The SlugLab was in full force at the 2023 meeting of the Chicago Society or Neuroscience.
Zayra, Jackie, and Jash presented a poster reporting the very-long-term sensitization project we worked on this past summer.
Theresa snuck in some science before escaping for her softball team’s spring break trip.
We got to catch up with Cristian, a SlugLab alum now working as a lab technician at Rush.
And, nearly all of C-J’s neurobio class attended, soaking up some fantastic neuroscience.
A big highlight was the address by Carl Hart: “Exaggerating Harmful Drug Effects on the Brain Is Killing Americans” — it was a heartfelt, heartbreaking, and fascinating talk. Bravo to cSFN for highlighting Dr. Hart’s work and perspective.
Yesterday (12/14) was our slug lab and neuroscience holiday party. Please ignore the fact that we had food in the lab; focus instead on the festive fun time (complete with a crackling fireplace broadcast on the lab projector… toasty!).
We celebrated the graduation of our mid-term neuroscience majors
Steven Proutsos, who is graduating with a 4.0! (well, hopefully, depending on how he does on C-J’s molecular biology final) and just scheduled his MCAT
Christian Gonzalez, who just accepted a job working as a research technician in a neuroscience lab at Rush medical school!
We also celebrated birthdays, off-campus departures, successful TA-ships, the holiday, and anything/everything else worth celebrating about our wonderful lab students and neuroscience majors (a few non-majors even snuck in; the more the merrier!)
Yesterday, two Slug lab members had their first chance to present their ongoing research projects, premiering their work at the 2022 PUMA-STEM summer research conference:
Jaqueline Gutierrez presented work on very long-lasting sensitization in Aplysia
Monica Lopez presented work on developing earthworms to study long-term sensitization
It was a great event, and both Jaqueline and Monica did themselves proud–they had really nicely designed posters, presented with confidence, and did a fantastic job fielding question.
DU school photographer Ryan Pagelow stopped by this week to immortalize the intense work the Sluglab has been conducting this summer (thanks, Ryan!). Here are some cool images featuring Hannah Danha, Christian Gonzalez, Emma Gray, Jaquelin Gutierrez, Zayra Juarez, Monica Lopez, Steven Proutsos, Theresa Wilsterman, Jashui Zarate Tores, and Octavian Calin-Jageman.
It’s July of 2022 and for the past 2 months the SlugLab has been lurching back into life.
For the first time since 2019, the sluglab welcomed a new cohort of summer research students: a record 10 students!
Start of the summer celebration with Tavi, Theresa, Emma, Jas, Zayra, Monica, and Jaquelin (all seated); Christian, Steven, and Hannah.
We’ve so far been confronting the many problems associated with getting the lab back up and running. All previous SlugLab students had graduated, so training had to start from scratch with everything: tank maintenance, siphon-withdrawal reflex measurement, sensitization training, dissections, RNA isolation, qPCR, and data analysis.
Not only has getting everyone up to speed been a challenge, there have also been many challenges to confront from raising up the lab from dormancy. We had challenges with our RNA isolation protocol, an unhealthy batch of animals, a tank that shut down mysteriously over the weekend (and a tank monitoring system that didn’t sound the alarm!), a new file sharing service imposed by the university (which has been terrible), a simulator set up wrong… it’s really been an uphill fight almost every step of the way.
While the list of challenges has been lengthy, it’s turned out to be a lot of fun overcoming them. Our new and large group of sluglab scientists has brought tremendous enthusiasm and camaraderie, a surprisingly deep level of artistic talent, donuts, and a whole lot of fun to the lab. We’ve been knocked down, but we’ve made funny memes about it, and got back up again.
Nothing but great concentrations in the SlugLab!
Maybe we’re also smiling because as we finally seem to have kick started the engine in the lab. We switched to hand homogenization and RNA yields have been amazing. We fixed the stimulator, got healthy animals, and doubled-down on training how to measure behavior, and viola–behavioral data has been pretty fantastic. With data starting to roll in we were finally able to have a lab meeting to work through how to analyze qPCR data, and students have been adding plate after plate of new data for us all to ponder.
At this point, it’s late July and things are really cooking! We have developed and pre-registered (https://osf.io/wvx6z/) an experiment to examine the transcriptional correlates of a very long lasting memory, and it looks like we might end the summer with all behavioral data and tissue collection complete (or at least close to it!). This is an exciting experiment. It’s very clear that forming new long-term memories changes gene expression. What is less clear, though, is if these transcriptional changes are needed to help create the memory, or if they are needed both to create and maintain the memory. Neuroscientists have generally assumed an important role in maintenance, and some models specifically imagine transcriptional feed-back loops that help perpetuate transcription to help maintain memory expression1. But this would be a costly way to store a memory. Maybe instead, memories can become transcriptionally independent–perhaps by re-allocating resources within a neuron rather than permanently increasing them.
Our lab has had some hints that transcription might not persist throughout maintenance, at least not for the form of long-term sensitization we study in Aplysia. First, we’ve found that transcriptional changes after sensitization fade within 5 days, 2 days earlier than the memory lasts2. This might mean that transcription isn’t needed for maintenance, but it could also mean that there is a slight lag between gene expression decaying and memory expression decaying (2 days isn’t that much of a gap). A second line of evidence is that we’ve found that re-activating a seemingly forgotten memory requires no new changes in gene expression (at least none we could detect), suggesting an uncoupling between memory expression and transcription3. This is all suggesting, but not at all definitive.
Now we are collecting data that might help illuminate what role (if any) transcription plays in maintaining a long-term sensitization memory. To do this, we’ve cranked up our training protocol to 11– we are training each animal for 4 consecutive days rather than 1. Work in the Byrne lab4 and other labs has suggested that this extended training protocol produces very long-lasting sensitization, and indeed we’re seeing robust behavioral expression 11 days after training (in our typical 1-day training protocol, behavior was almost always back to normal within 7 days). With this longer-lasting training protocol we can examine if transcription also lasts a long time (more than 5 days) or it it still fades quickly. Specifically, we’ll conduct microarray on samples harvested 1 and 5 days after the end of training, and compare the levels of gene regulation at those two time points. If we see that the widespread transcritptional changes at 1 day are still present at day 5, this would suggest a potential role in memory maintenance. However, if we see a decay in transcription at day 5, it would suggest something else is going on…. perhaps transcriptional changes are offset by compensatory mechanisms? Or perhaps memories can be maintained without an ongoing transcriptional change?
At this point we have no idea how the new study will work out… will transcription persist as long as behavior? Will it fade early? We don’t know, but we’re excited to find out. At this point, it looks like we might end the summer with all behavioral data collected and tissue harvested… so it won’t be too much longer now before we have an answer (hopefully).
It’s been a grueling but fantastic summer.
1.
Zhang Y, Smolen P, Baxter DA, Byrne JH. The sensitivity of memory consolidation and reconsolidation to inhibitors of protein synthesis and kinases: Computational analysis. Learn Mem. Published online August 24, 2010:428-439. doi:10.1101/lm.1844010
2.
Patel U, Perez L, Farrell S, et al. Transcriptional changes before and after forgetting of a long-term sensitization memory in Aplysia californica. Neurobiology of Learning and Memory. Published online November 2018:474-485. doi:10.1016/j.nlm.2018.09.007
3.
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
4.
Wainwright ML, Byrne JH, Cleary LJ. Dissociation of Morphological and Physiological Changes Associated With Long-Term Memory in Aplysia. Journal of Neurophysiology. Published online October 2004:2628-2632. doi:10.1152/jn.00335.2004
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 ago1 . 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.
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
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.
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
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.
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
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
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
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.
