Students

DU Connections and a New Slug Home

- rcalinjageman

The slug lab is kicking off summer research with a brand new aquarium and mixing station for housing Aplysia.  It’s a great upgrade and an even better story that involves some strong DU connections.

The slug lab has been running for 10 years now (gasp!) and our aquariums were showing signs of wear.  Like the wooden stand on one of the tanks starting to collapse.  Pretty strong sign.  (fortunately a student was in the room as the tank started to tip; she called for help, we drained the tank, and disaster was averted).  By fall of 2017 we were down to just 1 tank and worried about how we’d get back to 2 in time for our blitz of summer research.

DU Connection Number 1: In late fall 2017 we were thrilled to receive a McNichols grant from a Dominican Alumni.  This grant was specifically targeted at funding science education at Dominican. We had some meetings and identified several great projects that could be helped by this generous gift–work to improve our greenhouse, a new measurement instrument for the PChem lab, and… a new tank for the slug lab.  Hooray, and a big thanks to the McNichols family.

DU Connection Number 2: We knew we wanted to upgrade beyond a hobbyist tank.. but there were so many options and it was difficult to determine the best path forward.   Enter DU connection #2, Romney Cirillo and his company Something Fishy.  Romney was a business major at Dominican.  When he graduated he wasn’t entirely sure what to do.  But he remembered Al Rosenbloom’s advice to find something he was passionate about and to find a way to make it a life’s work.  Combining that advice with a great entrepreneurship class he had completed, Romney decided to start a business related to his life-long interest in raising exotic fish.  He recruited a great friend as a business partner.  Something Fishy was quickly born as a full-service aquarium design and maintenance company.   Since its founding, Something Fishy has thrived by providing great service and incredible craftsmanship.  Things were going well, so Romney started giving back to DU–installing a gorgeous salt-water tank in Parmer hall.  That’s how I met Romney and got to know Something Fishy.  So, naturally, when it came time for a new tank, Romney was the first person to call.  Thank goodness for these strong DU connections.

The amazing tank.  Romney and Mike visited the slug lab, walked us through options and designed a customized setup exactly suited for our needs:

  • a bigger tank with a better filter system
  • lower to the ground with a huge lid to make experimental access easier (our students say thank you!)
  • incredibly tough and corrosion resistant tank stand (no more collapses from wooden stands)
  • better insulation to make our chillers work less hard
  • and an incredible mixing station for making salt water, complete with a DI line and an auto-shutoff (no more leaks down into the classroom below).

We just finished our first round of experiments with animals housed in the new tank… wow!  Even on the day of shipment the tank water stayed at crystal clear.  Good water -> healthy animals -> a good platform for good science.

Not only is the tank *way* better than what we had, it looks amazing–the install is clean and sharp; it really looks space age.  Best of all, the cost was not astronomical.

So – thanks to two great DU alum we have a great new home for our animals.

Romney (right) showing me the features of the tank on install day.

Here are some photos, but they don’t really do the tank justice for how cool and clean it all looks.

First fillup. Water has just had salt added.
Smiles even on tank cleaning day! The new tank setup is soooo sharp. (Melissa, Ushma, and Leticia… there are slugs in the tank, but all are hiding in the back).

Slug Lab 2018 – Summer Edition

- rcalinjageman

Summer is here, so the Slug Lab is running full speed.

We’re lucky to be joined once again by a really talented and dedicated team of students.  Here’s most of us at a pizza party to inaugurate a summer of research.  

From far left we have

  • Kayla Hall, joining us from Amherst for the summer
  • Ushma Patel, who has graduated but will stay in the lab for the start of the summer (and then on to study biomedical illustration at UIC)
  • Athira Jacob, lab alum now studying for her MCAT
  • Derek Steck, lab alum who this summer will be in the UCLA summer research program this summer
  • Steven Farrell, who has graduated but is also sticking with the lab for part of the summer while prepping for the MCAT
  • Dr C-J and myself (end of the table)
  • Tanya Rosiles, new lab member
  • Everett Krause, new lab member
  • Leticia Perez, lab alum sticking around for part of the summer before heading to UofI for veterinary medicine
  • Melissa Nguyen, new lab member and post-bac student

And not yet in the photo but planning on joining when she returns from Ireland: Shannon Wilcox

I hope I don’t jinx anything when I say that we’re off to a great start, with a very successful round of behavioral experiments and RNA isolations.  Looking forward to another great slug lab summer.

 

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

- rcalinjageman

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]

An unforgettable experience talking about forgetting

- rcalinjageman

Wow! Our lab just returned from the 2017 Society for Neuroscience meeting.  It was the typical maelstrom of neuroscience–with more than 20,000 neuroscientists bustling about trying to share the latest and greatest about their research.

This turned out to be an especially great year for the Slug Lab.  Leticia Perez, who has been working in our lab for the past two summers, submitted an abstract to present the work she and others in the lab have been doing on forgetting.  We’ve been really excited about the results of this project.  It turns out the SFN organizers were excited, too–they selected Leticia’s abstract for a 10 minute talk during a mini-symposium on the mechanisms of learning and memory.

Leticia absolutely crushed it–she gave a concise, clear, and exciting presentation on what happens in the Aplysia nervous system as a long-term memory is forgotten.  She handled the questions wonderfully, and was soundly congratulated by many researchers in the learning and memory community.  Of the 20,000+ in attendance, I’m willing to be she was the only undergraduate to give a talk at this year’s meeting.  It was *such* an accomplishment.

In case that wasn’t enough, Leticia also brought along a poster presenting the research.  She gave the poster at the pre-meeting on molecular and cellular neuroscience and at the undergraduate poster session.  Yes, that means she gave 3 presentations last weekend!  Wow!  And, again, all went wonderfully.

Part of the reason Leticia was able to attend the meeting to earn all this acclaim is that she was awarded an Excel scholarship through Dominican University–this paid her registration, hotel, and airfare to make it affordable to attend the meeting.  She still had to work like crazy to collect the data, refine the presentation, and clear her class schedule to attend.  Lab alumnnus Marissa Rivota also attended–so her and Leticia also got to see the capital and the White house.

We’re so proud of Leticia, and of the many other students who have worked so hard in the lab for the past summers to make this forgetting project such a success.  There will be a paper on it coming out very soon in Learning and Memory.  It’s tremendous work to do good science–we’re so happy to have wonderful students who want to get involved and excel.

Below are photos of Leticia giving her talk, giving her poster, and celebrating with me, Irina, and Marissa.  Congrats, Leticia!

Maintaining Memories, Changing Transcription

- rcalinjageman

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

The Amazing Slug Lab – circa 2017

- rcalinjageman

This summer DU’s photographer stopped by the lab to take some snazzy photos of the Slug Lab in action.  Here’s one of the photos, featuring the amazing roster of talented students who devoted so much time and effort to the lab this summer.  Back row (left to right) is Steve Farrell, me (Bob), and Derek Steck.  Front row is Marissa Rivota, Ushma Patel, Leticia Perez, and Irina.  Also, check out the cool slug lab logo that Ushma designed!

APS Presentations

- rcalinjageman

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. [cite source=’doi’]10.1126/science.1215647[/cite]. 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 [cite source=’doi’]10.1037/0022-3514.95.5.1150[/cite] and women rating men [cite source=’doi’]10.1037/a0019689[/cite] . 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 [cite source=’doi’]10.1177/1948550612447114[/cite]. Eileen’s studies were recently published [cite source=’doi’]10.1177/1948550616639649[/cite]. 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.

Rest easy — organic food probably does not make you into a jerk…

- rcalinjageman

My student Eileen Moery and I have a new paper out today in Social Psychology and Personality Science. It’s a replication paper that I’m quite proud of [cite source=’doi’]10.1177/1948550616639649[/cite]. It represents some evolution in how I’m supervising replication projects.

The new paper replicates a study purporting to show that being exposed to images of organic food produces a strong decrease in prosocial behavior and a strong up-tick in being morally judgmental [cite source=’doi’]10.1177/1948550612447114[/cite]. This is a potentially fascinating phenomenon–something like ‘moral licensing’, the ironic effect of good behavior fostering subsequent bad behavior.

The original paper caught fire and the media covered these findings extensively. Rush Limbaugh even crowed about them as evidence of liberal hypocrisy. I noticed the media coverage, and this is how the original study made it onto my ‘possible replication’ list. Eileen found it there, read the paper, and developed a fantastic honors project to put the initial study to the test.

For her project, Eileen contacted the original author to obtain the original materials. She planned and executed a large pre-registered replication attempt. She included a positive control (Retrospective Gambler’s task) so that if the main study ‘failed’ we would have a way to check if it was somehow her fault. She also devised a nice memory manipulation check to be sure that participants were attending to the study materials. She conducted the study and found little to no impact of organic food exposure on moral reasoning and little to no impact on prosocial behavior. She did find the expected outcome on the positive control, though–so sorry, doubters, this was not an example of researcher incompetence.

One of the things I don’t like about the current replication craze is the obsessive emphasis on sample size (this paper is not helping: [cite source=’doi’]10.1177/0956797614567341[/cite]). Sure, it’s important to have good power to detect the effect of interest. But power is not the only reason a study can fail. And meta-analysis allows multiple low-power studies to be combined. So why be so darned focused on the informativeness of a single study? The key, it seems to me, is not to put all your eggs in one basket but rather to conduct a series of replications–trying different conditions, participant pools, etc. The pattern of effects across multiple smaller studies is, to my mind, far more informative than the effect found in a single but much larger study. I’m talking about you, verbal overshadowing [cite source=’doi’]10.1177/1745691614545653[/cite]

Anyways, based on this philsophy, Eileen didn’t stop with 1 study. She conducted another larger study using Mechanical Turk. There are lots of legitimate concerns about MTurk, so we used the quality controls developed in Meg Cusack’s project [cite source=’doi’]10.1371/journal.pone.0140806 [/cite]–screening out participants who don’t speak English natively, who take way too long or too short of a time to complete the study, etc. Despite all this care (and another successful positive control), Eileen still found that organic food produced about 0 change in moral judgments and prosocial behavior.

Still not finished, Eileen obtained permission to conduct her study at an organic food market in Oak Park. Her and I spent two very hot Saturday mornings measuring moral judgments in those arriving at or leaving from the market. We reasoned those leaving from had just bought organic food and should feel much more smug than those merely arriving or passing by. Yes, there are some problems of making this assumption–but again, it was the overall pattern across multiple studies we cared about. And the pattern was once again consistent but disappointing–only a very small difference in the expected direction.

Although Eileen and I were ready to call it quits at this point, our reviewers did not agree. They asked for one additional study with a regular participant pool. Eileen had graduated already, but I rolled up my sleeves and got it done. Fourth time, though, was not the charm–again there was little to no effect of organic food exposure.

With all that said and done, Eileen and I conducted a final meta-anlysis integrating our results. The journal would not actually allow us to report on the field study (too different!?), but across the other three studies we found that organic food exposure has little to no effect on moral judgments (d = 0.06, 95% CI [0.14, 0.26],N=377) and prosocial behavior (d=0.03, 95% CI [?0.17, 0.23],N=377).

So–what’s our major contribution to science? Well, I suppose we have now dispelled what in retrospect is a somewhat silly notion that organic food exposure could have a substantial impact on moral behavior. We are also contributing to the ongoing meta-science examining the reliability of our published research literature–it gives me no joy to say that this ongoing work is largely painting a relatively bleak picture. Finally, I hope that we have now gained enough experience with replication work to be (modestly) showing the way a bit. I hope the practices that are now becoming routine for my honors students (pre-registration, multiple studies, positive controls, careful quality controls, and synthesis through meta-analysis) will become routine in the rest of replication land. No, strike that–these are practices that should really be routine in psychology. Holding my breath.

Oh – an one other important thing about this paper–it was published in the same journal that published the original study. I think that’s exactly as it should be (journals should have to eat their own dog food). Obviously, though, this is exceptionally rare. I think it was quite daring for the journal to have published this replication, and I hope the good behavior of its editors are a model for others and a sign that things really are changing for the better.

Grant Awarded to study the mechanisms of sensitization maintenance and decay

- rcalinjageman

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:
grant*

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.

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

- rcalinjageman

A nice way to wrap up 2014–we have a new paper out [cite source=’pubmed’]25486125[/cite] 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 [cite source=’pubmed’]25117657[/cite]. 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: http://dx.plos.org/10.1371/journal.pone.0114481. Also, you can download our raw data to examine for yourself at the Open Science Framework: https://osf.io/ts9ea/.