How do you remember?

Memory processes like formation, maintenance and consolidation have been the subjects of extensive research and, as a result, we know quite a bit about them. And just when we thought that we are getting a pretty clear picture of the memory tableau and all that is left is a little bit of dusting around the edges and getting rid of the pink elephant in the middle of the room, here comes a new player that muddies the waters again.

DNA methylation. The attaching of a methyl group (CH3) to the DNA’s cytosine by a DNA methyltransferase (Dnmt) was considered until very recently a process reserved for the immature cells in helping them meet their final fate. In other words, DNA methylation plays a role in cell differentiation by suppressing gene expression. It has other roles in X-chromosome inactivation and cancer, but it was not suspected to play a role in memory until this decade.

Oliveira (2016) gives us a nice review of the role(s) of DNA methylation in memory formation and maintenance. First, we encounter the pharmacological studies that found that injecting Dnmt inhibitors in various parts of the brain in various species disrupted memory formation or maintenance. Next, we see the genetic studies, where mice Dnmt knock-downs and knock-outs also show impaired memory formation and maintenance. Finally, knowing which genes’ transcription is essential for memory, the researcher takes us through several papers that examine the DNA de novo methylation and demethylation of these genes in response to learning events and its role in alternative splicing.

Based on these here available data, the author proposes that activity induced DNA methylation serves two roles in memory: to “on the one hand, generate a primed and more permissive epigenome state that could facilitate future transcriptional responses and on the other hand, directly regulate the expression of genes that set the strength of the neuronal network connectivity, this way altering the probability of reactivation of the same network” (p. 590).

Here you go; another morsel of actual science brought to your fingertips by yours truly.

99-dna-copy

Reference: Oliveira AM (Oct 2016, Epub 15 Sep 2016). DNA methylation: a permissive mark in memory formation and maintenance. Learning & Memory,  23(10): 587-593. PMID: 27634149, DOI: 10.1101/lm.042739.116. ARTICLE

By Neuronicus, 22 September 2016

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CCL11 found in aged but not young blood inhibits adult neurogenesis

vil - Copy
Portion of Fig. 1 from Villeda et al. (2011, doi: 10.1038/nature10357) describing the parabiosis procedure. Basically, under complete anesthesia, the peritoneal membranes and the skins of the two mice were sutured together. The young mice were 3–4 months (yellow) and old mice were 18–20 months old (grey).

My last post was about parabiosis and its sparse revival as a technique in physiology experiments. Parabiosis is the surgical procedure that joins two living animals allowing them to share their circulatory systems. Here is an interesting paper that used the method to tackle blood’s contribution to neurogenesis.

Adult neurogenesis, that is the birth of new neurons in the adult brain, declines with age. This neurogenesis has been observed in some, but not all brain regions, called neurogenic niches.

Because these niches occur in blood-rich areas of the brain, Villeda et al. (2011) wondered if, in addition with the traditional factors required for neurogenesis like enrichment or running, blood factors may also have something to do with neurogenesis. The authors made a young and an old mouse to share their blood via parabiosis (see pic.).

Five weeks after the parabiosis procedure, the young mouse had decreased neurogenesis and the old mouse had increased neurogenesis compared to age-matched controls. To make sure their results are due to something in the blood, they injected plasma from an old mouse into a young mouse and that also resulted in reduced neurogenesis. Moreover, the reduced neurogenesis was correlated with impaired learning as shown by electrophysiological recordings from the hippocampus and from behavioral fear conditioning.

So what in the blood does it? The authors looked at 66 proteins found in the blood (I don’t know the blood make-up, so I can’t tell if 66 is a lot or not ) and noticed that 6 of these had increased levels in the blood of ageing mice whether linked by parabiosis or not. Out of these six, the authors focus on CCL11 (unclear to me why that one, my bet is that they tried the others too but didn’t have enough data). CCLL11 is a small signaling protein involved in allergies. So the authors injected it into young mice and Lo and Behold! there was decreased neurogenesis in their hippocampus. Maybe the vampires were onto something, whadda ya know? Just kidding… don’t go around sucking young people’s blood!

This paper covers a lot of work and, correspondingly, has no less than 23 authors and almost 20 Mb of supplemental documents! The story it tells is very interesting and as complete as it gets, covering many aspects of the problems investigated and many techniques to address those problems. Good read.

Reference: Villeda SA, Luo J, Mosher KI, Zou B, Britschgi M, Bieri G, Stan TM, Fainberg N, Ding Z, Eggel A, Lucin KM, Czirr E, Park JS, Couillard-Després S, Aigner L, Li G, Peskind ER, Kaye JA, Quinn JF, Galasko DR, Xie XS, Rando TA, Wyss-Coray T. (31 Aug 2011). The ageing systemic milieu negatively regulates neurogenesis and cognitive function. Nature. 477(7362):90-94. doi: 10.1038/nature10357. Article | FREE Fulltext PDF

By Neuronicus, 6 January 2016

Will you trust a pigeon pathologist? That’s right, he’s a bird. Stop being such an avesophobe!

pigeon

From Levenson et al. (2015), doi: 10.1371/journal.pone.0141357. License: CC BY 4.0

Pigeons have amazing visual skills. They can remember facial expressions, recall almost 2000 images, recognizes all the letters of the alphabet (well, even I can do that), and even tell apart a Monet form a Picasso! (ok, birdie, you got me on that one).

Given their visual prowess, Levenson et al. (2015) figured that pigeons might be able to distinguish medically-relevant images (a bit of a big step in reasoning there, but let’s go with it). They got a few dozen pigeons, starved them a bit so the birds show motivation to work for food, and started training them on recognizing malignant versus non-malignant breast tumors histology pictures. These are the same exact pictures your radiologist looks at after a mammogram and your pathologist after a breast biopsy; they were not retouched in any way for the pigeon’s benefit (except to make it more difficult, see below). Every time the pigeon pecked on the correct image, it got a morsel of food (see picture). Training continued for a few weeks on over 100 images.

For biopsies, the birds had an overwhelming performance, reaching 99% accuracy, regardless of the magnification of the picture, and for mammograms, up to 80% accuracy, just like their human counterparts. Modifying the pictures’ attributes, like rotation, compression or color lowered somewhat their accuracy, but they were still able to score only marginally less than humans and considerably better than any computer software. More importantly, the pigeons were able to generalize, after training, to correctly classify previously unseen pictures.

Let’s be clear: I’m not talking about some fancy breed here, but your common beady-eyed, suspicious-sidling, feral-looking rock pigeon. Yes, the one and only pest that receives stones and bread in equal measures, the former usually accompanied by vicious swearings uttered by those that encountered their slushy “gifts” under the shoes, on the windshield or in the coffee and the latter offered by more kindly disposed and yet utterly naive individuals in the misguided hopes of befriending nature. Columba livia by its scientific name, at the same time an exasperating pest and an excellent pathologist! Who knew?!

The authors even suggest to use pigeons instead of training and paying clinicians. Hmmm… But who do I sue if my mother’s breast cancer gets missed by the bird, in one of those 1% chances? Because somehow making a pigeon face the guillotine does not seem like justice to me. Or is this yet another plot to get the clinicians off the hook for misdiagnoses? Leave the medical profession alone, birdies – is morally sensitive as it is -, and search employment in the police or Google; they always need better performance in the ever-challenging task of face-recognition in surveillance videos.

P.S. The reason why you didn’t recognized the word “avesophobe” in the title is because I just invented it, to distinguish the hate for birds from a more serious affliction, ornithophobia, the fear of birds.

Reference: Levenson RM, Krupinski EA, Navarro VM, & Wasserman EA (18 Nov 2015). Pigeons (Columba livia) as Trainable Observers of Pathology and Radiology Breast Cancer Images. PLoS One, 10(11):e0141357. doi: 10.1371/journal.pone.0141357.  Article | FREE FULLTEXT PDF

By Neuronicus, 19 November 2015

The F in memory

"Figure 2. Ephs and ephrins mediate molecular events that may be involved in memory formation. Evidence shows that memory formation involves alterations of presynaptic neurotransmitter release, activation of glutamate receptors, and neuronal morphogenesis. Eph receptors regulate synaptic transmission by regulating synaptic release, glutamate reuptake from the synapse (via astrocytes), and glutamate receptor conductance and trafficking. Ephs and ephrins also regulate neuronal morphogenesis of axons and dendritic spines through controlling the actin cytoskeleton structure and dynamics" (Dines & Lamprecht, 2015, p. 3).
“Figure 2. Ephs and ephrins mediate molecular events that may be involved in memory formation. Evidence shows that memory formation involves alterations of presynaptic neurotransmitter release, activation of glutamate receptors, and neuronal morphogenesis. Eph receptors regulate synaptic transmission by regulating synaptic release, glutamate reuptake from the synapse (via astrocytes), and glutamate receptor conductance and trafficking. Ephs and ephrins also regulate neuronal morphogenesis of axons and dendritic spines through controlling the actin cytoskeleton structure and dynamics” (Dines & Lamprecht, 2015, p. 3).

When thinking about long-term memory formation, most people immediately picture glutamate synapses. Dines & Lamprecht (2015) review the role of a family of little known players, but with big roles in learning and long-term memory consolidation: the ephs and the ephrines.

Ephs (the name comes from erythropoietin-producing human hepatocellular, the cancer line from which the first member was isolated) are transmembranal tyrosine kinase receptors. Ephrines (Eph receptor interacting protein) bind to them. Ephrines are also membrane-bound proteins, which means that in order for the aforementioned binding to happen, cells must touch each other, or at least be in a very very cozy vicinity. They are expressed in many regions of the brain like hippocampus, amygdala, or cortex.

The authors show that “interruption of Ephs/ephrins mediated functions is sufficient for disruption of memory formation” (p. 7) by reviewing a great deal of genetic, pharmacologic, and electrophysiological studies employing a variety of behavioral tasks, from spatial memory to fear conditioning. The final sections of the review focus on the involvement of ephs/ephrins in Alzheimer’s and anxiety disorders, suggesting that drugs that reverse the impairment on eph/ephrin signaling in these brain diseases may lead to an eventual cure.

Reference: Dines M & Lamprecht R (8 Oct 2015, Epub 13 Sept 2015). The Role of Ephs and Ephrins in Memory Formation. International Journal of Neuropsychopharmacology, 1-14. doi:10.1093/ijnp/pyv106. Article | FREE FULLTEXT PDF

By Neuronicus, 26 October 2015

It’s what I like or what you like? I don’t know anymore…

The plasticity in medial prefrontal cortex (mPFC) underlies the changes in self preferences to match another's through learning. Modified from Fig. 2B from Garvert et al. (2015)
The plasticity in medial prefrontal cortex (mPFC) underlies the changes in self preferences to match another’s, through learning. Modified from Fig. 2B from Garvert et al. (2015), which is an open access article under the CC BY license.

One obvious consequence of being a social mammal is that each individual wants to be accepted. Nobody likes rejection, be it from a family member, a friend or colleague, a job application, or even a stranger. So we try to mould our beliefs and behaviors to fit the social norms, a process called social conformity. But how does that happen?

Garvert et al. (2015) shed some light on the mechanism(s) underlying the malleability of personal preferences in response to information about other people preferences. Twenty-seven people had 48 chances to make a choice on whether gain a small amount of money now or more money later, with “later” meaning from 1 day to 3 months later. Then the subjects were taught another partner choices, no strings attached, just so they know. Then they were made to chose again. Then they got into the fMRI and there things got complicated, as the subjects had to choose as they themselves would choose, as their partner would choose, or as an unknown person would choose. I skipped a few steps, the procedure is complicated and the paper is full of cumbersome verbiage (e.g. “We designed a contrast that measured the change in repetition suppression between self and novel other from block 1 to block 3, controlled for by the change in repetition suppression between self and familiar other over the same blocks” p. 422).

Anyway, long story short, the behavioral results showed that the subjects tended to alter their preferences to match their partner’s (although not told to do so, it had no impact on their own money gain, there were not time constraints, and sometimes were told that the “partner” was a computer).

These behavioral changes were matched by the changes in the activation pattern of the medial prefrontal cortex (mPFC), in the sense that learning of the preferences of another, which you can imagine as a specific neural pattern in your brain, changes the way your own preferences are encoded in the same neural pattern.

Reference: Garvert MM, Moutoussis M, Kurth-Nelson Z, Behrens TE, & Dolan RJ (21 January 2015). Learning-induced plasticity in medial prefrontal cortex predicts preference malleability. Neuron, 85(2):418-28. doi: 10.1016/j.neuron.2014.12.033. Article + FREE PDF

By Neuronicus, 11 October 2015

I can watch you learning

Human Stereotaxic System. Photo credit: The Mind Project
Human Stereotaxic System. Photo credit: The Mind Project

Recording directly form the healthy living human brain has always been a coveted goal of many neuroscientists, thus bypassing the limitations of non-invasive techniques or animal work. But, understandably, nobody would seek or grant approval for inserting an electrode in the healthy living human brain, on moral and ethical grounds. The next best thing is to insert an electrode into the not so healthy living human brain.

Ison, Quiroga, & Fried (2015) got lucky and gained access to 14 patients with intractable epilepsy that had electrodes implanted in their brain to find where the seizure focus is (for possible surgical resection later on). Using these electrodes, they recorded the activity of single neurons within the medial temporal lobe (MTL, a brain area paramount for learning) while the patients performed some simple association tasks. First, they presented images of places, people, and animals to the patients to see “which (if any) of the recorded neurons responded to a picture” (p. 220). When they got a neuron responding to something, they rushed out, did some data and image processing, and after an hour they started the experiment. Which was showing the patient the picture to which the neuron responded to (e.g. Stimulus 1 = patient’s daughter) overimposed on a background that the neuron did not respond to (e.g. Stimulus 2 = the Eiffel tower). After one single trial (although there was some variability), the patients learned the associations (i.e. Stimulus 3 = daughter in front of Eiffel tower) and this learning was mirrored by how the neuron responded. Namely, the neuron increased its activity by 200% to 400% (counted in spikes per second) when shown the previously un-responded to image alone (i.e. Stimulus 2).

Excerpt from Fig. 5 from Ison, Quiroga, & Fried (2015).
Excerpt from Fig. 5 from Ison, Quiroga, & Fried (2015). “Average normalized neural activity (black squares) and behavioral responses (green circles) to the non-preferred stimulus as a function of trial number. Data were aligned to the learning time (relative trial number 0)”, i.e. when they showed the composite image between Stimulus 1 and Stimulus 2. “Note that the neural activity follows the sudden increase in behavioral learning”.

The authors recorded from over 600 neurons from various MTL regions, out of which 51 responded to a Stimulus 1. From these, only half learned, that is, they increased their activity when Stimulus 2 was shown. For the picky specialist, the cells were both Type 1 and Type 2 neurons, located 6 in the hippocampus, 4 in the entorhinal cortex, 11 in the parahippocampal cortex, and 1 in the amygdala. And the authors controlled for familiarity, attentional demands, and other extraneous variables (with some very fancy and hard to follow stats, I might add).

The paper settles an old psychology dispute. Do we learn an association gradually or at once? In other words, do we learn gradually that A and B occur together, or do we learn that the first time we are shown A and B together and the next trials serve just to refine and consolidate the new knowledge? Ison, Quiroga, & Fried (2015) data show that learning happens at once, in an all-or-none fashion.

Reference: Ison, M. J., Quian Quiroga, R., & Fried, I. (1 July 2015). Rapid Encoding of New Memories by Individual Neurons in the Human Brain. Neuron, 87(1): 220-30. doi: 10.1016/j.neuron.2015.06.016. Article | FREE PDF

By Neuronicus, 4 October 2015

Obscure protein restores memory decline

In the not-too-distant-future, your grandma may give you a run for your money on your video games. Photo credit: http://www.funtoosh.com/pictures/
In the not-too-distant-future, your grandma may give you a run for your money on your video games. Photo credit: Funtoosh

Aging comes with all sorts of maladies, but one of the most frustrating is the feeling that you are not as sharp as you used to be. Cognitive decline has been previously linked, at least in part, to a dysregulation in the neuronal calcium homeostasis in the hippocampus, which is a brain region essential for learning and memory. One player that keeps in check the proper balance of calcium use is the protein FKBP1b, and, not surprisingly, its amounts are reduced in aging rats and Alzheimer’s suffering patients.

FKBP1b overexpression in hippocampal neurons reversed spatial memory deficits in aged rats. Fig. 3 (partial) from Gant, J. C., Chen, K. C., Kadish, I., Blalock, E. M., Thibault, O., Porter, N. M., Landfield, P. W. (29 July 2015). Reversal of Aging-Related Neuronal Ca2+ Dysregulation and Cognitive Impairment by Delivery of a Transgene Encoding FK506-Binding Protein 12.6/1b to the Hippocampus. The Journal of Neuroscience, 35(30):10878 –10887. doi: 10.1523/JNEUROSCI.1248-15.2015.
FKBP1b overexpression in hippocampal neurons reversed spatial memory deficits in aged rats. Fig. 3 (partial) from Gant et al. (2015): doi: 10.1523/JNEUROSCI.1248-15.2015.

Gant et al. (2015) sought to increase the expression of the FKBP1b protein in the hippocampus, in the hopes that its increase would result in better calcium homeostasis and, as a result, better memory performance in aging rats. They built a virus that carried the gene for making the FKBP1b protein and they injected this directly in the hippocampus. After they waited 5-6 weeks for the gene to be expressed, they tested the rats in the Morris water maze, a test for spatial memory. The old rats that received the injection performed as well as the young rats, and far better than the old rats who didn’t get the injection. Then the researchers made sure that the injection is the one responsible for the results, by checking the levels of the FKBP1b protein in the hippocampus (increased, as per specs), by recording from those neurons (they were awesome), and by imaging the calcium to make sure the balance was restored (ditto).

Reference: Gant, J. C., Chen, K. C., Kadish, I., Blalock, E. M., Thibault, O., Porter, N. M., Landfield, P. W. (29 July 2015). Reversal of Aging-Related Neuronal Ca2+ Dysregulation and Cognitive Impairment by Delivery of a Transgene Encoding FK506-Binding Protein 12.6/1b to the Hippocampus. The Journal of Neuroscience, 35(30):10878 –10887. doi: 10.1523/JNEUROSCI.1248-15.2015. Article + FREE PDF + Journal of Neuroscience cover