A short report from a Cold Spring Harbor lab course

One of the best things of being a PhD student is that one is supposed to learn new things. As part of this mission, I attended a two-week laboratory course in the Cold Spring Harbor Laboratories on ‘Advanced Techniques in Molecular Neuroscience’ (ATMN), a field of neuroscience to which I had been exposed only passively before.

Ausblick auf den Harbor

Overview of neuroscience methods courses

Before writing about the course in more detail, here’s a brief overview alternatives for high-quality and hands-on methods courses that could be relevant for neuroscience PhD students and PostDocs.

  • Cold Spring Harbor in proximity of New York hosts a variety of different courses, most of them very dense and practical and typically 2-3 weeks long.
  • The Marine Biological Lab in Woods Hole, Massachusetts, offers also a variety of specialized courses. In addition, there are some more general and longer (up to two months!) ‘discovery courses’, that might be ideal e.g. for computer scientists, physicists or biochemists who transition to neuroscience without previous exposure.
  • More recently (starting in 2017), FENS has set up a program named CAJAL that consists of a couple of practical courses. The courses take place at the Champalimaud centre in Portugal or in Bordeaux/France. I do not know how good these courses are, but the schedules look very promising and very similar to the two alternatives above.
  • A very interactive and hands-on course on constructing hardware for experimental neurophysiology, especially for imaging, is TENSS in Transylvania, Romania.
  • There are other courses that seem to be interesting and hands-on, but I do not have any first- or reliable second-hand experience: a neuroscience course in Paris [update 2019: new website link], France; and a course on imaging at the Max Planck Institute in Florida.

If you have any comments or if I forgot something, let me know! – I did not include computational neuroscience courses on purpose, because there are many – probably they are easier to organize since they do not require reagents and hardware apart from computers. I guess that any computational neuroscience course or summer school would be announced via the Comp Neuro mailing list.

But back to a short review of Advanced Techniques for Molecular Neuroscience:

ATMN review: The application

Nothing difficult here. I do not know anything about the acceptance rate, but the organizers tend to put an emphasis on diversity (different backgrounds, different countries of origin). Recommendations from two PIs are required. Together with the course application, an application for a scholarship that covers part of the fees can be filed (and it does not require a lot of effort to do so). There are dedicated scholarships for people coming from developing countries.

ATMN review: The location

Cold Spring Harbor is beautifully located on Long Island, an hour drive from New York City. Coming from central Europe, I especially enjoyed the lively nature and the diversity of species. On the campus, which is basically a village sitting in the middle of nowhere, squirrels and chipmunks are omnipresent. Horseshoe crabs sit on the sand shores, and during nighttime, fireflies are blinking everywhere once you leave the streets. I was housed together with another participant of my course in a small, but nice room in a wooden cabin (see picture below), with showers shared among 6 persons. You can go to the campus gym, go running, swimming, kayaking, use the tennis court or the beach volleyball fields – if there is time leftover. The food that is provided is good, also for people who do not enjoy typical american style.


ATMN review: The labwork

The main focus of the course is on bench work. The day starts at 9 a.m. with a lecture or an introduction to the next experiment. Then the experiments start, interrupted only by lunch, dinner and possibly further short lectures/instructions, until 7, 8, 9 p.m. or even longer. There is basically no free time, except before 9 a.m. and during some afternoons.

In total, there were 16 students (half of them female; half of them non-US; roughly half of them PostDocs or beyond). 8 pairs were formed that worked together on a single bench for the whole duration of the course. The equipment is great: High-end confocal or brightfield microscopes, PCR and qPCR machines, tape stations, nanodrops, centrifuges, dissection stations with large demonstration screens, etc.

As typical for molecular biology, there is a lot of waiting, pipetting, washing, shaking and centrifuging involved, but the organizers interleaved different modules in order to minimize the idle time. Sometimes it was challenging to follow several modules running in parallel, because the modules were using an overlapping set of techniques.

After each module, the results (this can be images, gel pictures, qPCR results) are presented by the teams to the whole group (+instructors) using the white board or power point. All of this is very loosely organized and improvised, since the duration of each experimental step cannot be predicted easily.

The instructors (who can be PIs, PostDocs, PhD students or TAs of the lab that organizes the respective module) were not from Cold Spring Harbor research groups, but from universities all over the US. All of them were very kind and helpful and extremely patient, sometimes explaining a procedure five times in a row to ensure that everybody understood it well. They were also always competent for any technical questions like ‘What does the addition of enzyme X do, and why do we increase the temperature to 43°C?’

ATMN review: The content

The 10 modules of the course each take 2-5 days:

  • BACs
  • Brainbow and multispectral imaging
  • In utero-electroporation
  • Translating ribosome affinity purification (TRAP)
  • Cross-linking immunoprecipitation (CLIP)
  • Slice and primary cortical cultures
  • FISH and IHC
  • Lentivirus and stereotactic injection
  • Clearing techniques
  • Single-cell electroporation

For example, in the CRISPR module, instructed by Le Kong from the Broad Institute, a couple of lectures covered the principles of gRNA and vector design. The lab work started with the generation of a small DNA fragment that was then cloned into a CRISPR backbone vector and transformed into E. coli cultures. Then, a set of different CRISPR activation systems and controls were transfected into mammalian cells. Efficiency of the gene insertions was checked using the T7E1 surveyor assay,  a reporter gene (imaging) and qPCR of mRNA from transfected mammalian cells. Overall, this took 4 days, running in parallel with other modules. For me, all of this was new, and I was glad to learn all these steps by doing them.

To give another example, the clearing module was instructed by Jennifer Treweek and Ryan Cho from the lab of Viviana Gradinaru. Whereas the CRISPR module had been a protocol that had to be followed precisely by each of the 8 groups, here we could go ahead and choose between a variety of protocols. I and my lab partner tried out PACT and ePACT (decribed here), both passive clearing techniques with (ePACT) and without (PACT) expansion of the tissue, on Thy1-GFP mouse brain slices. We used slices instead of whole brains due to the limited time available during the course. Other groups additionally combined the clearing methods with in situ labeling, using a so-called hybridization chain reaction for RNA labeling.

ATMN review: The participants

The course was attended by a wide variety of different backgrounds. Only two of the 16 (including me) were mostly interested in systems or circuit neuroscience. Some were more into epigenetics, genomics, or other fields that rely more strongly on molecular rather than physiological methods. I guess that the networking component might have been more important for other participants who are going to work precisely in the field of some of their ATMN instructors. But if I for example were to set up a clearing protocol in my home institute, I would not hesitate a single second to write back to the course instructors in case I encountered technical problems.

ATMN review: Summary

My motivation to take this course was, coming from a physics background, to learn some basic (and advanced) molecular biology, and the course clearly exceeded my expectation in terms of what I could get out of it. I can therefore only recommend the course (or other courses in Cold Spring Harbor) to anyone! Two weeks of time is not a lot, and the amount of new knowledge that I (and others) learnt from this course is huge.

I can easily recommend this course (or similar courses) to any neuroscience PhD student. Often, it appears as if there is no time at hand to go somewhere and learn new things unrelated to one’s PhD project. But if I’m honest, compared to the many days, weeks or months that I have spent with failed experiments or following up on ideas that turned out to be wrong, two or three weeks of time is not such a big deal!

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