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.

Google Scholar vs. Scopus & Web of Science

citation-battleA couple of interesting correspondences (here and here) just appeared in Nature on the legitimacy of Google Scholar for tracking citations. Interesting because I’ve recently been pondering the same issue but came up with the opposite conclusion, namely that Google Scholar is actually a better tool for tracking citations than either Scopus or Web of Science (and not only because it’s a pain to access the latter two).

The main concern by the authors is that citations for a given article are higher in Google Scholar than Scopus or Web of Science (well, one mainly focusses on the fact that they’re different). Higher because they include theses, patents, websites etc. Maybe also false positives.

I started thinking about this issue when I began applying for jobs. I didn’t have any fancy papers and so, for people outside of my field, noting the number of citations in my CV seemed like a decent way to make the point that some of these articles have had an impact. As I sent my applications I’d go back to Web of Science and check for the latest numbers and, this past year, I noticed that citations of some of my articles suddenly increased by up to 20%. Yay! But then I’d check the next day and they were low again (perhaps relating to changes in how citations were detected). So there was some glitch and I certainly didn’t want to appear to be inflating the numbers so I turned to Google Scholar. The numbers were higher, but consistent. For the most part the citations seemed completely legitimate as well.

So why were Google Scholar’s citation counts higher? Looking at my most cited paper, which has been cited 367 times (Google Scholar) or 267 times (Web of Science) or 287 times (Scopus) I found that Google Scholar included 11 Chinese articles, 10 book chapters, 15 theses, 4 patents, 1 blog (yours truly), 1 grant application, and 6 mysteries. Eliminating these 48 still leaves 319. Quite a bit higher than Web of Science and Scopus, probably because Google counts citations from articles that are still in press (my Neurobiology of Aging paper was published online but “in press” for 23 months, during which citations could be tracked in Scholar but not Web of Science). This is probably also why Google Scholar counts 17 citations (16 “normal”) of my most recent paper whereas Web of Science only counts 9 – many of these citing articles were recently published.

So should Chinese articles be excluded? Are book chapters irrelevant? Theses, well, no one reads theses so maybe there’s a bit of inflation there. I do think it’s a sign of impact when a blog, grant, or patent refers to your paper and believe that these things should be included in the citation counts (Google still isn’t great in this regard – I know of several blog posts on my papers that haven’t been detected by Google).

These are the reasons I specifically decided to use Google Scholar when adding citation counts to my CV. And so it’s funny to read about the “limitations of Google Scholar’s personalized citation reports” and how “I would not recommend using the reports for decisions that could affect careers”.

(for what it’s worth I did get a job, though clearly it’s all downhill from here)

The White House wants your thoughts on open access to scientific publications! Deadline January 12!

Do you live on planet earth? Then you probably pay taxes. And if you pay taxes then you’re supporting scientific research. Thanks a lot – that’s really great. Thanks to you scientists can make discoveries that lead to cures for diseases. And we’d really love to share these discoveries with you…but you can’t afford them.

There are lots of problems with the way scientific findings are communicated but this is perhaps the saddest one. The public pays for scientific research and then is charged again to read the results. People who do not have access to massive library holdings simply cannot access scholarly publications. Many scientists themselves cannot even access the papers they need because their institution cannot afford the subscriptions.

Fortunately, things are changing. For example, the National Institutes of Health requires that all federally-funded research be deposited into Pubmed Central where it is freely available to the public within 12 months of publication (this allows publishers to still make money off the article for a while, which is very kind of the US government). Another example is the new publishing model put forth by PLoS One and other journals, where the authors pay a fee that covers the costs of publication, archiving etc. Then the articles are made freely available to all because subscriptions are not needed to cover costs.

The way things are going, it is only a matter of time before scholarly publications and scientific information becomes freely communicated to those that paid for it. How long this transformation will take is the big question and there are two big movements in the US government that will play a big role. Two big movements that need your input. Continue reading The White House wants your thoughts on open access to scientific publications! Deadline January 12!

Astrocytes: a story in pictures. Ok, just a bunch of pictures.

One trick on the confocal microscope is to use a larger pinhole so that a greater thickness of the section is captured in the image. Images acquired this way are comparable to a bunch of thin sections that are then merged into a “z-stack” except that some of the tissue is out of focus, giving rise to the blurry “rushing water” look that you see here.
Continue reading Astrocytes: a story in pictures. Ok, just a bunch of pictures.

Can you enjoy a good cup of coffee in the thick of experimenting?

More specifically,

Can you enjoy a good cup of coffee when you have 8 straight hours of experimenting with maximum 10 minute breaks here and there but it takes you 5 minutes just to get to the lab kitchen from the behavior space let alone make a coffee and get back in time and you can’t make a coffee at home and bring it in a thermos or travel mug (which would be room temperature (the worst temperature for enjoying coffee) by the time you wanted it nay NEEDED it) because those items have already been moved to Canada where you’ll also soon be moving which explains why you couldn’t do these experiments according to a more relaxed schedule but instead have to get as much done as is humanly possible in the few weeks that remain?


Yes:ultrapure vacuum filtered coffee

*Stay tuned for “Can you enjoy a good meal when you have 8 straight hours of experimenting with maximum 10 minute breaks here and there but it takes you 5 minutes just to get to the lab kitchen from the behavior space let alone make a meal and get back in time and you can’t make a meal at home and bring it in a thermos or travel mug because it would lose its form upon being stuffed into a drinking vessel but then why are you so hung up on appearances stop being so superficial and just stuff it in a thermos.”

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

Enhanced integrative properties of immature neurons #sfn11

How do the physiological properties of new neurons translate to a behavioral role? Are they just like mature neurons or are they unique? One idea that’s been thrown around is that their plastic period, their critical period, might endow them with an enhanced ability to associate information and contribute to memory formation. While we know that hippocampal neurons are already plastic and very capable of physiologically linking together different stimuli the big hope seems to be that maybe immature neurons are even better at this.


A related question is how fewer synapses and unique inhibitory connectivity affects their information processing capabilities. The verdict is out on whether new neurons are more or less involved in information processing than their mature counterparts. Currently, the best information we have is from studies looking at activity, measured by immediate early gene expression, in response to behavioral stimulation. The true measure of whether a neuron is involved in information processing / representation is if it spikes, i.e. fires action potentials, in response to a specific stimulus. Since new neurons have fewer synapses it’s very possible that they aren’t able to represent many different types of information, and therefore aren’t capable of associating information during memory formation. On the other hand, new neurons synapses are more plastic, perhaps making them better able to associate information even if they have fewer synapses. Continue reading Enhanced integrative properties of immature neurons #sfn11

Neurogenesis and the septotemporal axis at #SFN11

As I’ve alluded, science, and therefore the SFN meeting where much science is unveiled, is a cycle of confusion and clarification. Currently, confusion may be prevailing in the adult hippocampal neurogenesis field since new neurons have been implicated in everything mammals do – spatial and nonspatial memory, anxiety, depression, addiction, social behavior, stress regulation, blinking etc. This should not be entirely surprising since the hippocampus itself, where these young neurons reside, has many different functions. But how can we reconcile these seemingly disparate functions?

Every time I get worked up about all these neurogenesis findings I think about two words that return me to a state of inner peace, calmness, and….mental turmoil that all of my experiments will have to be performed twice: Septal and Temporal. Neurogenesis aside, the septal and temporal ends of the hippocampus are connected to different brain structures that cause the septal hippocampus to be more involved in spatial processing/cognition and the temporal hippocampus to be more involved in regulating stress and emotion. Which has the potential to explain everything. Continue reading Neurogenesis and the septotemporal axis at #SFN11

What I learned while presenting at #SFN11

It’s hard to explore SFN when you’ve got your own poster to tend to. I thought I could hop around the development section before things got busy but there was no “before things got busy.” The design of the conference also can work against presenters because the presentations you’d like to see the most are being displayed simultaneously with your own. So next year I vow to present something really boring.

Of course, much can be learned while pinned down at your own poster. When you work in one lab, or one institution, your thoughts about the brain tend to have a specific focus based on the ideas of the people around you. Of course, new papers come out that challenge those thoughts but, man, papers move slooooowly. Scientists have not done a stellar job of using the internet to quickly communicate ideas. However, once a year at SFN a whole bunch of people come to your poster and give you their thoughts on the brain. Sometimes their thoughts are only presented in the language of distorted eyebrows and raised inflections but this is way better than typical social interactions with strangers, which usually go something like “You study brain cells/memory? Dude, I sure could use some more of those/that!”

So, what did my visitors think?

I had several visitors who specifically came by because they knew about me through the blog and through Twitter. Thank you for stopping by! You often never know if your online thoughts are useful, but I was happy to hear that several of you have used the blog as a teaching tool and a way to keep up with the field. I wish I could have these interactions with my readers more often than once a year at SFN. Then again I’d probably never be able to keep up with the comments so…no I didn’t say that – get engaged! I also heard one person, who does in vivo electrophysiology on my favorite brain regions, tell me that they’d tweet about neuroscience but they have nothing interesting to add to the conversation! Bollocks! Do you know how many in vivo electrophysiologists are on Twitter? Like, one? And how many experts are reviewing the literature on Research Blogging? Your knowledge is valuable. I would follow you in an instant.

“At first there was agreement on the behavioral function of neurogenesis but now everything is going in different directions.” Yes! Adult neurogenesis is a great example of the more you learn the more confused you get! Things may have seemed congruent 5 years ago but that was when there was only half a dozen studies that had examined the problems that arise when new neurons are ablated. Since then people have gone on to study more types of behavior and, as is also the case with the hippocampus, new neurons have been found to contribute to more and more types of behaviors. This has also given us additional opportunities for failed replication, and therefore doubt and confusion. One visitor commented on the recent paper that found memory impairments only if you kill new neurons after learning and we agreed that killing new neurons before behavioral testing could allow for other neurons to compensate, and make it appear that these new neurons are not doing anything significant. Of course, we have shown that often (e.g. at “baseline”) new neurons may be dispensable but that when an animal is stressed they are critical. And so explanations are emerging as to why some observe a behavioral function for new neurons and others do not, it’s just that it seems to be unbearably slow or remarkably fast depending on your mood.

I learned that there’s someone out there studying neurogenesis as related to maternal behavior….IN SHEEP! And they find that these neurons mature very slowly, like, primate slow. I love it when we think we have things completely figured out and then the data goes a totally different direction when you throw wool into the equation. Like, if we put cute little wool sweaters on our mice, would that make new neurons mature slower? One of the next big questions. Testable. Do it.

For those that missed my poster, fear not, for I have submitted it to Nature Precedings and will notify you here when they’ve posted it (couple days). For those that came to my poster today, sorry, you didn’t have to come to my poster.


Saturday Nov 12, #SFN11, poster A27 = me

Update: The poster is now available at Nature Precedings.

Still acquiring histological images for my SfN poster. My recurring problem is that I end up taking pictures of things because they’re pretty and not because they have anything to do with the task at hand. Today’s case in point:

Well, this does relate to my SfN poster a little bit. Red shows cell nuclei, most of which are dentate gyrus granule neurons. And white is GFAP immunostaining, which largely labels astrocytes but in this part of the brain also labels radial glia, the stem cells (or to be less controversial, “precursor” cells) of the hippocampus. Radial glia can be identified by the long process (almost like a dendrite) that they extend through the granule cell layer. There are a few in the above picture. Continue reading Saturday Nov 12, #SFN11, poster A27 = me

New neurons in the adult brain. How they work and what they're good for.