// Twitter Cards // Prexisting Head The Biologist Is In: October 2018

Monday, October 29, 2018

Domestication of Yeasts

Saccharomyces cerevisiae is known as the Baker's Yeast. It has helped us make bread, beer, and wine since before recorded history. These days we also use it to make fuel, pharmaceuticals, and for basic biology research. With the innumerable industrial, food, and research purposes we use it for, it is a thoroughly domesticated organism.

With the various mammals we've domesticated, researchers have identified a "domestication syndrome"; a set of features common across domesticated animals. They have shorter faces, milder temperaments, reduced weaponry (teeth, horns, claws), and color changes. In short, they've become cuter. To some degree these are traits that could have been actively selected for, but it turns out that if we only select on temperament, all of the other traits come along for free because all those traits are mediated by the action of neural crest cells throughout the body.

Now, yeast don't have neural crest cells, but they're still domesticated. It didn't evolve to have a more amenable temperament, but it did evolve to grow rapidly in the amenable conditions we provide for them. There's a different sort of "domestication syndrome" that it would have developed along the way. Any trait or ability it needed to live as a wild yeast, but did not need to live under our care, would be lost. This would happen because any lineage that dispensed with those traits would be able to grow faster without the energy drain they represent.

So. What traits would yeast lose under domestication? It's not entirely clear. We can't just look at the cells and see a difference. Nor do we exactly have the wild progenitor yeast around to make comparisons with.


Here we're going to take a bit of diversion.

My first major project in grad school was to figure out how to use flow cytometry to determine the genome size of a different yeast called Candida albicans. In the past, This analysis had proven difficult to do with this yeast for others. This difficulty had been generally blamed on the organism's ability to grow either as independent yeast cells or as elongated hyphal cells that get all tangled up in each other.
Figure showing genome content size of a population of yeast cells. One large peak near the left edge, with a smaller peak at twice the distance along the x-axis. Smaller peaks at 3x and 4x locations.

I started with protocols developed for S. cerevisiae. At three months in, I was testing yet another protocol variation and the data that came out of the experiment looked like the figure at right. Previous data had much broader, indistinct peaks. (I'm sure I have some of those early figures around somewhere, but I'm not going to spend a bunch of time digging for them.) I was amazed and quickly set up a repeat of the exact same experiment. It failed miserably.

I had made a mistake somewhere in the protocol which made things work. Because it was a mistake, it wasn't written down in my lab notes. You can only write down what you know you're doing.

It took me another frustrating month to figure out what it was I had done wrong. I had used way too much EDTA in the buffers for processing the cells. With this improved protocol, I could get good flow cytometry data from even the most difficult hyphal-growing strains of C. albicans. This disproved the previous theory as to why this species was difficult to work with while doing this assay.

Subsequently, the protocol proved effective with every random yeast species I was able to acquire for testing. I never tested them with the original S. cerevisiae protocol for comparison. In retrospect, I consider this to be an oversight.

The flow cytometry protocol has since then been used in numerous papers from several separate labs. The flow cytometry protocol and analysis tools I developed become the second chapter in my thesis. The idea of wrapping up the material into a paper did come up after I graduated, but I really didn't have the time/energy to dedicate to the process. Researchers should probably cite that chapter, but I know that thesis chapters tend to only get cited rarely. If you are interested in all the details, you are welcome to have a read.


I pretty quickly developed a working theory about what was going on. EDTA binds to divalent cations (Ca2+ and Mg2+) in solution, locking them up so other enzymes don't have access to them. Many enzymes require certain levels of these ions to function normally. For whatever reason, the endogenous nucleases of C. albicans were much less sensitive to low levels of divalent cations than those found in S. cerevisiae. Now, I couldn't think of any way to test this theory. I wasn't in a biochemistry or structural biology lab, so the techniques that would have been useful were well outside our wheelhouse.

This uncertainty has stuck with me for the roughly seven years since then. Just a couple days ago, I developed an idea that in some sense explains the results. Domestication.

S. cerevisiae is a thoroughly domesticated species. It hasn't had to fight for what it needs, so it could very well have evolved enzymes that are used to easier environments with more consistent levels of necessary ions. I strongly suspect the flow cytometry protocol for S. cerevisiae only works because of the domestication syndrome of traits found in S. cerevisiae.

I'm not sure how one would test this theory, but it sure seems to make sense of the observations so far.


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Monday, October 1, 2018

The Color of Beans

I've been looking for some blue-colored beans for several years. Its easy to find beans in a range of colors (red, pink, white, yellow, green, black), but blues are a rarity in beans. Early on I found an Italian bean called "Nonna Agne's Blue Bean", but the only seller in my country was out of stock. Sometime along the way I received an offer of some French heirloom blue beans via a facebook connection, but no seeds ever appeared. (She offered them for free, so I can't complain too much.) Blue beans are around, but they're rare.

Three black dry beans, with an almost bluish shine in the light.
Last year I received some beans from an online collaborator after I had mentioned my interest in blue beans. She said one of her plants that season had turned out to be an unexpected hybrid that produced blueish seeds. The three seeds that arrived are shown at left. To my eye they were basically black, but with maybe the slightest blue cast. I wasn't optimistic, but after the difficulty I'd had finding blue beans I was going to give them a try.

Square plastic pot with two bean seedlings.Two of those three beans sprouted. This was kinda a dramatic time, as those two sprouts could easily have died and then another possible blue bean lead would have gone nowhere. Fortunately, both plants thrived.

Mixed dry beans in shades of dark blue, brown, and a color in between that looks like a dark grey..A few months later I had a small pile of new beans. When I started shelling them I was very pleased to see some distinctive blue color. As the beans age and dry down, they start to produce some tan pigment which muddies up the pretty blue.

Next spring I'll plant enough of the more blue beans so I can grow enough to make a few meals of them. Right now I have too few to make a meal and have enough for planting.


How did I know that the biology of bean color should be able to produce a blue bean? The red color of beans is due to a group of biological pigments called anthocyanins. This same group of compounds is also responsible for the rare blue pigments we see in biology.

An analysis of black beans showed most of the anthocyanins to be delphinidin (at 56%), with lesser amounts of petunidin and malvidin (26% and 18%, respectively). Delphinidin and malvidin are responsible for blue color in various flowers. The petunidin is described as having a dark-red/purple color. All together, this suggests that black beans really are just super-dark blue beans. This is corroborated by references I've heard of black beans crossed to white beans sometimes producing distinctly blue beans in among the progeny.

So, why are blue beans so rare? I got nothing that explains it. Blue is such a lovely and generally rare color that I would have thought people would have been growing blue beans as much or more than the now-common red beans. Maybe I can help rectify the situation in time.


As I was writing this post I decided to look around again for vendors selling blue bean varieties. I found a European vendor that seems to have stock of the Italian "Nonna Agne's Blue Bean". I also found another unrelated blue variety called "Blue Shackamaxon Pole Bean". I might think about ordering some of each, but it'd be more fun to make my own now that I've got a start at it.


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