Remember My Name: the Rise of the Acronym

I’ve been thinking a lot about acronyms. It seems to me, that an acronym is a super sexy thing to have.

In the past few months, my little corner of Neuroscience has enjoyed the appearance of 4 new acronyms. Now, I’m not talking about the consonant-and-vowel salad used as shorthand for ever-more-sub-classified brain regions. Although, as a side note, I learned last Thursday during a lab meeting presentation that no matter how firm my intentions, I cannot seem to say dlPFC. Instead of a neat word-limit-approved acronym, I find myself pronouncing dorsolateral prefrontal cortex in a burst of desperate enunciation.

But the acronyms that float through my NCBI email alerts are not these brain region shorthands. Rather, they are the badges of newly minted techniques, or ideas, branded with a catchy, sexy acronym to help propel them into the neuroscience community’s awareness.

Remember my Name

(Aside - Attention: D. Bochner.)

There are a lot of neuroscientists out there. And all of us are constantly producing new research, new techniques, new publications. Standing out amongst all this noise can be an imperative; critical for attaining an elusive funding source, or a prized (by some) academic job. So it makes perfect sense to me that a researcher, armed with a novel technique (or combination of ideas) would seek to use a clever acronym as a way to catch the attention of her/his fellow researchers. Can we together admit to a feeling of professional jealous admiration for a colleague armed with an acronym? (Catherine, nicely done with SPLURgE. Casey, TRAP is so delightfully customizable: ArcTRAP, fosTRAP. Excellent work.)

Plus, how thrilling to hear your colleagues utter the creative symbol of your research efforts. The next best thing, perhaps, to the nomenclatural heights enjoyed by Golgi, Nissl, Purkinje, Brodmann; that age of naming, it seems, has passed. (Although vestiges persist; see the newly discovered Dua’s layer, so found and named by Harminder Singh Dua, U. Nottingham).

Acronyms are also clearly useful for condensing a complex technique into an easily stated verbal handle that can be readily passed along to PR departments, or thrown around in scientific discussions. My personal struggles with dlPFC aside, I think we can all agree that including “clear lipid-exchanged acrylamide-hybridized rigid imaging/immunostaining/in situ hybridization-compatible tissue-hydrogel” in a sentence would be a trial. Far easier to say “CLARITY”. And with the added benefit of an evocative name to entice readers, prospective users, and public audiences. Here too we find the BRAIN Initiative (Brain Research through Advancing Innovative Neurotechnologies). Open to some good-natured ribbing for using “Brain” as the B in BRAIN? Sure. But ever so ready for prime-time publicity.

A Final Thought

The other week, during a grant application planning session, I was counseled that using a particular acronym-ed technique (hopefully soon to be published from my lab), could help my grants score. An acronym bringing a sense of the official, the innovative, where a colloquial description of a technique is merely… there. After receiving Summary Statements that praise my scientific questions, only to declaim the innovation of my techniques, I can’t argue with the impulse. Will the technique be critically necessary to answer my scientific questions? Maybe. Nevertheless, as I construct my research strategy, I’ll be spending some quality time considering whether a sexy acronym could catch the attention of that NIH review committee, and secure me the funding I need to help my lab stay in business.

The Acronyms

SPLURgE. From Chrisitan et al (2013). Sniffer Patch Laser Uncaging REsponse (SPLURge): an assay of regional differences in allosteric receptor modulation and neurotransmitter clearance. J Neurophysiol. Epub ahead of print. Link

TRAP. From Guenthner et al (2013). Permanent Genetic Access to Transiently Active Neurons via TRAP: Targeted Recombination in Active Populations. Neuron. 78(5):773-84. See previous blog post.  Or go see the paper directly. 

CLARITY. From Chung et al (2013). Structural and molecular interrogation of intact biological systems. Nature. 497(7449):332-7. Link

BRAIN Initiative. Via the NIH and the White House.

Comment

Astra Bryant

Astra Bryant is a graduate of the Stanford Neuroscience PhD program in the labs of Drs. Eric Knudsen and John Huguenard. She used in vitro slice electrophysiology to study the cellular and synaptic mechanisms linking cholinergic signaling and gamma oscillations – two processes critical for the control of gaze and attention, which are disrupted in many psychiatric disorders. She is a senior editor and the webmaster of the NeuWrite West Neuroblog

PhDs in Press: TRAPing Neurons and Tracking Temporal Lobe Epilepsy

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Part 7 in an occasional feature, highlighting recently published articles featuring an author (or authors) affiliated with the Stanford Neuroscience Ph.D program. This round, we've got two lovely first author papers, by Casey Guenthner and Izumi Toyoda.

Let's begin with my year-mate, Casey Guenthner (Luo Lab), who published his development of a technique, TRAP (Targeted Recombination in Active Populations), that allows genetic targeting of populations of neurons that are defined by whether they were activated in vivo by a set stimulus. For details, check out Casey's abstract, below.

Targeting genetically encoded tools for neural circuit dissection to relevant cellular populations is a major challenge in neurobiology. We developed an approach, targeted recombination in active populations (TRAP), to obtain genetic access to neurons that were activated by defined stimuli. This method utilizes mice in which the tamoxifen-dependent recombinase CreER(T2) is expressed in an activity-dependent manner from the loci of the immediate early genes Arc and Fos. Active cells that express CreER(T2) can only undergo recombination when tamoxifen is present, allowing genetic access to neurons that are active during a time window of less than 12 hr. We show that TRAP can provide selective access to neurons activated by specific somatosensory, visual, and auditory stimuli and by experience in a novel environment. When combined with tools for labeling, tracing, recording, and manipulating neurons, TRAP offers a powerful approach for understanding how the brain processes information and generates behavior.

Guenthner, Miyamichi, Yang, Heller and Luo. Permanent Genetic Access to Transiently Active Neurons via TRAP: Targeted Recombination in Active Populations. Neuron. 2013: 78(5):773-84. doi:10.1016/j.neuron.2013.03.025

I will leave you all with the comment that Casey's cartoon of the mouse whisker pad is glorious in its anatomical accuracy. And it's pretty cute, too. Figure 3b. Check it out below, along with data demonstrating targeting of active neurons in the whisker barrel system.

Figure 3. FosTRAP in the Barrel Cortex of Whisker-Plucked Mice.(A) Experimental scheme: FosTRAP mice had either all whiskers except C2 plucked unilaterally or had only the C2 whisker plucked. After a 2 day recovery period, mice were injected with 150 mg/kg TM, and recombination was examined 7 days later.(B) Tangential views of flattened layer 4 of the primary somatosensory barrel cortex (top) or coronal views through the C2 barrel (bottom). White dots indicate the corners of the C2 barrel on the basis of dense DAPI staining of the barrel walls. Compared with controls (left), removal of only the C2 whisker results in elimination of TRAP signal from the C2 barrel (middle), whereas removal of all whiskers except C2 results in absence of most TRAPed cells in all barrels except C2 (right). The left and middle images are from the same mouse. Images are representative of at least 3–4 mice for each condition. The scale bar represents 250 μm. Guenthner et al 2013.

Just last week, Izumi Toyoda (Buckmaster lab) published her work recording spontaneous seizures in rats with temporal lobe epilepsy. Using 32 recording electrodes per rat, Izumi records from a massive number of brain structures, tracking the spread of seizures within the rodent brain. Her paper compares the propagation of the spontaneous seizures in the rats to known seizure activity in human patients with temporal lobe epilepsy. The results validate the pilocarpine model of temporal lobe epilepsy, showing seizures begin in similar brain locations in human patients and rodent subjects.

Temporal lobe epilepsy is the most common form of epilepsy in adults. The pilocarpine-treated rat model is used frequently to investigate temporal lobe epilepsy. The validity of the pilocarpine model has been challenged based largely on concerns that seizures might initiate in different brain regions in rats than in patients. The present study used 32 recording electrodes per rat to evaluate spontaneous seizures in various brain regions including the septum, dorsomedial thalamus, amygdala, olfactory cortex, dorsal and ventral hippocampus, substantia nigra, entorhinal cortex, and ventral subiculum. Compared with published results from patients, seizures in rats tended to be shorter, spread faster and more extensively, generate behavioral manifestations more quickly, and produce generalized convulsions more frequently. Similarities to patients included electrographic waveform patterns at seizure onset, variability in sites of earliest seizure activity within individuals, and variability in patterns of seizure spread. Like patients, the earliest seizure activity in rats was recorded most frequently within the hippocampal formation. The ventral hippocampus and ventral subiculum displayed the earliest seizure activity. Amygdala, olfactory cortex, and septum occasionally displayed early seizure latencies, but not above chance levels. Substantia nigra and dorsomedial thalamus demonstrated consistently late seizure onsets, suggesting their unlikely involvement in seizure initiation. The results of the present study reveal similarities in onset sites of spontaneous seizures in patients with temporal lobe epilepsy and pilocarpine-treated rats that support the model's validity.

Toyoda, Bower, Leyva, Buckmaster. Early Activation of Ventral Hippocampus and Subiculum during Spontaneous Seizures in a Rat Model of Temporal Lobe Epilepsy. J Neurosci, 3 July 2013, 33(27):11100-11115. doi:10.1523/JNEUROSCI.0472-13.2013

And because I showed a figure from Casey's paper, here is one from Izumi's, highlighting a subset of 16 recording electrodes on which a spontaneous seizure is recorded in an epileptic, pilocarpine-treated rat. Let there be no doubt in your mind - the skill required to implant 32 recording electrodes into a rat is large. I suggest being very impressed with Izumi's surgical skills.

Figure 2. Spontaneous seizures in epileptic pilocarpine-treated rats. A, Seizures spread quickly and extensively. Recordings from a subset of 16/32 electrodes implanted in various brain regions. The approximate seizure offset (arrow) and onset window (bar), bracketed by the latest normal activity and earliest clear seizure activity, are indicated. L indicates left; M, medial; EC, entorhinal cortex; sub, subiculum; R, right; amyg, amygdala; SNpr/c, substantia nigra pars reticulata/compacta; sept, septum; D, dorsal; hipp, hippocampus; olf ctx, olfactory cortex; vdb, ventral diagonal band; dm thal, dorsomedial thalamus; endo n, endopiriform nucleus. B, Precise seizure onsets (arrows) in three regions. C, Seizure durations. Bars represent averages; symbols indicate durations of individual seizures. D, Behavioral seizure onset latencies. Electrographic seizure onset is at 0. Positive (negative) values indicate that behavioral onset followed (preceded) electrographic onset. Bars represent averages; symbols indicate individual seizures. From Toyoda et al, 2013.

1 Comment /Source

Astra Bryant

Astra Bryant is a graduate of the Stanford Neuroscience PhD program in the labs of Drs. Eric Knudsen and John Huguenard. She used in vitro slice electrophysiology to study the cellular and synaptic mechanisms linking cholinergic signaling and gamma oscillations – two processes critical for the control of gaze and attention, which are disrupted in many psychiatric disorders. She is a senior editor and the webmaster of the NeuWrite West Neuroblog

Brains & Bourbon Ep. 3: neuroinflammation, brain parasites, zombie mice, and Sazerac

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A new week, means a new episode of Brains and Bourbon! Our guest this week is Egle Cekanaviciute, a 5th year graduate student in Marion Buckwalter's lab, who teaches us how to make a Sazerac, and talks to us about teaching, neuroinflammation, and brain parasites and zombie mice!

This week, we have two versions: one shorter, one longer (including additional and expanded sections).

The Shorter Version

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The Longer Version

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You can also stream or download the shorter version of the episode here: Brains & Bourbon Ep3 Neuroinflammation/Sazerac/EgleCekanaviciute SHORT or the longer version of the show here: Brains & Bourbon Ep3 Neuroinflammation/Sazerac/EgleCekanaviciute Full You can subscribe to "Brains and Bourbon," and all of the Neuwrite West podcasts, by searching for "Neuwritewest" at the iTunes store and subscribing to our channel.

Thanks for listening! Erica Seigneur Forrest Collman Nick Weiler

Framing the Debate

As someone on the outside of the connectomics debate looking in, I thought I’d more or less figured out what everyone was talking about, and what the major arguments were. But as it turns out, a recent experience with someone who’s closer to the discussion taught me not to take my assumptions for granted, and got me thinking about why the debate might look the way it does now, and whether it ought to look differently.

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A Myriad of Problems

Human genes can’t be patented. So said the Supreme Court in their June 13 decision in Association for Molecular Pathology v. Myriad Genetics, Inc.  I heard the news that morning on NPR and cheered aloud, even though I was alone. Then I paused. Myriad Genetics had patents on the genes BRCA1 and BRCA2, which are associated with breast and ovarian cancer. The value of these genes, for now at least, rests mostly in the information they contain (that is, they are not drug targets). People with a strong family history of breast or ovarian cancer can have samples of their own DNA tested by Myriad to determine if they have inherited particular mutations in these genes that put them at risk for developing cancer themselves. The stakes of this testing are high: many people who test positive for cancer-causing BRCA mutations opt for radical surgical procedures like double mastectomies and ovariectomies. Yet Myriad’s tests are quite expensive and, until the Supreme Court decision, only Myriad could legally run them – no shopping around, no second opinions.

Myriad Genetics (along with various partners, including, notably, publicly-funded scientists at the University of Utah, the University of Pennsylvania and the National Institute of Environmental Health Sciences) cloned, sequenced, and identified key mutations in BRCA1 and BRCA2 in the 1990s. The research was costly (though again, it is important to note that some of that cost was born by the American taxpayer), so Myriad wanted to patent the BRCA genes in order to profit from their discoveries. Without patent protection, anyone could have come along and provided low-cost BRCA testing. That’s because the techniques involved in BRCA testing are not actually that complicated. The valuable discoveries that Myriad and its collaborators made didn’t have to do with developing the testing process (i.e. gene sequencing), but with telling testers where and what to test for. Once those things were known, anyone could run a test, or rather, anyone could have run a test had Myriad not been granted gene patents.

Depending on your perspective, competition in the BRCA testing market could have been good or bad. Low-cost testing would have been better for patients and insurance companies. But if competition had been allowed, would Myriad have even bothered with the investments necessary to develop the test in the first place? Probably not. Why put in all that money and effort and risk of failure when you won’t be able to reap the profits? Why not wait around and see if some other sucker will try it? In the absence of patent guarantees, the private sector will not make risky investments in nascent biotechnologies. That’s not to say no test would ever have come along. There were probably some selfless science heroes out there who would have done it without a profit motive (Jonas Salk, inventor of the polio vaccine, famously refused to patent his invention, lest that limit its availability), but it would have taken longer. It also would likely have required government funding of the Salk-esque scientists who would be willing to do it.

For a stark illustration of public vs. private approaches to science, look no further than the Human Genome Project. The public Human Genome Project, which officially began in 1990 and was led primarily by the current director of the NIH Francis Collins, was plugging along slowly but surely on sequencing a human genome, dumping its sequences into a giant open-access database called GenBank as it went, every 24 hours. Then, in 1998, along came Celera, Craig Venter’s company, which was using “shotgun sequencing” techniques to piece together genetic information much more rapidly and cheaply than the government project had been doing. Celera’s work on the Human Genome Project accelerated its progress substantially. The final Human Genome Project came in several years ahead of time and under budget. But Celera also changed the nature of the project by delaying the release of its data (it agreed to release data yearly instead of daily), refusing to release data into the government’s open-access database, and seeking to patent the genes it had sequenced first, sometimes without knowing anything about what they did (in total, it filed 6500 preliminary “placeholder” gene patents).

In summary, Celera was good for genomics in that it accelerated progress toward a specific goal, but bad for science in that it impeded the efforts of others to make use of and build on Celera’s achievements. So, the question for us, as citizens, taxpayers, consumers and patients, is this: do you want specific projects done fast and cheap? Or do you want to pay, with your tax dollars, for open academic exchanges of information that will drive further innovation? Do you want the private sector to pay for research to develop new genetic tests and pharmaceuticals, in exchange for which we will grant them temporary monopolies? Or do you want to pay, with your tax dollars, for the research, which will permit the immediate availability of generics from a variety of competing companies?

Perhaps there is a middle ground between these two extremes. For one thing, it is unrealistic to think that all science could be government funded. It’s too expensive and a complete lack of competition would lead to profound inefficiencies. On the other hand, gene patents are too broad and cause too much restriction (thus my happiness and relief on hearing they are gone). A gene is not so much a material thing as it is information, and granting one entity the exclusive legal right to make use of information restricts intellectual freedom and scientific progress. What might make sense is to issue patents only for specific applications. We do currently allow patents on ideas in the form of “inhibit protein X to treat disease Y.” We can do the same for genes, allowing companies to pursue gene therapies under patent protection without allowing them to own the actual genes they’re seeking to manipulate.

Another idea percolating in the background is to offer monetary rewards for specific discoveries. If the rewards offered are sufficient, such a system could provide incentives for individuals or companies to pursue worthy goals independently of offering them patent protection. The XPrize Foundation has incentivized some amazing inventions, including the design of commercially viable passenger space shuttles. A new prize, the Archon Genomics XPrize, is offering $10 million for the complete, accurate whole-genome sequencing of 100 centenarians. The XPrize model is interesting, but there are still issues simmering in the background over the issue of who will retain intellectual property rights on the inventions made by XPrize competitors and how that will affect participation in the competitions. Another issue is the prize money. $10 million is a lot, but probably not enough to cover the costs of the eventual winner of the prize, so the XPrize as it is can’t replace patent rights as the sole incentive to achieve this feat.

As we consider pragmatically what can be done to reform biological patent law, it is impossible to ignore the fact that we are talking about biology, the study of life. The question of whether human genes, or living organisms, or any parts of living organisms are patentable is not just a pragmatic question, but also an ethical one. The Myriad case notwithstanding, we are trending more and more towards granting patents on life.  There are patents on genetically engineered viruses, bacteria, plants, animals, and even human stem cells. It sounds very creepy, but I still can’t help questioning whether some of those patents really are justified in the name of promoting innovation. As scientists develop more and more ways to use biomolecules as machines (e.g. to make computers), we are blurring the lines between invention and discovery, between innovation and information, between synthetic and natural. As a result, we are going to need to think long and hard about how to handle biological patents in the future. Preferably, we would do this as a society, through open debate and clear legislation, rather than waiting for the courts to do it for us.

Brains & Bourbon Ep.2: neuronal plasticity, religion, and green Chartreuse

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A new week, means a new episode of Brains and Bourbon! Our guest this week is George Vidal, a 4th year graduate student in Carla Shatz's lab here at Stanford, who talks to us about neuronal plasticity, and the intersection between science and religion, and shares with us his favorite cocktail -- green Chartreuse.

This week, we have two versions: one shorter, one longer (including additional and expanded sections).

The Shorter Version

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You can also stream or download the shorter version of the episode here: Brains & Bourbon Ep2 Plasticity/Chartreuse/George Vidal SHORT or the longer version of the show here: Brains & Bourbon Ep2 Plasticity/Chartreuse/George Vidal FULL You can subscribe to "Brains and Bourbon," and all of the Neuwrite West podcasts, by searching for "Neuwritewest" at the iTunes store and subscribing to our channel.
Thanks for listening! Erica Seigneur Forrest Collman Nick Weiler

Vampire Worms

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Illustration of the fabled Mongolian death worm, via Neatorama

What comes to mind when I say the word "worm"? If you're not acquainted with invertebrate neurobiology, it's probably that squiggly, segmented creature with five hearts that you accidentally cut in half with a spade once while digging around in your garden. If you're familiar with the nematode Caenorhabditis elegans, you may instead think of a tiny roundworm with exactly 959 somatic cells that develop in the same way every time in every worm.

Nope. What you should really be thinking is 'fangs.' Or, more precisely, 'tooth-like denticles,' though unfortunately, 'worms with tooth-like denticles' doesn't quite conjure up the same imagery as 'worms with fangs.'

Dorsal tooth outlined in blue, from Bento et al. 2010

To be fair, not every worm has a fang. But we can take advantage of the similarity between nematodes with and without fangs to learn how variations in their neural circuitry may contribute to differences in their feeding behavior.

C. elegans is a bacterivore. It crawls around in soil, foraging for bacteria and gulping them down into its bicameral pharynx. When the bacteria get to the posterior chamber, they run into a grinder, a hard structure that breaks them down mechanically, like the stones in the gizzards of chickens and herbivorous saurians.

Pristionchus pacificus, a predatory cousin of C. elegans, instead develops one or two teeth akin to the fangs of a snake. It can then use its dorsal tooth to puncture another worm and suck out its viscera. To help digest its prey in the absence of a grinder, P. pacificus plays host to a set of gut bacteria that do the work for it.

Now here’s the fun stuff: in the first 20-30 seconds of the video below, you can see the back-and-forth pumping motion as the pharynx moves food down the gut. In the last 30 seconds, when the C. elegans stops moving, the tooth and movement of the mouth muscles are more clear. Warning: graphic nematode-on-nematode violence.

If I were a nematode, a cannibalistic vampire worm would certainly be the stuff of nightmares. Luckily, I am 1600 times taller than P. pacificus is long.

Since these two types of feeding behaviors require different sets of muscle movements, it stands to reason that the neurons of the pharynx might be wired somewhat differently. Daniel Bumbarger, a postdoctoral fellow in the Sommer lab at the Max Planck Institute in Tübingen, borrowed from Google and graph theory to compare the anatomical circuitry of these two species. He took advantage of the fact that the pharyngeal nervous system in both of these species is almost a closed system, connected to the rest of the worm’s sensory and motor functions by only a single neuron. In a marvelous stroke of luck that probably made up for the tedious work of creating a 3000-slice EM reconstruction of the P. pacificus pharynx, it turned out that the identities and locations of the 20 C. elegans pharyngeal neurons are preserved almost perfectly in P. pacificus – it’s only their connectivity that differs (although we can argue about how connectivity may define identity, neuron identity in C. elegans is defined by lineage as well as function). The muscle cells pm1 and pm3, which contract rhythmically in predatory feeding as P. pacificus punctures its prey, are more highly innervated in P. pacificus. Conversely, pm7, the cell that normally drives the grinder in C. elegans, exists but receives no neural input at all in P. pacificus.

Comparison of pharynx cells in C. elegan and P. pacificus from Bumbarger et al. 2013

It's a classical comparative neuroanatomy study, but on a much smaller scale. The qualitative information is interesting, but what else can we do with a map of anatomical connections between neurons? The authors decided that they might be able to tease something more out of this connectivity map by integrating mathematical algorithms from other disciplines. In this case, the field they drew from was that of the search engine – specifically, Google. The PageRank system, named not for the fact that it ranks webpages, but for Google co-founder Larry Page, is meant to rank the importance of any given node in the network, based recursively on the number and weight of other nodes that link to it. To put it simply, if important people think you’re important, then you’re considered more important, which in turn affects the rank of people you think are important.

In comparing the two worm neural networks, the authors found that neurons controlling the behavior of the anterior pharynx (where the tooth is) were more important in P. pacificus, while neurons controlling the posterior pharynx (where the grinder is) were more important in C. elegans. What does this actually mean? Well, it suggests that more information is flowing through that particular part of the circuit, and that the physical behavior of the worm is most dominated by what those particular neurons say.

To look at where these specific interneurons were getting information from, the researchers then used a measure of focused centrality from graph theory (a branch of mathematics that focuses on the links between pairs of objects in a network). This revealed that neurons I1 and I2 receive a lot of indirect input from the motor neuron M4, and send out a whole lot of indirect input to the muscle cell pm4. The authors suggest that this higher proportion of indirect information flow in P. pacificus as opposed to C. elegans may correlate with more complex functions and the ability to switch between different behaviors.

It is a little difficult to understand what some of these methods could actually teach us about the system – do we really need to do a closeness centrality analysis to find that muscle cells that move the tooth receive more inputs in P. pacificus? We could just compare the number of synapses onto each of those cells between the two species. There is still a lot of work to be done here in finding what kinds of analyses might actually yield biologically relevant insights, but once we've identified the best methods in a small, isolated system such as this, we could expand their use to understanding indirect information flow through larger networks of neurons. We might also find something interesting if we take a look at the characteristics of the information being passed to these important-looking neurons. We can integrate this kind of information flow analysis with knowledge of whether the synapses are excitatory or inhibitory, the strength of each synapse, the changes that might arise with learning, and the effect of neuromodulators like dopamine and serotonin (which are especially important in regulating worm feeding behavior and which play large but poorly understood roles in the human alimentary system as well).

I'm hopeful that we will soon see functional data to correlate with the behavior, from ablation studies, optogenetic inhibition, in vivo electrophysiology, or even imaging with voltage indicators. In addition to testing the predictions made about the importance of certain cells, such data could shed light on various unanswered observations, such as why pm4, a muscle in the middle of the pharynx, and the gland cell, whose function is unknown, seem to be so central and important in the network analyses. And maybe we can even solve the mystery of why worms with fangs are so cool.

References

Bumbarger, D. J., Riebesell, M., Rödelsperger, C. & Sommer, R. J. System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes. Cell 152, 109–119 (2013).

Bento, G., Ogawa, A. & Sommer, R. J. Co-option of the hormone-signalling module dafachronic acid-DAF-12 in nematode evolution. Nature 466, 494–497 (2010).

Can neurofeedback go deeper?

Feedback, a word with more than 100 years of history, is one of the most crucial concepts to understanding how the brain works. Feedback occurs both at the cellular level – neurons are wired to feed information forward and back – as well as at a more behavioral level. We understand feedback colloquially as the reactions we get from the people around us that help to shape our behavior, but the brain uses feedback at multiple levels, down to individual cells and circuits. For example, you use visual feedback to correct the position of your hand if you can not find the light switch at first try, or mostly tactile feedback if the room is dark. At a more cognitive level, negative feedback from people around us is discouraging, while positive feedback encourages us to repeat the same behavior. Inside the brain, one can find signals that reflect something like this higher-level behavioral feedback information from the outside world. One famous example is the dopaminergic neurons in midbrain encoding reward and the lack thereof. The brain, a highly dynamic structure fed by these feedback information, changes in order to optimize actions that maximize reward. This continuous learning process provides adaptation to our changing environment.

To get a sense of what might be happening at the neural level, let's go back to the first example of the motor system's ability to control your arm and hand as you flip a light switch. The motor cortex controls the basics of intentionally moving your hand to the correct location, but if you miss the switch for some reason, the cerebellum takes charge of solving the mysterious discrepancy by comparing outgoing motor commands against sensory feedback, which acts as an error signal. This feedback controller continuously compares the desired output ("hit switch") with the actual result ("there's no switch here!"), and makes adjustments until the desired movement is achieved.

Scientists feed back to the disordered nervous system

Increasingly, clinical applications take advantage of the feedback mechanisms that are extensively used by the brain. The most prominent clinical applications so far are brain-computer interfaces (BCI) using implanted electrodes, such as those used to control neuroprosthetics, and EEG neurofeedback (NFB). BCI is a kind of brain computer interaction where a device provides direct communication between brain and computer. This approach is being used for neuroprosthetics that might substitute sensory, motor or cognitive modalities. There are devices, for example, that assist individuals with quadriplegia. These invasive devices decode the neural activity in motor cortex that are received from implanted electrodes, while the patients think about moving their limbs in a certain way and command a robotic limb that executes the movement. While they get trained for the device, individuals learn to use their neural activity to manipulate computer cursors on screen in order to command the device perform simple motor tasks just by thinking about the task and seeing the visual feedback. Thus, visual feedback provides the cues for the accuracy of the aimed movement, just like the real thing.

EEG NFB uses brainwaves recorded from electrodes placed on scalp and conveys them to a computer, which decodes these signals. The signals are then visualized on the screen so that the individual learns to self-regulate the underlying neural signals picked up by the electrodes. Thus, NFB is distinguished from the BCI approach in several aspects. Unlike the implanted BCI electrodes used for neuroprosthetics, NFB is not invasive, relying instead on EEG electrodes placed on the skull. While implanted electrodes can record from multiple neurons in a very defined region, EEG recordings reflect an aggregate activity, recorded from a rather large, indistinct region, resulting in low spatial resolution. Similarly, temporal resolution of implanted electrodes are better than the EEG electrodes. However, the invasiveness makes neuroprosthetics available only to patients whose conditions are not treatable with any other method, while NFB is basically available to everyone.

BCI and NFB are used for different clinical purposes. While BCI has mainly been developed to assist individuals with severe neurological deficits, ongoing NFB research often aims to ameliorate various psychiatric conditions such as addiction, ADHD, depression, autism and anxiety, besides initial successes with Parkinson’s disease, tremor and dystonia. Neuroprosthetics with implanted electrodes can be considered as a last resort for the patients whose lives are severely affected by the disease, and who cannot benefit from any other therapy. In the case of psychiatric disorders, medication and psychotherapy can generally keep the disease under control, or the patients can live a somewhat normal life without intervention. As a result, individuals with these disorders cannot yet benefit from the more advanced, but also more invasive methods used with BCIs.

In recent years, researchers have begun experimenting on invasive methods for the treatment of pychiatric conditions. One example where implanted electrodes have been used to treat psychiatric disorders is deep brain stimulation (DBS) which has been successfully used to treat major depressive disorder in recent years and found to be effective in many conditions that are otherwise incurable . In addition, there are clinical trials ongoing for DBS treatment of obsessive compulsive disorder. DBS requires implantation of deep brain electrodes as in the BCI approach, but does not require any feedback training as the treatment is comprised of continuous stimulation of an affected brain area.

Neurofeedback for DBS patients

Stimulation of specific brain regions seems to be effective against some psychiatric disorders, but these approaches have not yet harnessed the power of feedback that has been so effective in EEG NFB treatments. Here, I would like to argue that we can, and maybe should, take advantage of these invasive electrodes that are implanted for DBS, and perform neurofeedback. This would be an invaluable opportunity for those individuals to focus on how to feel better (less anxious, less sad, more attentive etc). Currently, DBS is thought to work through altering the abnormal activity in affected regions in a way that decreases symptoms. The patient has no control over the stimulation or its influence on the symptoms. I propose that it might be better to have patients learn to self-regulate this activity in real time rather than just applying standard stimulation. In the development of neuroprosthetics, we have become aware of the importance of feedback to the patient to allow self-regulation. Currently, for instance, a paralyzed patient can move a robotic arm by just thinking about it, but because there is no sensory feedback, the simplest movements are at best slow and clumsy, leaving patients with a lot of frustration. Researchers now are working on providing sensory feedback to make the robotic arm closer to a real one. Similarly, neural feedback can be applied to DBS patients to improve the quality of the improvement.

An important note here is that psychiatric problems are inherently more complex than the neurologic ones such as paralysis in terms of the subjective awareness of the existing problem and capacity to imagine what it would be like to be “normal”. During BCI training, a paralyzed patient needs to imagine herself moving a limb, which is a very easy task. Additionally, research shows that the brain activity is similar when a particular movement is performed vs. imagined. However, let's say for a patient experiencing depression, imagining to be happy or motivated might not be as intuitive. Similarly for an individual with ADHD, being more focused and attentive is a difficult state to attain. Revealing neural correlates of these deficits have thus been crucial in providing the connection between the brain activity and what the patient experiences. NFB shows that patients can self-regulate the brain activity if it is presented to them in the form of a sensory stimulus.

There are two steps that need to be taken to make invasive NFB possible: First is to explore how the neural activity recorded by DBS electrodes correlates with the symptoms of the condition of interest. There are several human imaging and animal electrophysiology studies that begin to address this, but we need to be able to precisely interpret the correlation of symptoms to neural activity in real time. The success of EEG NFB in various psychiatric conditions suggests that this is an achievable goal. Secondly, the electrode placement for invasive NFB might be slightly different than DBS, which would require more research. Additionally, there are technical challenges, such as the need to both stimulate and record from the same electrodes, that will eventually need to be addressed.

Incorporating neurofeedback to DBS not only has the potential to improve the quality of the treatment, but it might give rise to longer term, persistent effects. If the patients learn to control the abnormal activity, or even just get a feedback on how it is changing with stimulation, they might eventually learn to suppress or change the symptoms by themselves. This obviously opens a whole new avenue of research about how plasticity and learning may come about with neurofeedback.

To conclude, it is crucial to benefit from the existing technologies as much as possible. neuroprosthetics, DBS and NFB are rapidly developing, promising techniques and I believe that invasive NFB is worth exploring with the hope of open a new avenue for long incurable psychiatric conditions.

Inflammatory comments on ageing

Cell-signalling.png

None of us is getting any younger. In fact, most of us can expect to live longer than ever. The world’s oldest man died just last week aged 116 and, as global life expectancy continues to increase, we’re going to have to tackle age-related frailty and functional fragility to avoid unbearable healthcare costs and provide quality of life for a growing population of centenarians. With rates of dementia as high as 60% in the over 85s1, neurodegeneration is a big issue; but treating age-related diseases in isolation may not be the most effective solution. Scientists now think of ageing as an intricate process during which tissues and cells change the way they communicate and interact, resulting in a gradual loss of function. Not exactly a simple cause-effect pairing that can be hit with a youth pill.  

So how can we even start to pick apart the elaborate tapestry of ageing? What exactly happens when a cell changes the way it communicates? To perform effectively, neurons need to pick up signals from the outside world. Indeed all cells, tissues and organs function by responding to external signals, thus allowing an organism to respond and adapt to changes in environment. It is difficult to show in a static diagram the dynamic nature of these interactions. But I tried anyway. ↓

 Cell signalling

The majority of signals are chemical compounds, floating around outside a cell, waiting to contact their receptor protein. Once in range, the signal and the receptor are drawn closer and dock together. In response to the signal, the receptor twists and changes; not only on the surface, but also through the cell membrane and into the cytoplasm – the inner world of the cell. The shifting and gyrating receptor can hit other proteins, slapping on new chemical groups, removing others and sending these messengers on through the internal cellular space on a collision course with target proteins of their own. This molecular line of dominoes almost always ends at the cell’s control centre – the nucleus. It is here that messages are converted into changes in gene expression, protein production and, in turn, cellular behaviour. The proteins that directly interact with DNA to bring about such changes are called transcription factors.

 

Different signal molecules and receptors trigger distinct domino effects in the cell, which scientists refer to as signalling pathways. Though different cells are tuned to pick up different signals, many of the intracellular proteins used to transmit the message have been the same for millions of years. Throughout evolution, cells have taken the Heath Robinson* approach to signalling. Rather than inventing new proteins every time a new function had to be performed, cells used the tools already at their disposal. As a result, the same proteins can be found in different types of cells, across species and even across kingdoms. You share molecular signalling pathways with almost everything – from bears, to bananas to bacteria.

*Americans see Rube Goldberg

 

One versatile and highly abundant transcription factor, and the focus of a new study in Nature2, is NFkB (nuclear factor kappa B). This molecule is a hallmark of inflammation and once activated, perpetuates inflammatory responses. However, many different cells use this molecule to transmit all sorts of messages and, as a consequence, its role in a particular signalling pathway is often difficult to pin down. In their new study, Zhang and colleagues used several tricks to see just what NFkB is up to in the brain and how its activity relates to ageing. By linking it to a fluorescent molecule, the authors were able to visualise NFkB activity in the brain. The more active the transcription factor, the brighter the signal. In this case, brains got brighter with age supporting the idea that inflammation in the brain increases as we get older. While not always bad, inflammation in the brain is a sign of altered equilibrium and contributes to several neurodegenerative diseases3-6. By injecting a non-functional version of the protein, the authors were able to interrupt NFkB activation in the brains of old mice. Interestingly, reducing NFkB activity not only reduced inflammation, but also improved cognitive function (measured by maze navigation), decreased muscle degeneration (measured by grip tests) and even extended life span.

 

So why is inflammation increased in older brains? It turns out that in mouse middle age, the majority of NFkB activity comes from the microglia –the brain’s resident immune cells. A change in the calibration of these cells over time increases their sensitivity in old age. Instead of waiting for an infection, the microglia are active all the time and mount an inappropriate inflammatory response. This is when NFkB first gets activated and it makes the microglia produce other inflammatory molecules, which perpetuate the rumour that there is some kind of infection and that inflammation is necessary. Neurons take up these signals from the microglia and NFkB inside these cells also becomes active. This form of molecular baton passing between the immune microglia and the neurons of the hypothalamus is possible because they share the same signalling molecules, and is likely to bounce back and forth in an escalating feedback loop. In this way, an inappropriate response by one cell type (the microglia) can result in another cell type getting the wrong idea. As the signals feedback, the neurons change their behaviour. One consequence is that they gradually reduce production of an important molecule called gonadotropin-releasing hormone (GnRH). The decline of GnRH is responsible (along with other things) for the loss of reproductive function with age; but this new study showed that GnRH injection can also improve neural regeneration in old mice and strengthen cognitive and muscle function. In addition, by specifically removing a gene controlling NFkB in microglia, the authors were able to restrain inflammatory microglia in middle-aged mice. This nipped inflammation in the bud, prevented the involvement of neurons in the inflammatory process, reduced GnRH decline and extended lifespan. Hurray! A new miracle drug, right? Well, maybe not quite yet.

 

Unfortunately, we’re still a long way from using NFkB inhibition or GnRH replacement to extend human lifespan. The fact that many cells are using the same molecules to transmit messages makes targeting specific molecules very difficult. During evolution, different cell types adopted different roles as they became more specialised. However, having come from the same ancestral cell, they use the same old machinery to perform new and different tasks. Now, when a signal from one type of cell gets picked up by another, there is a level of cross-communication that can have unexpected and sometimes undesirable outcomes. If we try and remove a protein that is misbehaving in one cell type, we risk interrupting its routine function in another. The complex crosstalk between biological molecules is a caveat worth remembering whenever a new protein or gene hits the headlines as the root of all ageing or instigator of disease. These genes and proteins did not evolve to make us old and sick. They evolved to perform a task that is almost certainly essential for survival. It is the misuse of a protein or its appearance in the wrong cell at the wrong time that causes problems. A “disease-causing” protein is, in all probability, performing an essential role elsewhere in the body so cannot just be eliminated.

 

It will take incredibly sophisticated techniques to iron out exactly how best to recalibrate cellular function following an undesirable change like the increase in NFkB activity in older neurons. Unravelling the mysteries of ageing is not an easy task and is likely to involve the integration of many different scientific disciplines. By identifying how different cells and organs communicate, we hope to get a better idea of when and how signalling wires get crossed and so identify the right target to prevent disease and maybe even slow the ageing process.

 

1)         Alzheimer’s Association (2013). 2012 Alzheimer’s Disease Facts and Figures. http://www.alz.org/downloads/facts_figures_2012.pdf OPEN ACCESS!

2)         Zhang et al. (2013). Hypothalamic programming of systemic ageing involving IKK-β, NF-κB and GnRH. Nature 497: 211-216.

3)         Wright et al. (2013) Neuroinflammation and Neuronal Loss Precede Aβ Plaque Deposition in the hAPP-J20 Mouse Model of Alzheimer’s Disease. PLoS ONE 8(4): e59586. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0059586 OPEN ACCESS!

4)             Ugur Tufekci et al. (2012). Chapter Four – Inflammation in Parkinson's Disease. Advances in Protein Chemistry and Structural Biology Vol. 88 pp. 69–132. http://dx.doi.org/10.1016/B978-0-12-398314-5.00004-0

5)         Holmes (2013). Systemic inflammation and Alzheimer's disease. Neuropathology and Applied Neurobiology 39 (1): 1365-2990 http://dx.doi.org/10.1111/j.1365-2990.2012.01307.x

6)             Hauser and Oksenberg (2006). The Neurobiology of Multiple Sclerosis: Genes, Inflammation, and Neurodegeneration. Neuron 52 (1): 61–76 http://dx.doi.org/10.1016/j.neuron.2006.09.011