The PostDocs Forum

Our featured scientist this month is Professor Dana L. Miller. Dana’s Lab is located in the Department of Biochemistry at the University of Washington School of Medicine. The lab works on understanding how cells and organisms maintain homeostasis and survive when environmental conditions change. The main research focus in Dana’s lab is investigating responses to decreased oxygen, or hypoxia, and how they are integrated with adaptation to hydrogen sulfide.
Our interview below delves into Dana’s research, her clever advice to researchers, and the advantages of worms as a model system.

What was it that first brought you to take an interest in science?
Well, when I was a kid I liked playing outside and do science-like things; I just never outgrew it. I think most kids are scientists, and most outgrow it, but some don’t.
I grew up on a farm in the middle of the US, and I spent a lot of time out picking up bugs, which I kept in shoe boxes in our garage, and playing with snakes. Somehow, that was OK with my mom (as long as they were all kept outside the house), and also a lot of fun for me, so, it just stuck with me.

Tell me about your early days as a young biologist.
Technically, I started my scientific path in learning chemistry. One of the courses I had to take was a biochemistry course, which I was very excited about, since when I went into college what I really wanted to study was how chemistry came together to make things be alive. I enjoyed that course very much, and the professor who taught it recruited me into his lab to work over the summer in a molecular biology research project. It was fun! And so, I decided to go to graduate school in a biology program, and I got pulled more and more into biology. Now I’m pretty much a biologist, I think I can’t claim to be a chemist at all anymore.

Can you pinpoint what made you realize you wanted to be a researcher?
This was a moment I still remember very clearly, it happened when I was 12. I grew up in the middle of Kansas, and it didn’t even occur to me that you can do research for a living. One of my aunts was a postdoc at the NIH, and my mother and I went visiting her in her lab one day. That was the first time I’d ever been in a lab, and as I walked in I was astounded. I remember there were beakers all the way up to the ceiling, and although I had no idea what it was that they were actually doing in that lab, I thought to myself that this was the coolest thing I’d ever seen in my life, and that this is what I’ll be doing when I grow up. I somehow managed not to ever change my mind about it, because, honestly, up until that point, I was gonna be a baseball player.

Tell me about the current research in your lab and how you chose the research topics.
My lab topics were derived from interesting findings obtained during my postdoc, which was performed in the lab of Mark B. Roth at the Fred Hutchinson Cancer Research Center in Seattle. Mark’s lab has found that if you leave C. elegans embryos in an environment with no oxygen they do not die, but they stop all cell divisions and just “wait” up to 24 hours. This state is called suspended animation. Then, when you add oxygen back they start dividing again, continue to develop, and grow to be normal healthy adults. It was also found in Mark’s lab that if you don’t take out all the oxygen from the atmosphere but leave a very low concentration, the embryos will try to keep performing cell divisions, but would make all kinds of errors, leading to their death.
The question I dealt with in my postdoc was why can’t those embryos respond well to low oxygen concentrations. I found that embryos can’t stop divisions in a very low oxygen concentration since normally, when they are inside the uterus of their the mom, the uterus environment is what causes them to do suspended animation in low oxygen concentrations. I also found that when mobile adults are exposed to the same low oxygen concentration, they try to escape, but at the same time they enter a phase of energy saving, and stop performing processes unnecessary for survival or escaping.
One of the things we work on in my lab now is what are the mechanisms that allow animals to change and allocate where their energy gets spent, especially under stressful conditions such as lack of oxygen.
Another topic in my lab was derived from an interesting observation made by a graduate student in Mark’s lab, who was trying to induce suspended animation in mammals. Together with Mark he performed an experiment in which he lowered the temperature of a mouse’s chamber and added a very small amount of hydrogen sulfide. The metabolic rate of the mouse dropped within 5 minutes, its core body temperature became almost equal to that of the environment, and the mouse remained alive and breathing very slowly. After 6 hours he reheated and removed hydrogen sulphide and the mouse reheated and returned to normal behavior. It looked like he’d induced hibernation in a non-hibernating animal. The whole lab went for a beer after that experiment, we were thrilled!
After that I began trying hydrogen sulphide on worms, and found that they don’t do suspended animation under these conditions, but rather they keep performing all life processes normally, and in fact live 70 % longer. So, the other half of my lab uses those hydrogen sulphide phenotypes I found in worms to dissect the genetics and the biochemical pathways that respond to the hydrogen sulphide, and then translate that sensing of this compound into the changes in physiology that result in increased stress resistance and increased life span.

What do you find difficult as a scientist, and how do you deal with this difficulty?
The hard part for me is staying focused on one thing, since I’m easily distracted. If I’m researching a paper to write I’ll start all focused, writing what I’m supposed to, and read papers, but then I find myself clicking on links and reading stuff completely unrelated. More pragmatic difficulties: I’ve started my own lab about a year ago. When you’re a new assistant professor, you deal with things you never even thought as a postdoc you’d have to deal with, such as accounting and administrative issues and student tutoring. You basically run a small business, but you’re not trained at all in running one. I am a big believer that you shouldn’t try and reinvent the wheel, so, to deal with these difficulties I ask other people who’ve already done it what they did.

During the past 8 years you have been working with the nematode C. elegans. Please explain about this model system and its advantages.

Worms are great!! Some of their advantages:

• C. elegans has a stereotyped embryonic development, meaning it is just the same when looking at every single embryo. You can map the entire embryonic lineage of C. elegans. This makes it a great system to work with if you are interested in development. A Nobel Prize was recently awarded to Sydney Brenner, H. Robert Horvitz and John E. Sulston for using worms to understand development and apoptosis.
• The genome of C. elegans was the first Metazoan genome sequenced, so you have full genomic information.
• The worms are transparent, so you can watch all the developmental stages in a complete living animal by using a rather simple microscope. You can express GFP in the organism and watch its expression and localization in a living creature.
• Worms are self-fertilizing hermaphrodites, which makes it very easy to perform forward genetics studies just by mutagenizing one organism and allowing it to replicate itself.
• On the other hand you can easily perform reverse genetics studies using RNAi, simply by soaking the worms in a certain RNA, or feeding them with bacteria expressing a double stranded RNA. Both will turn off gene expression of that RNA. Today there are commercially available libraries of bacteria that can knock down every gene of the worm; each bacterial strain knocks down a single gene. You can actually screen the entire genome for whatever phenotype you are interested in. Another Nobel Prize was recently awarded to Andrew Z. Fire and Craig C. Mello for the discovery of RNAi using worms.
• Since I’m interested in cellular responses to the gas concentrations in the environment, and in how different cells within a tissue are coordinated, for me, another great thing is that worms cannot regulate their cellular oxygen uptake, in contrast to mice, for example. This means that in C. elegans, each cell performs gas uptake by diffusion, enabling me precise control over what oxygen concentration each cell will obtain. I have control both on the genetics and the environment, making worms a very powerful tool.

Can you recommend some useful databases and tools that are helpful for those beginning to work with C. elegans?
The worm community is a fantastic community, and I love it! We all gladly share reagents, ideas and useful information.
We mainly use the WormBase, which contains links to all the first papers about C. elegans, detailed and elaborated information about any gene in the worm genome, including links to all the relevant references, and links to pages, such as WORMATLAS, where you have all the anatomical data about worms, and WormBook, which has chapters about any aspect of C. elegans biology.
We also have a forum for worm researchers, and there’s the worm breeders gazette, where we share informal information between labs, tips, updates about strains we use, protocols etc. Also, every 2 years we have a giant community meeting “The International Worm Meeting” in LA, and we all get together there.

What is your favorite feature in this nematode?
The thing that is really great for me, is that they are very fast; they have a short life cycle: they complete embryogenesis in 9-12 hours, and become fertile adults in about 48 hours. Their post reproductive life span is 1-2 weeks. This provides you with the possibility to perform studies of embryonic development, life span and genetics all really quick.
Another thing I like about worms is looking at them in the microscope. I think it’s beautiful to watch them, and since they’re transparent you can actually see their entire intestine and how they eat, watch their germ-line, and how it is arranged; you can basically see the entire process of germ-line generation in a live worm. It’s so fascinating that I’ll take any excuse I can to go look at them in the microscope.

What are the common problems you are faced with during your day-to-day work in your lab?
Lab managing, which is still something I’m in the process of learning. I don’t want to have a very hierarchical lab, so I consider my graduate students as my colleagues, and I expect them to correct me if they think I’ve said something wrong, whereas my job is to help them learn the field. But, at the same time I need to to make sure that routine lab work is being done. We’re working on this together every day, and still learning how to do this. I try to protect my students from being overwhelmed by keeping them, as much as I can, from doing too many administrative things, and things unrelated to their research work. On the other hand, I encourage them to give a lot of talks, and to help high school students, since I believe graduate school is not just about learning how to do experiments. So, perhaps, sometimes I pile a lot on them, but I also let them know that my job is to be here and be as helpful as possible, and that’s a hard thing, to get a sense of where’s somebody else’s level of comfort is in multitasking.
Basically, I want my lab to be a safe place for everyone to be wrong, because if you’re scared to be wrong you cannot do anything as a scientist. I want my students to be able to tell me when they think I did something wrong, or inappropriate, and still feel that’s an OK thing.

How do you manage and organize your lab and your research?
For data organization I have a central electronic lab notebook that I expect everyone to use, and the idea is that anyone can look at anyone’s data at anytime.
I also have a server and a lab drop box folder that contains all our protocols and a folder for each member of my lab to put data in. The drop box folder is backed up by my lab server, and that’s how we keep most of our data. I have a central place on my server where I keep all the grants I’ve written, and I encourage my students to open it and read all the grants, especially, the ones related to what they work on. I try to be as transparent as possible about the data in my lab, I make sure everyone know what info is on the server and in the drop box folder. Probably I’ll need something more official if my lab gets much bigger.
My orders are all kept in an excel file, which I think is actually not the best way to go about it. Somebody told me that you can organize all orders on LabLife, so I’m currently looking into doing that.

Please share with our readers how you store your specimens and samples and how you keep track of them.
I have a database containing all information about the worm strains and their locations in the freezers and liquid nitrogen. Our freezers are kept very organized and all strains in the database are linked to their location in them. In much the same manner I have built a freezer database for antibodies and bacterial strains, and all these databases are on the central server for anyone in my lab to view.

Can you give a tip to researchers just starting to work with nematodes from your own experience?
Go back and read the old papers. If you begin working with worms you should first read Sydney Brenner and John White’s papers, even if they are not directly related to what you’ll be doing. You need to learn first how this field was built up. Next, I recommend to find an areal work meeting. Many places, including Seattle, have these meetings, which are small joint group meetings between all the different worm researchers in that area, enabling you to learn about worms biology. In Seattle, for example, I coordinate these meetings, and we have people working in different fields of worm research, such as biochemistry, molecular genetics, developmental biology, life span. I recommend going to these meetings and simply asking a lot of questions! I believe that’s the only way you can really learn about our system, or about any new system for that matter.

Can you give a tip to other new PIs starting up a lab?
The best advice I can give someone starting as a PI is to remember that it is not your job as a PI to do bench work. It’s highly important to take time every day and talk to your colleagues; ask and learn what they’re doing, and make sure they’ll know what you’re doing. These are people who will be voting on your tenure some day, and they need to know you and to feel invested in you.
If you do that you’ll have people to ask for help with things that come up during your work, who are the people working in the same academic and administrative environment as you are, and they have already invented the wheel.
That’s my big advice; always ask people for help! I know it is not that easy to do for some people, but you need to first accept that you’ll be wrong most of the time, and then it will be easier to ask for help.

Professor Dana Miller has received a K99/R00 Pathway to Independence award, and is about to enlarge her lab by recruiting postdocs. If you are interested in working in her lab or know of someone who will be, please contact her at: dlm16@uw.edu.