Fly feelings and feelings about flies

Last time I titled my blog 'getting to know you'. So do I know you? I was reminded today about how the 'lecture plan' has nothing to do with the 'what I would like to know plan'. What I wanted to skim, the group wanted to explore.  What I thought would provoke discussion passed quietly, and the ethical treatment of flies and how exactly dsRNAs get chopped up took center stage. Believe me when I say this is not a complaint but rather a plug for exchange and group discussion. Which reminds me- thank you for your interesting questions at the beginning of the session- Madras and Hyderabad.  

Nusslein-Volhard and Wieschaus conducted a Nobel-prize winning screen defining many genes that are required for the segmentation process in Drosophila.  The mutants they created had altered body plans and by looking at these 'broken' embryos the way a wild-type embryo is constructed emerged. A huge breakthrough for the field and a monumental forward genetic screen. I also showed Ed Lewis' amazing four-winged fly. I know we are all thinking about ethics,  in part because Dan Farrell's session on the ethical conduct of research is next week, but I didn't expect to be asked about the ethical considerations that come into play when so many fly embryos are used (well doomed) in an experiment.  Let me say straight away that I am the person who saves worms from the sidewalk on rainy days and I never met an animal I didn't like (except lions), but well flies.... I hope I answered the question sensitively because I do actually care about my flies quite a bit.  

This led to our lunch discussion and what kinds of animals feel pain- fish, frogs, cockroaches? Flies avoid odors associated with electric shocks but what does that aversion amount to? The vegetarians out number the meat eaters in the Columbus part of our class.  So then I felt bad about discussing the cow genome, because needless to say one of the driving forces behind that project is learn more about cows because they are a food product.  But at least Dominette, the DNA donor, looked fit and healthy! 

So let's stick to talking about dicing dsRNA and how you express it in one group of cells in the body and how long the double strand should be. All the things I thought would be less interesting than all the things I talked about instead!  

But I cannot resist showing you a picture of a fly with eyes all over its body. Repeating the classic experiment by my colleague Georg Halder when in 

Gehring's  lab - we make these every year in the undergraduate lab I teach! 

Getting to know you

Today's session was exciting. Venkat and I had learned a great deal from your feedback last time and incorporated questions and group work to make our lectures more interactive. Through this to and fro, we really are getting to know you! Thank you all for your great questions- Hyderabad, Columbus, and Madras.

At lunch following the session, we asked the OSU students what they expected to get from the course. One student remarked that she didn't really expect to learn new material, but that in fact much of it is new to her. I concur- a lot is new to me too, as I found out while preparing my lectures- the science we are covering will transform biology. On the other hand, another student was expecting to learn new material, but has been surprised by just how interesting the international component is. We were happy to learn that she had been chatting to student colleagues in India and then got to connect the names to the faces during the video introductions. How cool is that? (Sorry but in this case it seems to be the appropriate word.)

Next time I will be discussing functional genomics and as luck would have it a brand new fantastic paper was just published on genome wide RNAi in flies looking for Notch pathway genes. The Notch pathway is important in human disease and this is another case of using a model genetic organism for discovering the 'genes we share'.

It is a privilege to part of this joint enterprise and I thank you all for energizing me for the rest of the weekend!

Friday 17th - the view from my window

I have been thinking quite a bit about next generation sequencing versus microarrays. I am involved in a collaboration with a colleague at Harvard. The goal is to identify changes that occur when cells become 'immortal'. We planned to look for changes in the transcriptome using Agilent arrays. But why not also survey the genome for mutations? Next generation sequencing allows both in a single experiment because you get abundance (transcript level) and sequence information. So in the spirit of competition my last slide is to ask students and instructors at all the sites for their views on the relative power and merits of arrays and next generation sequencing for a given application.

Meanwhile here in Columbus it is sunny and beautiful. This is the view from my window. So you will see both kinds of 'football' represented in the video - the 100,000-seat stadium for watching the game with the oddly-shaped ball and some guys running around after a little round ball.

Thoughts after the first session

There are many levels on which to think about the first session. How was it technically? Good- we had one glitch with the graphics, but pointing the camera at the screen solved that. As someone who likes to make videos, I am going to use the remote next time and actively record Venkat as he speaks and switch to the audience for the questions. Let me compliment Madras- I think you had the most dynamic coverage! How was the content? There is no doubt the material is interesting. For my part, I know I rushed the next-generation sequencing and need to cover some of it again. I will do that- a recap that will fit well with the next topics anyway. Mike thanks for bringing the Scope and starting the STR analysis. I will be down to film you on Monday as you process the samples! Venkat, you have thrown down the gauntlet- I see this is a genomics versus proteomics competition. It is interesting how many 'omics' must be considered. Your point is well taken, as was an audience point that it is in fact the activity of factors (proteins, RNAs, and other molecules, comments on these anyone?) that really represent the phenotype of the cell. I look forward to the next installment!

After the session we adjourned to the room next door and ate pizza and Ruth's delicious homemade chocolate cake! We talked. Two main subjects: how did it go and what topics would be good for the student presentations? The students thought that more interaction during the session would be good. Together we came up with the idea of pairing students between the sites- so that we can learn more about each other. Probably most of this will go on behind the scenes. Venkat reminded us that this course is an experiment and that we could write it up as a paper for a science education journal. So I encourage you to do what I am doing now- write down your thoughts privately or publicly. Then we will have data.

Topics for student presentations. 1) The $1000 genome was the first idea and I have already blogged about it. 2) Functional genomics and/or genetic engineering. These topics are rife with Nobel prizes, science, technology and ethical issues. We struggled with a third equally interesting idea. Then Sathiya suggested: 3) Biology and law. A wonderful idea- how do findings in science get made into products? And if they do what happens next ? -an interesting mix of patents, generic drugs, money, egos and more!

Next generation sequencing- the movie

I met with Jeff and Tim who gave me a tour of the SOLiD system in the Department of Human Cancer Genetics. To tell the story I made this movie. Thanks, to you both. 

My interest in next and next-next generation sequencing is increasing the more I learn. Venkat and I discussed student projects and agreed that the quest for the $1000 genome (personal genomics) would be a very interesting topic. It could combine a Nobel prize (Sanger), technology (single molecule sequencing) and ethics (what are the implications?).