Sunday afternoon reading: Genetic tools "primer"

I came across this fantastic review of tools for the Genetic Dissection of Neural Circuits in Neuron a few days ago. It’s by Liqun Luo, Ed Callaway, and Karel Svoboda. I highly recommend it, as it spans the gamut from genetic targeting (recombination, binary logic, viral delivery) to circuit reconstruction (super resolution LM, EM, brainbow) to activity modulation and functional mapping (uncaging, artificial GPCRs, light-gated channels, MIST). I don’t think I’ve ever seen quite a review of so many cutting edge neurotechnologies in one place. I can’t recommend this piece enough really. For me, with my lack of molecular expertise, the first sections on combinatorial gene targeting/expression techniques were great, pulling together Gal4, Cre/Flp, and Tet systems into a unified framework, along with more general concepts like site-directed integration, enhancer-trap, and repressor trap (eg. Thy1 mice).

Neuroengineering memory: Something old, something new

Over the last week, it seems like everyone has sent me this NYT piece on PKM-zeta (about work in Todd Sacktor’s lab). I’m not sure why this work is being featured in the Times right now, since it’s a few years old. But it was news to me and I think it is of interest to anyone trying to understand structure-function relationships in the brain. In the original Science paper (from 2007), a pseudosubstrate inhibitor of PKM-zeta caused irreversible loss of a conditioned taste aversion memory (news and views here). I was unfamiliar with PKM-zeta, which appears to be a constitutively active form of PKC-zeta (a kinase that some might be more familiar with) and that lacks the autoinhibitory regulatory domain of PKC. The amazing phenomena is that, after treatment with ZIP (the pseudosubstrate that ties up PKM-zeta), the memory is permanently erased and doesn’t seem to return.

What’s going on? One tantalizing possibility is that the enzyme itself is directly related to the memory trace. This contradicts the (unproven) assumption of modern neuroscience that memories are stored solely in the synaptic strengths (ie. membrane-bound receptors) of a neuron. The other suggestion is that PKM-zeta is actively maintaining synapses and that enzymatic inhibition disrupts the precise maintenance of receptors or synaptic machinery. The effects happen quite fast (within 2 hours after drug injection), which seems short for receptor recycling but perhaps long enough for structural change to occur. I’m no expert on receptor movement: Is 2 hours long enough to add/remove a significant number of receptors?

Fascinating work but the method is blunt, wiping all experimentally-induced memories (and probably others too). Last month, another group reported (also in Science) selective erasure of a fear-conditioned memory using an interesting new genetic tool. Here, neurons in the amgydala that overexpressed CREB were found to be preferentially recruited into a fear memory trace (as shown in a previous Science paper). Incorporation into the memory trace was assayed by expression of the immediate-early gene (ie. activity-dependent) Arc. In the present study, they combine overexpression of CREB in a subset of neurons with cell death (via Diphtheria toxin in a transgenic mouse vulnerable to diphtheria). Apparently, normal mice lack the receptor (here a simian version is used) that confers pathogenicity for diphtheria. Thus, the viral construct both overexpresses CREB in a subset of neurons and selectively makes the same subset vulnerable to diphtheria. Ablation of just these neurons causes a permanent loss of the memory. Subsequent similar learning proceeds just fine (using the remaining neurons).

Can we say that the race is officially on to ablate just the synapses involved in the memory? I think so. Extra points if the ablation is reversible too!

Deisseroth on new step ChR2

Nature methods has a small piece interviewing Karl Deisseroth on properties of the new step ChR2.

Some shortcomings of step ChR2 and future research directions:

Deisseroth expects ongoing efforts to improve key features of these channels. “One disadvantage is that some of the mutants have reduced current compared to wild type, so multiple mutations may help to bring those current levels back up to wild-type levels,” he says. Projects designed to improve membrane targeting and to apply a composite of opsins, including the red light–responsive channelrhodopsin from Volvox carteri, are also in the works in his laboratory.

A return to integrative medicine

Today’s NYT has a fascinating article about NIH‘s new Undiagnosed Diseases Program.

The program’s methodology is still evolving, but for the first dozen or so patients it worked this way: A primary-care physician sent in a letter describing the case, followed by reams of records documenting the diagnostic dead ends the patient had already confronted. Gahl personally reviewed all the cases and discarded about three-quarters of them, usually because the problem was insufficiently documented, seemed to be psychosomatic or, for some other reason, left Gahl with the impression that the N.I.H. had little new to offer. Then he took the most promising cases to his medical-review board, made up of several dozen clinical investigators from all over the N.I.H. The board reviewed 10 or so cases at each monthly meeting, out of which it accepted just a handful, the ones that seemed most likely to lead to a new insight into a known disease, or, even better, to a diagnosis of a disease never before seen. Then Gahl’s staff arranged to bring in each patient for a week of assessment in Bethesda. There, the patient would meet an array of specialists who did physical exams, took histories and conducted whatever additional tests they needed: ultrasound scans, M.R.I. scans, X-rays, electroencephalograms, maybe a spinal tap or a biopsy of skin or other tissue.

This approach seems in many ways more fruitful than bouncing patients from one specialist to another. Instead get the specialists together for a short period and focus on the patient. But even more tantalizing are the long-term goals:

Gahl’s projected success rate is so low because his aim is so high. His holy grail is a molecular diagnosis: finding not just a description of a new disease but also an understanding of how it works at the level of the gene. With this goal, the Undiagnosed Diseases Program aspires to be a model for how genomic medicine will be done in the 21st century.

The article documents NIH use of a “one-million SNP chip” on these patients and discovering potential molecular targets by combining insertion-deletion analysis with standard practice differential diagnosis. Combined with the recent addition of the National Center for Complementary and Alternative Medicine, NIH seems to be focusing on building clinical expertise in more integrative medicine.

Evidence of similar linguistic capabilities in Neaderthals

Apparently, in a few years, we will be able to bring Neaderthals back to life with the complete Neaderthal genome [NYT]. Currently, there is good sequence data available over 63% of the genome. (I’m amazed that, given fragmented DNA from bone, Neanderthal sequence can be distinguished from human DNA contamination but perhaps this problem is solved by having high enough coverage/multiple fragments of the same region.)

Also, it looks like Neanderthals share the FOXP2 variant that humans have:

Archaeologists have long debated whether Neanderthals could speak, and they have eagerly awaited Dr. Pääbo’s analysis of the Neanderthal FOXP2, a gene essential for language. Modern humans have two changes in FOXP2 that are not found in chimpanzees, and that presumably evolved to make speech possible. Dr. Pääbo said Neanderthals had the same two changes in their version of the FOXP2 gene. But many other genes are involved in language, so it is too early to say whether Neanderthals could speak.

UPDATE: A few days ago, I heard Wolf Enard, one of Paabo’s postdocs, speak on a fascinating project, where human version of FOXP2 was knocked in to mice (replacing the endogenous mouse version). Although the phenotypic effects were subtle, the approach itself is quite revolutionary: Putting human versions of genes into model organisms to see how the subsequent evolution of the gene changes its function. I wonder what other genes might be amenable to this approach.

sCRACM: ChR2 circuit mapping

As has become a hallmark of the Svoboda lab, this new paper in Nature (advance online publication) combines several cutting edge technologies (rAAV-delivered ChR2, most prominently, and 2-photon 1-photon laser stimulation) to do some interesting synaptic physiology.

The subcellular organization of neocortical excitatory connections : Article : Nature.

They used ChR2 (with TTX and 4-AP to block action potentials) to find where on the dendritic tree particular inputs synapsed onto L3 and L5 cells and to measure the strength of those inputs. ChR2 depolarizes the input axon locally (60um spot diameter) at points of (potential) axodendritic contact. If you’ve heard the term “potential synapse” before, then think of this technique as a way of checking potential synapses and seeing if there really is an actual synapse there.

The technique allowed them to map on a L3 barrel cortex pyramidal cell where different thalamic inputs (VPm, POm) and cortical inputs (M1, barrel L2/3, barrel L4):


sCRACM stands for subcellular ChR2-assisted circuit mapping.

Bistable current photoswitches in neurons

Bi-stable neural state switches : Article : Nature Neuroscience

Another channelrhodopsin breakthrough from Deisseroth’s lab. This time light is not required to keep the channel open. Light merely triggers opening and closing behavior. Blue-shifted light opens channels and red-shifted light closes them. This looks like another potentially powerful neurotechnology for interrogating circuits and systems.

Relevant fig:

photoswitching channelrhodopsin traces

Personal genomics: Some details for the curious

There’s an article in this weekend’s NYT magazine from Steve Pinker on what he’s learned from the first stages of genetic screening (recall he’s part of George Church’s Personal Genome Project, which is attempting to sequence many genomes and make them publicly available along with phenotypic data).

The most interesting tidbits in the story relate to data from SNP array analysis retailer 23andme. Given that the SNP analysis reported that Steve has a large chance of being bald, I have to agree with him that personal genomics has a way to go.

Neuroengineering mosquito repellents

There has been a few articles recently in the NYT about the neural mechanisms used by mosquito repellents. What a wonderful idea: Do some ephys recordings to find which neurons are sensitive to DEET (the current standard for mosquito repellents, which I can attest both doesn’t work very well and eats holes in synthetic clothing) and then build targeted compounds for those receptors/neurons/pathways. I always like this type of simple and practical neuroengineering.

Right now, it appears that there’s a bit of controversy in the field. Earlier this year, in Science, a group from Rockefeller found that DEET masked sensitivity to human odors by interfering with a particular odorant receptor. This impressive result was recently question by entomologists from UC-Davis in a PNAS paper claiming that DEET acts directly on a particular olfactory receptor neuron and does not attenuate the response to the same human-emitted odorant, as found in the earlier paper. Although the results appear to be conflicting, the studies use different techniques and thus it is likely that DEET’s action might be more complex than either paper claims. Still, the idea of identifying a target for chemical intervention by looking at electrophysiological responses to DEET is smart.

In related work, earlier this year a group from Colorado State University, as described in this PNAS overview, “conducted a rigorous search of a library of N-acylpiperidines, using an artificial neural network to identify strong candidates, and then tested them in the laboratory on human volunteers.” They found a candidate molecule that has a ~4X longer repellency effect than DEET. Here’s a photo from the experiments (DEET vs. untreated hand)… ouch!

Lots of flies on the untreated hand!