Building Blogs of Science

How to build a [water] brain

Posted in Science by kubke on June 18, 2010

Whenever I try to teach some aspects of neuronal integration in class, I run into trouble, since most of the neuronal properties are defined by mathematical formulae that describe the electrical properties of neurons that are sometimes difficult for the students to grasp. Without a basic knowledge of electricity, it is hard to build a conceptual image of what neurons are doing.

Or is it?

I was invited to talk about the brain to a group of 9-11 year old pupils in a primary school in the North Shore yesterday, when I thought it might be fun to try to build neurons and discover how they worked. So, here is my water neuron:

The water neuron

It turns out, this little water neuron (which can be built with pretty much household items) has a lot to show about the passive properties of neurons.

Synaptic currents:

The pipette dropper was used to inject [current] water into the different dendrites. Because of the properties of the dropper, there is a limit to the amount of current that can be injected at a given time, and the injection of current is not instantaneous but has a time course that is analogout to the time course of the synaptic potential.

Spatial and temporal integration:

Current can be injected in one or more dendrites with different time patterns. Injecting into all dendrites at the same time, or into one or more dendrites at different time intervals provides a good idea of how the output of the neuron is shaped by spatial and temporal integration.


By tilting the ‘soma’ to different degrees the amount of current needed to be injected into the dendrites to allow for an output of the axon will increase. Therefore, one can build neurons with different thresholds and see how that affects the output of the neuron.

Leak currents:

One can poke tiny holes into the soma so that some of the current injected into the neuron leaks out. Combining this with changing threshold and the temporal patterns of injection into the dendrites is a good way of showing how temporal and spatial integration work in different ways to produce an output through the axon.  One can also put some leaks into the axon, and ‘myelinate’ it with saran wrap to show the insulating  properties of the myelin sheath.

Although this ‘water neuron model’ cannot illustrate the active properties of the neurons, it does contribute to an intuitive construct of how currents may be acting in individual neurons. The different neurons can be connected to form a circuit, and then one could examine how the output of the circuit is affected by changing things likethreshold, leak and number of inputs into individual neurons.

Well, it was fun. I may give this a go in my next neuro class at Uni.

Ed Rubel: The 21st century, a new era for hearing habilitation

Posted in Health and Medicine, Science, Science and Society by kubke on February 10, 2010

It wasn’t easy to get Professor Ed Rubel down to New Zealand due to his busy schedule, but finally, and thanks to support from the University of Auckland School of Medical Sciences, we did.

Yesterday, Prof Rubel delivered a public talk at the Med School: “The 21st Century: A New Era for Hearing Habilitation”.

Ed Rubel has a long trajectory, and has contributed to many aspects of neuroscience, ranging from how brains are put together in the embryo, how and when auditory processing is set up, how the way that neurons are connected determine how information is coded, and much more.

But among all his contributions one stands out: the discovery that the sensory hair cells in the inner ear of birds can regenerate after damage. His team found this, as he describes, serendipitously in the mid 1980’s. In mammals, once the sensory hair cells are damaged due to noise exposure or chemical toxicity (like exposure to certain antibiotics), the cells are not replaced, and as a result, the hearing loss is permanent. Thus, the question is: what is different between birds and mammals that allows one, but not the other to repair their damaged ears?

This answer has eluded us since then. There are basically two possibilities: One, that damage induces the mechanisms of repair in birds, but not mammals. The other is that the repair mechanisms are inhibited in mammals (and that damage removes this inhibition in birds). In order to get to the bottom of this, one would need to understand what are the cellular mechanisms that are either inhibiting or inducing hair cell replacement.

Zebrafish labelled lateral line, from Owens et al PLoS Genetics 2008

And here is where the Rubel group in Seattle came up with a rather clever solution: Let’s look in the zebrafish. One reason to do this is that zebrafish, like many other fishes, have hair cells on the lateral line on the surface of the body in structures called neuromasts. And like in birds, fishes are able to replace these cells.There are two advantages to the zebrafish approach. First, because the neuromasts are on the surface of the body it is possible to load the sensory hair cells and support cells with fluorescent molecules and monitor what is happening over time with different treatments. Second, the genetics of zebrafish are well-known, which facilitates the identification and manipulation of genes to see what their effects are on the ability to regenerate those cells.

Zebra fish neuromast, From Owens et al PLoS Genetics, 2008

Ed Rubel teamed up with David Raible’s group, and examined genes that may be involved in different susceptibility to induced hair cell death by neomycin, as well as what drugs that may confer protection to the hair cells. Their work was published in PLoS Genetics (doi:10.1371/journal.pgen.1000020) and you can go and read it thanks to the magic of Open Access.

Their ultimate goal is to use this approach to screen for genes and pharmaceutical compounds that protect hair cells from damage in the zebrafish and, once identified, determine whether their findings apply to mammals as well. As the authors state in their summary:

Variation in the genetic makeup between individuals plays a major role in establishing differences in susceptibility to environmental agents that damage the inner ear. […] The combination of chemical screening with traditional genetic approaches offers a new strategy for identifying drugs and drug targets to attenuate hearing and balance disorders.

You can also read more about the project in a feature by Shirley S Wang in the Wall Street Journal.

About Professor Ed Rubel: Professor Rubel is the Virginia Merrill Bloedel Professor of Hearing Science at the University of Washington. He was the founding Director of the Virginia Merrill Bloedel Hearing Research Center and is currently the Scientific Director. Professor Rubel’s work is geared towards understanding the development, plasticity, pathology and potential repair of the inner ear and auditory pathways in the brain. His work throughout the years has focused on the cellular processes underlying the development of the auditory system and how these processes are influenced by early experience.

The ever-changing world of dendritic spines

Posted in Science by kubke on December 18, 2009

ResearchBlogging.orgSantiago Ramón y Cajal originally described spines in the dendrites of neurons in the cerebellum back in the late 19th century, but it wasn’t until the mid 1950’s with the development of the electron microscope that these structures were shown to be synaptic structures. Although it has been known that the number of dendritic spines changes during development and in association with learning, most studies have inferred the changes by looking at static time points rather than monitoring individual spines in the same animal over time, partly, due to the difficulty of tracking a single structure of about 0.1 micrometer in size (0.0001 mm). But new advances in imaging technology have allowed researchers to ‘follow’ individual spines over time both in vitro and in the whole animal.

Purkinje Cell by S Ramon y Cajal

Dendritic spines are no longer thought of as the static structures of Ramón y Cajal’s (or even my) generation, but rather dynamic structures that can be added and eliminated from individual dendrites. And because each spine is associated with a synaptic input, and because their structure and dynamic turnover is known to have a profound effect on neuronal signaling, one cannot but be tempted to propose that they are associated with specific aspects of memory formation.

Two developments have made it possible to monitor individual dendritic spines at different time points in the same animal: the ability to incorporate fluorescent molecules into transgenic mice that make the spines visible under fluorescent illumination, and the development of in vivo transcranial two photon imaging that allow researchers to go back to that individual dendrite and monitor how the dendritic spines change over time. Two papers published in Nature make use of these techniques to look at how dendritic spines change in the motor cortex of mice that have learned a motor task.

In one, Guang Yang, Feng Pan and Wen-Biao Gan looked at how spines changed when either young or adult mice were trained in to learn specific motor strategies. They observed that spines underwent significant turnover, but that learning the motor task increased the overall number of new spines and that a small proportion of them could persist for long periods of time. They calculated that although most of the newly formed spines only remained for about a day and a half, a smaller fractions of them could still persist for either a couple of months or a few years. Based on their data they suggest that about 0.04% of the newly formed spines could contribute to lifelong memory.

Dendritic spine by Tmhoogland

Another study by Tonghui Xu, Xinzhu Yu, Andrew J. Perlik, Willie F. Tobin, Jonathan A. Zweig, Kelly Tennant, Theresa Jones and Yi Zuo did a similar experiment, but using a different motor training task. Like the Yang group, they also saw that training leads to both the formation and elimination of spines. Although newly formed spines are initially unstable, a few of them can become stabilized and persist longer term. Further, training made newly formed spines more stable and preexisting spines less stable. The authors interpret their results as an indication that during learning there is indeed a ‘rewiring’ of the network and not just addition of new synapses.

The two papers were reviewed by Noam E. Ziv & Ehud Ahissar in the News and Views section. Here they raise the issue that, if such a small number of spines are to account for the formation of stable memories, then what are the consequences of the loss of a somewhat larger number of spines on the neuronal network?

For someone like me that more than once as an undergraduate used a microscope fitted with a concave mirror to use the sunlight to illuminate the specimen, the ability to monitor individual synaptic structures over time in a living organism can only be described as awesome. But, as pointed out by Ziv and Ahissar,

“[…] although it remains to be shown conclusively that these forms of spine remodeling are essential components of long-term learning and not merely distant echoes of other, yet to be discovered processes, these exciting studies make a convincing case for a structural basis to skill learning and reopen the field for new theories of memory formation.”

Yang, G., Pan, F., & Gan, W. (2009). Stably maintained dendritic spines are associated with lifelong memories Nature, 462 (7275), 920-924 DOI: 10.1038/nature08577
Xu, T., Yu, X., Perlik, A., Tobin, W., Zweig, J., Tennant, K., Jones, T., & Zuo, Y. (2009). Rapid formation and selective stabilization of synapses for enduring motor memories Nature, 462 (7275), 915-919 DOI: 10.1038/nature08389
Ziv, N., & Ahissar, E. (2009). Neuroscience: New tricks and old spines Nature, 462 (7275), 859-861 DOI: 10.1038/462859a

Synapse #fail, Science #win

Posted in Science by kubke on November 25, 2009

ResearchBlogging.orgThe endbulb or calyx of Held is a very large synapse found in the auditory system. It consists of a very large ‘calyceal’ ending, literally wrapping around the cell body of the postsynaptic neuron. It was first described by H Held in the late 1800’s and has since been shown to characteristically be present in neuronal circuits that require very high temporal precision. (It is, by the way, my favourite synapse.)

Because the synapse is so large, there are numerous sites of contact where the neurotransmitters are released, which will happen whenever an action potential reaches the synaptic terminal. Because of this, it has always been thought that these synapses never fail to produce a response (action potential) on its target (postsynaptic) neuron, that is, that it is a fail-safe synapse: every time that there is neurotransmitter release, the postsynaptic neuron produces an action potential.

Endbulb of Held

Barn owl endbulb of Held (by Kubke)

But is this true?

Jeannette Lorteije, Silviu Rusu, Christopher Kushmerick and Gerard Borst examined precisely this, and they did so in a series of really elegant experiments in mice. They examined whether the discrepancies in the data regarding the degree of reliability at the enbulb or calyx of Held could be attributed to different methodological approaches or differences in the interpretation of the raw data. To examine this they did a series of recordings from cells in the Medial Nucleus of the Trapezoid Body (MNTB), which is part of the mammalian auditory system. The authors conclude that that there is a significant incidence of failures of transmission at this level of the system.

This is in contrast with the results reported by Bernard Englitz, Santra Tolnai, Marey Typlt, Jürgen Jost and Rüdolf Rübsamen. Here the authors recorded the failure at the endbulb of Held in the auditory cochlear nucleus AVCN and the calyx of Held in the MNTB in mongolian gerbils. They report that although failures of transmission were often found in AVCN, this was not the case in MNTB.

Synaptic structures analogous to the endbulb or calyx of Held are found in neuronal circuits that require high temporal precision. In the auditory system high temporal resolution is necessary for the measurement of interaural time differences, which in mammals are used to localize low frequency sound in the horizontal plane. Benedikt Grothe has argued that low frequency hearing appeared later in mammalian evolution, and that anatomical differences in a nucleus that receives inputs from the MNTB and is involved in the detection of interaural time differences (MSO) reflect this evolution. He argues that although MSO may have evolved to detect ITDs in low frequency hearing mammals (such as gerbils), its function may be different in higher frequency hearing mammals. On therefore wonders whether the differences in the data between the two studies may be related to adaptations associated with different temporal processing requirements in mammals with different frequency hearing ranges.

What did Lorteije and collaborators do?

In order to decide whether there are times in which synaptic release fails to elicit an action potential on the target cell, one needs to simultaneously monitor the activity happening at the synapse as well as at the postsynaptic neuron. There are traditionally two ways of doing this: One is to record the currents near the synapse that are produced by the electrical activity of the synapse and the cell, and the endbulbs of Held are large enough to produce sufficient current that can be detected. The other is to actually record the activity simultaneously from the cell and the synaptic terminal, which is usually done in an ‘in vitro’ preparation.

Lorteije and colleagues produced a set of data that is simply amazing, and their findings explain many of the discrepancies that can be found in the literature. They answered some very straightforward questions:

  1. Are the extracellular recordings done in vivo representative of what is actually going at a single endbulb-neuron contact? (the answer is yes)
  2. Is there synaptic  release that fails to produce an action potential in the postsynaptic neuron? (the answer is also yes)
  3. Is the short term synaptic depression seen in vitro also seen in the whole animal (in vivo)? (Short term depression is a reduction in the effect of synaptic release on the postsynaptic cell.). (The answer is basically no)

The authors recorded from cells in the Medial Nucleus of the Trapezoid Body (MNTB), which receives inputs in the form of the large calyces of Held and is involved in auditory processing. They did this by recording the spontaneous and auditory-evoked activity extracellularly (as most people do) as well as directly from the cells with a patch pipette in anaesthetized mice. They then repeated these experiments in vitro, this time simultaneously recording extracellularly and in whole cell patch, which allowed them to confirm that the extracellular recordings in vivo did indeed represent the activities of the terminal and the cell and that it could also provide information as to the size of the synaptic potential. Their results have two important findings:

  1. in vivo there is no observable short term synaptic depression. The synaptic depression observed in vitro may be partly due to the concentration of Calcium in the bathing solution, but other factors may be involved.
  2. They also found that the release of neurotransmitter at the synapse often failed to produce an action potential in the postsynaptic cell. A similar rate of failure to that observed in vivo can be obtained in vitro by lowering the calcium concentration of the bathing solution.

The authors summarize their findings by saying:

“Due to its low release probability and large number of release sites, its average output can be kept constant, regardless of firing frequency. Its low quantal output thus allows it to be a tonic synapse, but the price it pays is an increase in jitter and synaptic latency and occasional postsynaptic failures.”

This is a carefully designed study, and despite my concerns as to whether their results are generalizable to other mammals, they do provide data that will be welcome by many auditory neurophysiologists. Their ability to record from a patch in vivo is no small feat, and the correlation between intracellular and extracellular data is extremely useful. Further, there is a cautionary tale around the way that data obtained from in vitro data can be interpreted.

And if you think this post is long, try reading the paper! (There are heaps more gems in there.)


Lorteije, J., Rusu, S., Kushmerick, C., & Borst, J. (2009). Reliability and Precision of the Mouse Calyx of Held Synapse Journal of Neuroscience, 29 (44), 13770-13784 DOI: 10.1523/JNEUROSCI.3285-09.2009
Englitz, B., Tolnai, S., Typlt, M., Jost, J., & Rübsamen, R. (2009). Reliability of Synaptic Transmission at the Synapses of Held In Vivo under Acoustic Stimulation PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007014
Grothe, B. (2000). The evolution of temporal processing in the medial superior olive, an auditory brainstem structure Progress in Neurobiology, 61 (6), 581-610 DOI: 10.1016/S0301-0082(99)00068-4

[Open] Science Sunday – 1-11-09

Posted in Science, Science and Society by kubke on November 1, 2009

Random samples of my reading list brought to you through the magic of the internet, bloggers and Open Access.

This has been a busy week, but I managed to get some reading in anyway.

A nice piece of news is that it looks like Canada’s Science Media Centre is ready to go, adding to the family of SMCs. (via Peter Griffin, SMC-NZ)

I loved this article in PLoS Computational Biology (Getting Started in Gene Expression Microarray Analysis) by Slonim and Yanai. It is a great “do’s and don’t’s” of the technique. I love articles that spell out techniques I don’t have personal experience with, because they give me the information I need to be able to make a critical assessment of the literature that make use of them. I will be coming back to this article a lot!

Steve Wilbanks has a great post: “Open Source Science? Or distributed science?” He starts his blog by saying:

I was asked in an interview recently about “open source science” and it got me thinking about the ways that, in the “open” communities of practice, we frequently over-simplify the realities of how software like GNU/Linux actually came to be. Open Source refers to a software worldview. It’s about software development, not a universal truth that can be easily exported. And it’s well worth unpacking the worldview to understand it, and then to look at the realities of open source software as they map – or more frequently do not map – to science.

And that was enough to hook me. Very interesting read.

Misha (from Mind Hacks) has a great post on brain stories and neuronovels, or about how neuroscience is seeping into literature. The post is a comment on a story by Marco Roth (n+1) which is a must read for those that love both literature and the brain.

My favourite tweet this week is by @gnat, pointing to the historical thesaurus of the Oxford English Dictionary. Lust, indeed!