Why yeast? Part II

In Part I, I talked about the convenience of using yeast in terms of cost, space, ease of care, and regulations. And all of those are really good reasons to use yeast. But those aren’t the only things that have made yeast a popular model organism for cell and molecular biology and genetics research.

First, because it’s easy to grow and maintain and because yeast is small, you can easily grow up a lot of yeast at once. This can be important if you want to do something like purify a protein for biochemical analysis. In order to do biochemistry you often need a lot of protein and, depending on the protein, you can get that from yeast.

The yeast genome can be easily manipulated. One thing you can do is knockout a gene, that is, essentially remove it from the genome. This is useful if you want to study the function of that gene. That sounds counterintuitive but, basically, the idea is that you get rid of the gene then see what effect that has on the cell. From that you can infer the function of the gene. Another thing you can do is add DNA to the genome. Let’s say you want to be able to see where your favorite protein is in the cell. You can insert DNA encoding a fluorescent protein (a protein that glows when exposed to a particular kind of light) just after the gene that codes for your favorite protein in such a way that now the fluorescent protein will be attached to your protein of interest allowing you to watch the movement of your protein in the cell. These kinds of tricks are available in other model systems, but it’s much much more complicated to do them and it takes longer. It takes about three days to get the yeast you want after knocking out or adding a gene in yeast whereas in mice it takes weeks to months.

You can do genetics with yeast. This is probably one of the biggest advantages to working with yeast. Yeast can exist either as haploids (having one copy of every chromosome) or diploids (having two copies of every chromosome) and it is fairly easy for a researcher to manipulate the yeast into each of those states. Two haploid yeast can be mated to create a diploid and a diploid can be forced to undergo meiosis and become haploid. Let us say you want to see if a particular gene is essential for life. If you try to knockout that gene in a haploid, you may kill the cell if the gene is essential because you’ve gotten rid of the only copy of the gene the cell has. If you don’t get any cells after the knockout procedure, you won’t be sure if the gene is essential or if there was a problem with the procedure. However, you can use a diploid yeast strain and knock out one copy of the gene. Now the cell has one good copy to keep it alive. Then, you force the yeast to undergo sporulation during which the yeast goes through meiosis. The result is four haploid spores. These spores can be manipulated such that you can observe the growth of each individual spores. If the gene is not essential, all four spores will grow. If the gene is essential then some of the spores won’t grow.

Yeast are eukaryotes and have the same basic internal structures as other eukaryotes (including mammalian cells). All eukaryotes (unlike prokaryotes) have internal membrane structures called organelles. These organelles include the nucleus, the endoplasmic reticulum, the Golgi, and mitochondria among others. The advantage to yeast is that these structures are often simpler in form than in a higher eukaryote like mammals. For instance, there are only 3-6 of the particular subcellular structure I study present in yeast while there are hundreds in the mammalian cell. The protein that I’m interested in is present both in yeast and in humans, but in humans there are two different forms while in yeast there is only one. By studying the simpler system in yeast, we gain insights into how things might work in more complicated systems like mammalian cells. We (or some other researchers) can then take the information gained in the simple system as a starting point for investigating the same process in the more complex system.

Why yeast? Part I

I volunteered to be the speaker at a Jr. Science Cafe in a couple weeks. The idea is that middle school and high school students will come and listen to me talk a little bit about science and we’ll have a discussion. My topic is using yeast as a model system. However, last night, I tried explaining to a layperson why we use yeast and I found myself floundering a little bit. Why do we use yeast?

Well, for one thing, it’s easy to work with. You don’t need a lot of special equipment. Just a regular incubator set at 30 degrees Celsius and a shaking incubator set at 30 degrees celsius. Another couple of incubators are good so that you can change the temperature for temperature sensitive mutants. And you can grow yeast on your benchtop as well–it just takes a little longer. Contrast that with mammalian tissue culture (mammalian cells grown in dishes). You need a special hood to maintain sterility. You need fancy incubators that pump carbon dioxide into them.

Yeast don’t take up a lot of space. You just need space for the incubators and glassware. Mice, another good models system, take up a lot of space. And you have to have a special facility in which to house them, special protocols for the care and treatment of the mice and how you are going to use them in your experiments. There are very specific rules about how you take care of animals that are used for research purposes. Even fish, which seem pretty straightforward, have special protocols for maintenance.  Nobody cares how we treat the yeast.

And yeast are cheap. All of those special facilities for animals cost a lot of money to maintain, money that has to come out of your grants. Even tissue culture is expensive. Because it’s so easy to contaminate your cells, you use lots of disposable pipets and bottles, unlike with yeast where everything is reusable once it’s been cleaned and sterilized. Also, tissue culture requires the cells to be grown in special media which is bought pre-made and is quite expensive. Yeast media is cheap and you can make it yourself.

So, yeast are convenient. But there’s more to yeast than convenience (see Why yeast? Part II).

Acquiring Talking Points

So, Bora suggested I go here to get some talking points for the next time I’m confronted with a creationist while carrying on my everyday life.  I’ve started reading the Introduction to Evolutionary Biology FAQ which is pretty detailed.  It might even be a little too detailed, depending on who the target audience is.  It actually tells you how to calculate linkage disequilibrium and allele frequencies and when I saw the words Hardy-Weinberg equilibrium, I started having bad flashbacks to the population genetics section of my genetics classes.  Not pretty.  I’m not sure how a layperson would react to this introduction but it’s at the right level for me.  I think if it were to be geared toward laypeople, it would have to be simplified a bit and shortened.  I’m not sure how many laypeople care enough about evolutionary theory to read a 30 page introduction.  Though, I suppose you don’t end up at that particular site, reading that FAQ, unless you have an interest in learning more about evolution.

No common ground

Last Friday, I got into a cab that had the radio on to Science Friday. I wasn’t really paying attention (I was thinking about my upcoming trip to NYC) when all of the sudden, the cab driver says that the effort scientists are putting into figuring out the differences between chimps and humans is “a big waste of time and money.”

Uh-oh.

I knew what was coming. I knew that I was a biological scientist in the presence of a creationist and I knew I had a duty to make the case for evolution. But, the whole idea seemed overwhelming. First of all, I didn’t want to tick off the driver, I mean, I was sort of at his mercy sitting in the back of his cab. Second, I felt singularly unqualified to make a case for evolution. I accept evolution (I hate the term “believe in” as though it were in article of faith) but I don’t know enough to have an argument with a creationist about it. As I told my husband later, I don’t have any talking points prepared for this situation. All I’ve got is a set of disjointed facts that I can offer up (and several are molecular biology related so I’ve got to deal with the fact that most people don’t know a damn thing about molecular biology). My argument would have been something like, “Fossils! Homologous genes! In vitro evolution!” Hardly convincing.

So, first I asked why he thought looking for the differences between chimps and humans was a waste of time and money. As I thought it was because he believed that God created humans fully formed and since scientists did not want to take God into consideration, they were never going to find the answers they are looking for. I tried to explain that divine intervention is not a scientific argument and therefore scientists cannot take God into consideration as it were (despite their own personal beliefs about faith). Somehow this led to a discussion in which the driver asserted that Darwin wanted people to become atheist and that’s why he came up with evolution, as though the theory of evolution was simply a means to make people atheist.

So, I tried to shoot that down. But, unfortunately, Cab Driver had read about the life of Darwin and I haven’t (where he read about the life of Darwin, I am not certain and probably would be scared to find out) so he asserted that Darwin became atheist after the death of a child. Whether this is true I couldn’t say, but I could at least argue that if what Cab Driver said was true, that didn’t necessarily mean that acceptance of evolution leads to atheism because lots of people lose their faith in God after a tragedy. To which Cab Driver agreed so I guess I came out the winner (?) there despite my lack of actual knowledge.

I further tried to explain that there are scientists who believe in God and accept evolution. Cab Driver argued this was not possible, it had to be one or the other because the two were mutually exclusive. The problem here was that he was equating belief in creation with belief in God. Now, here we get into the idea of a literal interpretation of the Bible versus a non-literal interpretation of the Bible and this was really beyond my ability to debate.

Fortunately, we had arrived at my destination, so I paid Cab Driver, who thanked me for the good conversation (!) and I went on my way.

I left this conversation feeling very uneasy and even a little ashamed of my lack of knowledge. This is exactly the kind of situation in which contact between the public and a scientist can foster understanding of evolution and instead of diving right in, I held back because I wasn’t sure what to say. True, I also didn’t want the guy to kick me out of his cab on Lake Shore Drive, but still, the fact that I felt completely unprepared for this conversation while Cab Driver felt fully prepared for this conversation having “read up” on the subject because, he said, he wanted to know more about it was, well, embarrassing. Never mind the fact that where he got his information might not be a reputable source, the fact is he had actually bothered to become more informed and I haven’t. I just haven’t.

Beyond that, we had no common ground theologically, either. He’s right, you can’t believe in a literal interpretation of the Bible and accept evolution. You can’t believe in Adam and Eve and the Garden of Eden and simultaneously accept that people evolved from lower primates, you just can’t. So, where do you go in that sort of argument? There really isn’t anyplace.

I suppose I just have to accept that I did the best I could. There wasn’t anything more I could have said or done and I’m not sure that more knowledge on my part would have persuaded him that evolution is valid. What I hope, though, is that when he thinks about scientists and God and evolution, he’ll remember that once he had this girl in his cab who was a scientist, who believed in God, who accepted evolution and who was nice and didn’t yell at him and didn’t call him an idiot for his beliefs and tried to explain her point of view without being insulting. So that, when he hears about scientists and evolution he doesn’t automatically think of atheism, doesn’t automatically think of unreasonable people. I suppose that’s the best I can hope for.

A day in the life

People often ask me what it is I actually do in lab (not what I’m studying, but what I physically do with my time in the lab). Here’s a rundown of Thurs. Sept. 4:

10:20–Arrive in lab

10:30-11:30–extract DNA from bacteria

11:30-11:35–Label tubes, check yeast cultures to see if they are dense enough for an experiment (they’re not), watch a mock fight between two labmates who are using giant pillow boxing gloves

11:35-11:45–Set up and start running DNA gel of a PCR product.

11:45-12:00–Write on blog, check email, send email.

12:00-12:40–Buy lunch, come back to lab, eat lunch at desk while reading blogs.

12:40-12:50–Stop running gel from earlier, visualize DNA, swear because it looks like crap, print out picture of crappy gel, throw away gel, clean up gel running apparatus.

12:50-1:10–Design and set up new PCR and start running it.

1:10-1:30–Discuss with labmate possible alternative strategies to get around PCR problem.

1:30-2:30–Work on planning alternate strategy to get around PCR problem; check to see if yeast cultures are ready for another experiment (they’re not).

2:30-3:00–Hunted down reagents for yeast experiment. This took a lot longer than it should have.

3:00-4:00–One yeast culture finally ready for experiment. Start purifying protein from this culture. Freeze bacteria cultures in our frozen stock collection during the down time in the experiment.

4:00-4:20–Go get tea with labmates.

4:20-4:40–Freeze bacteria cultures in our frozen stock collection. While doing this, have discussion with labmates about letter in Science about publishing.

4:40-5:30–I have no idea what I did during this time. I forgot to write it down for the blog. How can I lose track of an hour? Probably checked email, wrote in lab notebook, planned experiments for tomorrow and chatted with a few people.

5:45-6:45–Other culture finally ready for experiment. Do protein purification experiment with yeast from this culture.

6:45-7:45–Streak yeast plates, start bacterial cultures to freeze and purify DNA from tomorrow, send DNA for sequencing (we have a facility that does all of our DNA sequencing).

7:45–leave lab

This was a pretty typical day.  Usually, I’d talk to my adviser once or twice in there but he’s out of the country at a conference.  Also, I came in a little later than usual.

The joys of shared equipment

I’ve written a little bit about the microscope that I use to look at the results of my experiments.  The scope belongs to the department, meaning it’s shared by several labs.  In order to use it, you have to schedule time on it.  Of late, it seems like it’s booked up like crazy–to the point that today I had to come into lab way earlier than usual in order to do this experiment so that I could look at the results this morning because the scope is booked until 8pm today.  I am not a morning person.  So, despite the fact that a large portion of the American population is at work at 8AM, for me to get here by 7:30AM (having showered and eaten breakfast beforehand and even *gasp* wearing makeup) is a miracle on the order of giving sight to the blind.  Usually, I roll in around 9 or 10 or sometimes even 11 (along with the majority of my lab, including my adviser).  This means that I stay later in the day (7 or 8pm) but for me that’s infinitely preferable to getting up at the ungodly hour of 6:30AM.

Cleaning out the cobwebs

Look at the dust that has accumulated on this thing!  It must be an inch deep at least!  There are dustbunnies the size of tumbleweeds rolling around in here.

I think it’s time I dusted this thing off, cleaned up the corners a little, and use this space for its intended purpose.  I can’t promise much, but a post a week seems reasonable.

Now, if  someone would pass me a broom and some swiffer cloths, I’ll get to work cleaning this place out and maybe put up a science-related post in a day or two….