Jageman, I. E. (2018). Transcriptional changes before and after forgetting of a long-term sensitization memory in Aplysia californica. Neurobiology of Learning and Memory, 155, 474–485. doi:10.1016/j.nlm.2018.09.007
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.046250.117