Lab course

Hi,

I recently accepted a position at the University of Buenos Aires to study aging using C elegans. I was surprised to find out nobody here use this model organism for their research. To educate students (and professors) on worm research, I’m planning to dictate a lab course. I was wondering if anybody could suggest me lab work for the course. It’s for approx. 20 students and is 2 weeks long.
Thanks!

Dani

Lots to go at here…and after a few glasses of an acceptable Spanish white wine ( :-[) I am suitably relaxed for the task.

So, you accepted a position in Buenos Aires to work with C. elegans on Ageing and then found out nobody was working with worms ;D? Did no one say anything at the interview like, “what"s C. elegans then?”. Forgive my surprise, but I would have thought they would have spotted the “gap” in the research expertise?

They must have realised there was a gap (e.g. we work with , let"s say, Drosophila, because like everyone does…but you want to use C. elegans…didn"t you already summarise the benefits of C. elegans in your presentation?

Perhaps you can clarify this point a little just to put us all in the picture?

Being based in Germany I find one has to be careful with phrases like 'dictate a lab course", you mean you have to put together a 2 week (seems a long time) course for students?

So, serious stuff now.

  1. What Department are you to be based in? That dictates (to some extent at least) how you present the salient features of C. elegans as a model organism.

  2. Related to 1., what do the other members of the Faculty do (besides look up C. elegans in the English-Spanish Online Translator)?

  3. Who are the students that you want to design a 2 week (still too long) course for?
    a. What skills/background knowledge have they got?
    b. what facilities do you have to draw upon?
    c. What should they learn and how does this integrate with their other studies?

  4. Who do you have to support you and what experience do they have (cell biology, molecular biology, etc etc.?

Steve

Maybe you can team up with some of the other worm people in Buenos Aires (Sergio Simonetta, Diego Golombek etc.)? I’m sure they could help you out.

Maybe you can also contact labs in Uruguay, they may want to join you for the course! Have you tried to contact Gustavo Salinas and Gianfranco Grompone?

You might look at this old thread, and at WormClassroom.org.

Beyond that, Steve’s comment has some great questions that will hugely influence what you do. Just to repeat a couple of them and expand on them a bit:
Are you looking to demonstrate/appeal to their interest in Mendelian genetics? RNAi and reverse genetics (or, heck, that CRISPR feeding could be fun)? Transgenesis? Neurobiology and behavior? Toxicology? Ecology?
How many students, for how many hours over those two weeks? How many people will be assisting you, and will you have time beforehand to teach them a bit about worms? How many dissecting microscopes (especially if they’ve never used C. elegans in lab before), how much other equipment or reagents?

PS In addition to the people Snug mentions, the CGC lists an A Parodi in Buenos Aires, and WormBase has more suggestions.

PPS Rosina suggests you might invite researchers in Uruguay to help or participate, and I’ll point out that the CGC and WormBase list the lab of Marcelo Doucet in Cordoba, Argentina, who might be interested. Beyond these suggestions, you might look into the nematology / invertebrate pathology world. Researchers in this community typically have extremely poor connections to the C. elegans research community and wouldn’t be listed in any of the databases linked above, but are likely to be very knowledgeable and may be interested in exploring the overlap between their areas of research and the more molecular-biological studies typically done in C. elegans, and might be very helpful to you.

Thanks everyone for the interest!
It’s my first post and don’t have the habit to open the discussion forums I guess I have to set it up to send me a notification when someone answers.

Regarding names; I don’t know the people from Uruguay, but I do know Diego Golombek and Sergio Simonetta. They are working at the University of Quilmes and Leloir foundation respectively. While there are a few groups working with C elegant in Argentina, surprisingly there are none at the University of Buenos Aires. I don’t see it as a problem; it’s actually an honor to start a C elegant tradition at this University.

I have not a clear idea how many hours is going to be the course. It’s intended to be for graduate students for their pHD program. In general, a 60 hours course is attractive for them, as they will earn 3 points (out of 20 they need). That’s my goal. I forgot to mention that in the course program I’ll include other model organisms, such as Drosophila, yeast, Xenopus and zebrafish.

I did a short 3 years old postdoc in a C elegans lab, but I worked in mammalian systems all my life studying cancer. I decided to keep working with worms because of the novelty here and also because it’s very expensive to work with cells or mice. The reason I’m saying this is because my goal is to study human diseases with worms. The topic of the course would be “modeling human diseases with model organisms”.

We have 4-5 dissecting scopes, incubators, a confocal microscope and basic stuff to do worm research. I have experience making transgenic worms, siRNA feeding, molecular biology, etc. The problem I see is that, in general, there’s a lot of stuff to prepare, but the experiment per se is quit short (for instance, takes long time to have worms ready for bombardment, but the bombardment per se is just a few minutes). To do siRNA feeding, you prepare plates, but experiment is just to move worms from a plate to another one.

Steveh: if you come to Argentina I’ll give you a good Malbec, not a white wine :relaxed:

Forgot to mention. I just checked worm classroom.com and it’s an awesome site. Thanks!!

Hmm…lots of observations, questions, suggestions here…first, the offer of the Malbec is something I will definitely keep in mind if ever I fly that far south.

In terms of Buenos Aires, great that you have decided to tread the path of the pioneer.

In terms of your outline of what you want to do;

  1. ~20 students would do 60 hours over 2 weeks, am I reading that correctly?
    (If so, you have a very intensive course which would only work (in my humble opinion) if you front-loaded short punchy sessions on basic descriptions, experimental use of and relevance to human disease of each of the model organisms, then lauched into the practical work).

  2. You would hit all the bases (C. elegans, Drosophila, Xenopus, Zebrafish, Yeast) but lab work would be exclusively using worms?
    (Given your comments regarding cost etc. I can’t see you being able to do much else (perhaps a bit of yeast work)).

  3. ‘Modelling Human Diseases with Model Organisms’?
    (Gives you plenty of scope for designing a series of grad level intro seminars + extended practical session, but for the practical therein lies the first issue of selecting something suitable from the myriad of C. elegans human disease models now in print).

  4. You say 20 students and 5 scopes?
    (You need teams and that decision kind of points you in a particular direction in terms of what you might focus on. It also makes organising the practical work a little easier.)

  5. You mentioned some possible techniques?
    (the practical work has to be bombproof, you have no room for failed transformations or RNAi experiments in such an intensive course even if worms do develop quickly. I would play it much safer and use the seminars to describe the more elaborate techniques).

OK…what would I do?

Assuming all of the above is correct (timing, numbers etc), then I would say, use the first day only for the theory (with suitable breaks). On the second day, you could outline the practical work the students are going to undertake, sort out groups, hand out protocols, familiarise the students with things like ‘what is a pipette?’, ‘why is it important to know how to use a microscope?’, ‘writing out experiments’ and all the things they never learned as undergraduates.

For the practical work, I guess it’s always a question of where your interests are…you have to go for a particular focus otherwise it will appear to be just a mishmash of techniques with no ultimate goal.

Of course, you can

a) go in the highly-structured, ‘like it would be done in a real lab’ way…perhaps a variation of this:

http://www.lifescied.org/content/11/2/165.abstract

The advantages are clear, you adapt something that has been used, apparently worked and details what was involved.

Or

b) you go it alone and develop a single focus perhaps and have each group look at a different aspect of the problem.

What about the effect of age on chemotaxis (I can hear the groans / WTF already), but hey, you have a well proven effect, mutants at the CGC, well-tried assay(s), a variety of explanations to be explored (insulin signalling, changes in locomotor activity, sensory neurone changes etc.), loads of background literature. It would be a blast (or even a BlastN).

Steve

just as a quick follow up…for those of us that do not work on ageing in C. elegans (we are few but mighty), here are a few examples of why chemotaxis (and mutations affecting chemotaxis) are interesting themes:

aristarless (alr-1) mental retardation
http://www.molbiolcell.org/content/16/10/4695.full.pdf

location of vulva/ (lov-1/pkd-2) polycystic kidney disease
http://www.nature.com/nature/journal/v401/n6751/full/401386a0.html

netrin (unc-6) cancer
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613020/

CREB transcription factor/insulin pathway (crh-1) memory impairment/loss/cognitive performance
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000372

Steve

Steve,

I have no words to thank you enough for the time you’re taking to help me. I’ve been even considering forgetting about World cup final game!
Some comments in between you’re suggestions…
The papers you sent me in the last thread were also very useful.

  1. ~20 students would do 60 hours over 2 weeks, am I reading that correctly?
    (If so, you have a very intensive course which would only work (in my humble opinion) if you front-loaded short punchy sessions on basic descriptions, experimental use of and relevance to human disease of each of the model organisms, then lauched into the practical work).

R: I absolutely agree. I was thinking of the same dynamics for this course.

  1. You would hit all the bases (C. elegans, Drosophila, Xenopus, Zebrafish, Yeast) but lab work would be exclusively using worms?
    (Given your comments regarding cost etc. I can’t see you being able to do much else (perhaps a bit of yeast work)).

R: My idea is to spend most of the time working with C elegans. Whether we can work with some other model organisms will depend on the other investigators.

  1. ‘Modelling Human Diseases with Model Organisms’?
    (Gives you plenty of scope for designing a series of grad level intro seminars + extended practical session, but for the practical therein lies the first issue of selecting something suitable from the myriad of C. elegans human disease models now in print).

  2. You say 20 students and 5 scopes?
    (You need teams and that decision kind of points you in a particular direction in terms of what you might focus on. It also makes organising the practical work a little easier.)

R: We’ll be a little tight on lab equipment, but in general we organize the student in groups. It’s normal practice here.

  1. You mentioned some possible techniques?
    (the practical work has to be bombproof, you have no room for failed transformations or RNAi experiments in such an intensive course even if worms do develop quickly. I would play it much safer and use the seminars to describe the more elaborate techniques).
    R: It’s a good point. I’ll leave elaborate techniques for the seminars.

OK…what would I do?

Assuming all of the above is correct (timing, numbers etc), then I would say, use the first day only for the theory (with suitable breaks). On the second day, you could outline the practical work the students are going to undertake, sort out groups, hand out protocols, familiarise the students with things like ‘what is a pipette?’, ‘why is it important to know how to use a microscope?’, ‘writing out experiments’ and all the things they never learned as undergraduates.

For the practical work, I guess it’s always a question of where your interests are…you have to go for a particular focus otherwise it will appear to be just a mishmash of techniques with no ultimate goal.

Of course, you can

a) go in the highly-structured, ‘like it would be done in a real lab’ way…perhaps a variation of this:

http://www.lifescied.org/content/11/2/165.abstract

R: This article is awesome. It’s exactly what I was looking for!

The advantages are clear, you adapt something that has been used, apparently worked and details what was involved.

Or

b) you go it alone and develop a single focus perhaps and have each group look at a different aspect of the problem.

What about the effect of age on chemotaxis (I can hear the groans / WTF already), but hey, you have a well proven effect, mutants at the CGC, well-tried assay(s), a variety of explanations to be explored (insulin signalling, changes in locomotor activity, sensory neurone changes etc.), loads of background literature. It would be a blast (or even a BlastN).

Steve