Category Archives: memory

New data on neurogenesis, pattern separation, context discrimination and stress

One of the leading hypothesized functions for adult hippocampal neurogenesis in memory is pattern separation. Loosely defined, pattern separation is the process of making similar patterns of neural activity more distinct. This is clearly relevant for learning and memory since we have many experiences that are similar to each other but nonetheless must be remembered as distinct. For example, the girl who sat behind me in 2nd year organic chemistry bore a striking similarity to the woman who later became the mother of my firstborn child (long, dark curly hair, sense of humour etc). But perhaps due to a dysfunctional hippocampus it wasn’t until halfway through the term that I was able to discriminate these 2 individuals.

In its true form, pattern separation is a neurophysiological computation that is very difficult to measure since we know very little about how information is represented, in terms of action potential firing patterns in assemblies of cells (i.e. how can you measure how information has changed if you don’t have a good handle on what the incoming neural activity meant in the first place?). There has been some progress suggesting the dentate gyrus may pick up on minor changes in the environment and perform such a function. And so behaviourists have been keen to test whether the dentate gyrus and immature neurons are important for this function, using tasks such as discriminative context fear conditioning (is this the place where I received a shock?) or object location tests (did these objects move just a tiny bit since I saw them last?). When the dentate gyrus is compromised, or when neurogenesis is reduced, we sometimes see deficits in these behaviours. If you have a look at the pattern separation blog you’ll see an impressive interdisciplinary discussion of what these findings mean (and don’t mean!). In short, they are consistent with a pattern separation role but they don’t prove that the dentate is actually performing pattern separation at a physiological level.

Here I present some new data on adult neurogenesis, context fear discrimination, and stress hormones. It’s been on my hard drive since 2008. Which is ridiculous since it reflects many long days of putting mice into boxes and the findings are pretty intriguing, if inconclusive.

So finally I wrote it up and have published it on FigshareDownload it there and read along.

The basic idea is that I was training neurogenesis-deficient GFAP-TK mice in a discriminative context fear paradigm. The hypothesis was that, if the dentate gyrus and adult neurogenesis is important for pattern separation, then we would expect that the TK mice would be impaired, and show similar levels of freezing in the so-called “safe” and “shock” contexts. This is now obvious given work by McHughTronel, Sahay, Niibori, Kheirbeck.

Figure 1 - circles vs stripes
Fig 1-circles vs stripes

To make the discrimination challenging, I started with a discrimination paradigm where the 2 contexts were quite similar and the only difference was the pattern on the walls of the 2 contexts: circles or stripes. During the training session it appeared to be too challenging – the mice showed no discrimination whatsoever. Interesting finding #1: when tested 1 week later, the WT mice did show a discrimination whereas the TK mice did not. To get the most out of the experiment, I re-tested the mice the following day: mice that were tested in the shock context on test 1 were tested in the safe context on test 2 and vice versa. Interesting finding #2: There was a carry over effect such that the WT mice again discriminated, but on test 2 they now froze more in the safe context! On test 2 corticosterone levels were also greater in the mice tested in the safe context.

This experiment (“Circles vs Stripes”) suggests to me that neurogenesis may indeed be involved in some sort of pattern separation function, since the TK mice never successfully discriminated. But it is interesting that WT mice only discriminated during the test. Usually, context fear memories become more generalized with time (see Wiltgen, Biedenkapp, Wang) but here they are becoming more accurate. I don’t have a solid explanation for this but wonder if the simplicity of the context difference plays a role. If mice were able to form a simple stimulus-shock association (circle-shock or stripe-shock association, rather than complex context-shock association) then these memories might not subject to the same generalization/interference processes that typically occur during consolidation. This result is also a reminder that memory may be intact, even when there isn’t behavioural evidence. Regarding the reversal effect, the paradigm is different but reminiscent of findings by Beracochea showing that stress can alter which of 2 context memories dominates at the time of retrieval. It is also worth noting that blood samples were taken 30min after testing for corticosterone measurements, using a submandibular cheek-lancet method. This is a stressful procedure and may have altered the memory retrieved on test #1, and contributed to the carryover effect on test #2.

Figure 2 - mo diff
Figure 2 – mo diff

To see if we could pull out a context discrimination difference during training, I repeated the experiment but changed many more features between the 2 contexts (shape, odours etc). This variation was code named MO DIFF since the contexts were made “more different” and I have kept that name since this isn’t a journal. If anything, the TK mice now did a better job of discriminating (at least during training). Compared to Circles vs Stripes there was weaker discrimination during Mo Diff testing and also fewer reversal/carryover effects between tests #1 and #2. TK mice had huge elevations in corticosterone compared to WT mice at the time of fear memory retrieval.

Figure 3 - stress+mo diff
Figure 3 – stress+mo diff

For the last experiment I had some mice that had been subjected to chronic stress so I figured why not then test them on Mo Diff? The mice in Mo Diff didn’t remember super well and chronic stress enhances fear conditioning so…we found that these mice indeed discriminated very well during training and testing. No difference between WT and TK mice during training but TK mice discriminated identically on tests #1 and #2. In contrast, WT mice again showed a carryover effect such that there was no discrimination on test #2.


Final thoughts: This dataset may raise more questions than it answers and for this reason my work with GFAP-TK mice then took a more straightforward route, eliminating memory from the equation and investigating whether new neurons are important for innate responses to psychological stress. In any case:

  1. The data support a role for neurogenesis in context discrimination, and potentially pattern separation, but it suggests that new neurons may bias towards both separation or generalization depending on the conditions.
  2. New neurons may be important for accurate consolidation of memory
  3. Neurogenesis regulates stress hormone levels during memory retrieval
  4. Testing order strongly influences whether mice express fear in the appropriate context

Reference: Snyder, Jason; Cameron, Heather A. (2013): Reduced adult neurogenesis alters behavioural and endocrine discriminative fear conditioning. figshare.

Forming and recalling memories. Artificially.

Memory manipulation has become one of the most hotly pursued topics in neuroscience. After all, much or of who are is based on what we’ve learned, including memories that we can consciously recall as well as acquired desires and habits that can lead to problems like addiction. In rodents, we’ve known for decades that damage to the hippocampus can erase recently-formed memories. Studies of reconsolidation have shown us that when a memory is retrieved it becomes labile and allows for new information to be added, thereby creating an updated version. More recently we (humans) have been able to identify the neurons involved in memory formation and show that killing them, and only them, results in memory erasure. Bringing us even closer to the stuff of movies, studies by Garner et al. in Science and Liu et al. in Nature have now artificially controlled memory formation and recall. We’re essentially talking about reactivating memory by pushing a button. Yes – you can say “dude, whoah” now. Continue reading Forming and recalling memories. Artificially.

Saving the best for last: neurogenesis, plasticity and memory. #SFN11

blue dcx

Previously, I wrote about new SFN data on the role for newborn neurons in regulating emotion. The second half of the SFN meeting rounded out the story because the bulk of the functional presentations focussed on the role of new neurons in that other, classic function of the hippocampus: memory. Spanning synaptic plasticity, circuit function, and then linking it all to behavior, we have quite a complete story here.


Every time I get worked up about all various neurogenesis findings I think about one acronym that returns me to a state of inner peace: ACSF-LTP. Yes, I plagiarized that last line from my previous post. We all know about LTP right? The ability of synapses to strengthen their connections in response to activity? It has been used for decades as a physiological model of memory formation. It’s pretty well accepted that newborn neuron ACSF-LTP is a unique form of LTP – one that is insensitive to GABAergic inhibition (hence “Artificial Cerebro Spinal Fluid” LTP, in contrast to LTP that also requires inhibition of GABA neurotransmission), one that requires a the NR2B subunit of the NMDA receptor, and one that is induced more easily than that of mature neurons. ACSF-LTP has quite a history: Continue reading Saving the best for last: neurogenesis, plasticity and memory. #SFN11

Random roundup

random roundup banner

“Random” roundup because any posts linking to articles or ideas I’ve recently found noteworthy will never occur on a regular basis (as others manage to do – I applaud you) but only when enough interesting material has accrued and I have a spare moment. The links will, however, not be random. For example, you can expect many links to point to articles on adult neurogenesis or hippocampal function but will likely find few links directing you to photos of puppy dogs.

Dopaminergic Modulation of Cortical Inputs during Maturation of Adult-Born Dentate Granule Cells. A pretty thorough examination of dopaminergic modulation of synaptic transmission and synaptic plasticity in the dentate gyrus. Dopamine reduced synaptic transmission in both immature and mature granule neurons, but through different receptor subtypes. Additionally, dopamine reduced long-term plasticity in immature neurons but not mature neurons. Given the suggestion that dopamine could gate the entry of information into long-term memory, these findings suggest young and old neurons could have quite different behavioral functions.

Mu Y, Zhao C, & Gage FH (2011). Dopaminergic Modulation of Cortical Inputs during Maturation of Adult-Born Dentate Granule Cells. The Journal of neuroscience : the official journal of the Society for Neuroscience, 31 (11), 4113-23 PMID: 21411652


Lidocaine attenuates anisomycin-induced amnesia and release of norepinephrine in the amygdala. Memory consolidation is the phenomenon by which memories are encoded through enduring structural changes in the brain and is often demonstrated by showing that memory loss occurs when you inhibit protein synthesis around the time of learning. This paper shows that one of the most commonly-used protein synthesis inhibitors, anisomycin, leads to increased norepinephrine release in the amygdala which could, by itself, impair memory.  The interesting final experiment showed that the effects of anisomycin on memory and norepiniphrine were reduced when the amygdala was totally shut down with lidocaine.

Sadowski RN, Canal CE, & Gold PE (2011). Lidocaine attenuates anisomycin-induced amnesia and release of norepinephrine in the amygdala. Neurobiology of learning and memory PMID: 21453778


Evidence for the Re-Enactment of a Recently Learned Behavior during Sleepwalking. I’ve written a number of times about how neuronal firing patterns observed during waking experience are replayed during sleep, and could therefore reflect consolidation of memory and even dream content. Of course no one knows what rats are experiencing during sleep or whether they dream like us. To get around this problem, these authors trained sleepwalkers on a motor task with very defined arm movements and then examined sleepwalking behavior on the following night. Indeed, a video shows one subject who wakes up the following night and, for a few seconds, seems to be performing the same stereotyped task movements. Only one subject but tantalizing evidence and a cool experimental strategy nonetheless.

Oudiette D, Constantinescu I, Leclair-Visonneau L, Vidailhet M, Schwartz S, & Arnulf I (2011). Evidence for the Re-Enactment of a Recently Learned Behavior during Sleepwalking. PloS one, 6 (3) PMID: 21445313


Increasing adult hippocampal neurogenesis is sufficient to improve pattern separation. One of the biggest questions in the neurogenesis field is whether adult-born neurons are important for behavior. Usually this is tested by examining behavior in animals that lack adult neurogenesis but many studies have correlated increased neurogenesis in enriched or athletic animals with “improved” behavior (smarter, less depressed etc). Of course, the major confound is that enrichment and exercise do many other things besides increasing neurogenesis. To get around this Sahay et al. made a mouse in which neurogenesis could be specifically increased in adulthood. These mice were better at discriminating between related contexts and, after exercise, showed much greater exploratory activity in an open field.

Sahay A, Scobie KN, Hill AS, O’Carroll CM, Kheirbek MA, Burghardt NS, Fenton AA, Dranovsky A, & Hen R (2011). Increasing adult hippocampal neurogenesis is sufficient to improve pattern separation. Nature PMID: 21460835


Necessity of Hippocampal Neurogenesis for the Therapeutic Action of Antidepressants in Adult Nonhuman Primates. This study potentially bridges a big big gap by extending the role of adult neurogenesis in the antidepressant response from rodents all the way to monkeys. Chronic stress induced anhedonic and subordinate behaviors and these effects could be reversed with fluoxetine, but not in irradiated monkeys that had reduced neurogenesis. Could someone follow this up with a transgenic model?

Perera, T., Dwork, A., Keegan, K., Thirumangalakudi, L., Lipira, C., Joyce, N., Lange, C., Higley, J., Rosoklija, G., Hen, R., Sackeim, H., & Coplan, J. (2011). Necessity of Hippocampal Neurogenesis for the Therapeutic Action of Antidepressants in Adult Nonhuman Primates PLoS ONE, 6 (4) DOI: 10.1371/journal.pone.0017600


Systemic 5-bromo-2-deoxyuridine induces conditioned flavor aversion and c-Fos in the visceral neuraxis. OH NOOO! Rats don’t like BrdU! These authors show that pairing a BrdU injection with exposure to a sweet palatable drink causes rats to avoid that drink in the future. It also leads to a mildly elevated stress response and elevated c-fos expression in areas of the brain that represent viscera, consistent with the possibility that BrdU could be exerting unpleasant effects in the gut, where there is a lot of cell division. The authors conclude that the effects on behavior in subsequent days and weeks are probably minimal (phew!), but I’d certainly keep these data in mind when considering injecting BrdU around the time of behavioral testing.

Kimbrough A, Kwon B, Eckel LA, & Houpt TA (2011). Systemic 5-bromo-2-deoxyuridine induces conditioned flavor aversion and c-Fos in the visceral neuraxis. Learning & memory (Cold Spring Harbor, N.Y.), 18 (5), 292-5 PMID: 21498563


Compensatory network changes in the dentate gyrus restore long-term potentiation following ablation of neurogenesis in young-adult mice. In an interesting study of plasticity following neurogenesis reduction, these authors find that LTP was dramatically reduced after arresting neurogenesis, but only transiently. LTP recovered within weeks, possibly because of compensatory reductions in inhibition and enhanced survival of neurons born before neurogenesis ablation. Hat tip to Sil for this one.

Singer BH, Gamelli AE, Fuller CL, Temme SJ, Parent JM, & Murphy GG (2011). Compensatory network changes in the dentate gyrus restore long-term potentiation following ablation of neurogenesis in young-adult mice. Proceedings of the National Academy of Sciences of the United States of America, 108 (13), 5437-42 PMID: 21402918


That’s it.

How does the brain pick which neurons to use?

ResearchBlogging.orgWiring. That’s one answer to this question. We know this from topographic maps in the thalamus and neocortex, where the basic units of sensory information are neatly represented in spatially-arranged populations of neurons – the various body parts are represented in specific locations, as are the different frequencies of sound, the different parts of the retina, and different odors and tastes. This basic sensory information has to be represented (i.e. we all need a faithful representation of visual elements, we all need to hear the various frequencies of sound that make up human speech etc.) so why not hard-wire it and make its representation the same for all of us?

It’s often thought that things change as you move into parts of the brain that represent more complex and abstract concepts. For example, in the hippocampus, many neurons receive the same inputs so it’s generally assumed that different neurons are equally capable of representing a given piece of information. While wiring between neurons must play a role in determining which neurons are activated, the diffuseness of the wiring means that related information need not be stored in spatially neighboring neurons as in the sensory regions of neocortex. Indeed, if you look at hippocampal neurons activated by a given experience they don’t appear to have any particular spatial arrangement but are randomly distributed, anatomically. Alternatively, it could be that certain hippocampal neurons are hard-wired to respond to specific stimuli, it’s just that we don’t understand the wiring. Continue reading How does the brain pick which neurons to use?

Pattern separation: 370,000,000 papers 2050?

pubmed 2If you’ve been paying attention to the adult hippocampal neurogenesis literature at all, you noticed that “pattern separation” is gaining popularity as a research topic. A few quick searches on Pubmed confirm that a trend is indeed afoot.  For the years prior to 1999, only 15 Pubmed-indexed papers answer to the keyphrase “pattern separation.”  This number holds roughly steady through about 2003, and then it begins to take off.  As of this moment (September 24, 2010 @ 3:27pm CST), we are up to 81 papers. According to my back-of-the-envelope calculations, we are in a period of exponential growth.  Should this trend hold –and I see no signs of it abating– we can expect upwards of 370 million pattern separation papers by 2050. Can you imagine what a comprehensive exam will be like?  Your child (grandchild?) will face a stack of journal articles almost 500 miles high!  Al Gore, from atop his famous scissor lift, will inveigh against the massive deforestation wreaked by our prolific little research community.  What’s that you say? We’ll all be using iPads? Fair enough.
Continue reading Pattern separation: 370,000,000 papers 2050?

Someone finally dissects the role new neurons play in fear conditioning

Based on a true story – how progress is made in the field of adult neurogenesis*

  1. A group of scientists reduce neurogenesis and report a memory deficit.
  2. A second group repeats the experiment, with only a few minor differences in protocol, and fails to find a memory deficit.
  3. A third group, using the same species as the first group but a protocol more similar to the second group, replicates the original finding but only when the experiment is performed on Wednesdays.
  4. Faith is restored.
  5. Five groups report no such neurogenesis-dependent memory deficit.
  6. It is reported that developmental exposure to strontium reduces adult neurogenesis by 40% AND produces the much sought after memory deficit. In a technical tour de force follow-up experiment, artisanal cheeses restore neurogenesis and reverse the memory deficits. Causation is established.
  7. BDNF.
  8. Everyone proclaims the role of neurogenesis in memory and is totally confused at the same time.
  9. Someone systematically examines all of the variables in the memory test to determine whether or not the whole thing is a hoax and they should just change careers**.
  10. We have never gotten this far.

Even at level 8, the neurogenesis-fear conditioning story was one of the more convincing arguments of new neuron functionality. With this study by Drew et al. we may soon be jumping for joy as we appear to be graduating to level 9.

The contribution of adult neurogenesis to contextual fear conditioning was greatest when mice were only given a brief training experience – mice lacking adult neurogenesis showed reduced fear of a context where they previously received a single footshock during a brief (3 min) exploration session. With longer exposures to the context, or additional footshocks, neurogenesis-deficient mice showed normal memory. This finding could be explained by the fact that young neurons have a lower threshold for synaptic plasticity, allowing them to encode fleeting experiences that would be forgotten if left to mature neurons.

So, brief training protocols may now likely be my first choice, at least when using mice. In fact, the only times I have observed contextual fear memory deficits in mice has been after brief training protocols almost identical to those used by Drew et al. So we just might have taken a big step forward. If not, check back in 5 years for my revised “How progress is made” list.

*or any other field for that matter
**this is not entirely a joke because, in this case, it both 1) appears to not be a hoax, and 2) marks the launch of the next phase of Michael Drew’s career (congrats)

Drew MR, Denny CA, & Hen R (2010). Arrest of adult hippocampal neurogenesis in mice impairs single- but not multiple-trial contextual fear conditioning. Behavioral neuroscience, 124 (4), 446-54 PMID: 20695644

Do new neurons go through a critical period and then retire, never to be used again? And here we have the latest, craziest hypothesis of granule cell function. Crazy not because the authors have lost their minds but because the story of the dentate gyrus, where adult neurogenesis occurs, is becoming more peculiar every day. The underlying premise of this paper by Alme et al. (which we will examine later) is that granule neurons go through a critical period during their development when they are more likely to contribute to memory encoding. Here it’s hypothesized that, once the critical period is over, they shut down. Forever. Hundreds of thousands of neurons never to be used again. It’s not every day you get to read such bold and novel ideas. Their hypothesis has similarities with that proposed by Aimone 2006, that adult neurogenesis causes different cohorts of neurons to be immature at different phases of an animal’s life, thereby separating memories according to time. The question here is whether these neurons can be reactivated once their critical period is over. Continue reading Do new neurons go through a critical period and then retire, never to be used again?

What IS the dentate gyrus doing to CA3?

Calbindin expression in the dentate gyrus/hippocampus is variable, and particularly weak in young neurons
A fundamental property of the hippocampus is its ability to rapidly encode memories while simultaneously keeping them distinct. Recording from hippocampal neurons one can clearly see that different populations of neurons are active as a rat explores two environments. This is thought to be one mechanism by which information is kept distinct in the brain.

For the last 15-20 years it has been thought that the dentate gyrus (DG), a major subfield of the hippocampus, serves to take small changes in incoming sensory information and orthogonalize them (i.e. make them more different). This idea was built in part on the fact that there are many more DG neurons than upstream cortical neurons. Thus, the DG could use completely different populations of neurons to represent different sets of incoming information and then pass on these representations to CA3, which may bind them into coherent events/memories (the interconnectedness of CA3 neurons, via “recurrent collatorals”, is thought to be a mechanism by which the different components of a memory are bound together).

However, a “problem” arose when Leutgeb et al. found that it is always the same population of dentate granule neurons (~1% of the total population) that are active as an animal explores different environments, even very different ones. This was a bit of a surprise. Still consistent with the proposed role of the DG in orthogonalizing information, however, was the fact that the DG neurons fired (i.e. generated action potentials, which transmit information from neuron to neuron) at different rates/frequencies in the different environments. Thus, changes in sensory information were represented by changes in patterns of activity within the same population of cells, not by recruiting different populations of cells. This is but one study – the question of how the DG encodes and extracts information is far from settled (e.g. what are the other 99% of granule neurons doing? Surely there is a situation in which they are active, no?). But the findings were robust and raise many questions, namely: How does the same population of DG neurons activate different populations of downstream CA3 neurons, during different experiences? Continue reading What IS the dentate gyrus doing to CA3?

(very) Young neurons – dying before they ever had a chance?

Yesterday I was taking pictures of 1-day-old neurons, which was irritating me for several reasons. First, at this age they’re small, irregular and uglier than the mature neurons I’m used to examining. Second, very immature neurons are located amongst a mess of proliferating cells and fellow young neurons so it becomes hard to discern one cell from the next.

One positive thing that came out of looking at these very immature neurons was that I got the chance to see several examples of pyknotic (dying) cells. Older, adult-born neurons also die, particularly after an experience (see here and here), but it’s infrequent and hard to visualize. However, a relatively large proportion of new neurons die within a few days of their birth making them easier to find – the cluster of cells shown below is an example that caught my attention.

1-day-old neurons undergoing cell death Continue reading (very) Young neurons – dying before they ever had a chance?