Friday, September 16, 2016

Lab meeting 1: The semester begins

I've been inspired lately by the open science movement, wherein scientific research is done out in the open where anyone can check it out.  I love being able to learn about other people's work on twitter or blogs and to read their manuscripts before they're published.  I think these are great ways to draw the public into the actual inner workings of scientific research and to show people what it's really like working on a research project, especially working through social media.

On the other hand, I'm also kind of a traditionalist, and I like to share my research mostly when I have a nice project that makes sense, with a beginning and ending.  I can tell the story of its significance and the work that I did and what I found.  But as I said, I'm becoming more and more enamored with the idea of drawing more people into my world of research and giving them a sense of what it's like to be a creationist researcher.

So I've decided to try out a virtual "lab meeting" that will summarize my weekly lab meetings with our Core Academy interns.  This is supposed to be mostly understandable to the general public, so if you can't follow it, let me know please.  I'm really trying here to translate our work, including all the weird wrong turns we make, so that you can understand.  I don't know how frequently I'll be able to post, since I'm very busy, but I'm going to make an effort to keep people up to date.

This semester I've got two intern projects I'm working on.  The first involves the created kinds of mammals.  I'll talk more about that in a future lab meeting post.  Here, I want to catch you up on the trillium project, which I've mentioned before.  Currently, we're trying to discover the genetic basis for flower appearance in trilliums.  In the picture above, you can see a mutant form of erect trillium.  Usually, erect trillium flowers have a deep red color, but this mutant is cream colored.  So what makes it do that?  Why is it not red like other erect trilliums?  That's what we want to find out.

This week, I had our intern look up different known genes from trilliums and compare them.  We found that most trillium genes (rbcL, ndhF, and matK, for those in the know) are nearly identical when you look at genes from different species.  That's pretty remarkable, because most trillium species look quite different when they flower.  The large-flowered trillium has big white petals, while the yellow trillium that blooms here on the Cumberland plateau has little yellow petals that barely open up at all.  How can these different species have such different flowers when the genes we've looked at are so similar?

We think the answer lies in the way the genes are used by the plants.  This is the standard story in this kind of research: When you have different species with very similar DNA, then the differences must be in the regulatory sequences, the parts of the genome that tell the plant cells when and where to turn on certain genes.  So we need to find not only the flower genes but also the regulatory parts of the genome that control when and where those flower genes get activated (or deactivated).

That's a bit of a different project than what we originally envisioned, and we talked during our real life lab meeting about how we can go about doing that on a limited budget.  We also discussed the possibility of just sequencing a trillium genome, but then we realized that the genome is HUGE (about 17 times bigger than the human genome).  That would require a bigger investment than we can make right now.  So we're going to try some lab tricks (with PCR in case you wondered) to try to find some genomic flower genes.  If this works, we'll be the first to sequence these genes, and that's very exciting!

Our job this week is to gather all the necessary materials to get started on the DNA extraction.  I'll do the ordering, but I've assigned our intern the job of telling me what to buy.  It'll be a good learning experience for her.

I definitely want to thank all the donors to Core Academy of Science.  Your contributions support this work, and our student interns greatly appreciate that support.  If you would like to help support our student scientists, please click on that donate button at the end of this post.

Feedback? Email me at toddcharleswood [at] gmail [dot] com. If you enjoyed this article, please consider a contribution to Core Academy of Science. Thank you.