Tuesday, November 29, 2016

Botanizing in Alaska: Low-Bush Cranberry

I still have some photos from my last trip up to central Alaska to go through. I found this plant on a drive in the vicinity of Fairbanks-AK. We drove up a mountain until we were at the tree-line. While walking around, we saw lots of this plant woven through thick mats of moss and other small plants. Though it didn't have any berries yet, I was able to find a few flowers.

Called Lingonberry or Low-Bush Cranberry (Vaccinium vitis-idaea), this plant has a circumpolar distribution. It is prominent in Scandinavian cuisine and is one of the plants I fondly remember from my childhood in Anchorage-AK. I was hoping to find a small specimen I could transplant to grow in Minnesota. The plants I found, however, spread over several feet wide (though most was hidden in the thick moss). I haven't found any research into how long the plants can live, but these were undoubtedly many years old. I didn't take any cuttings or plant samples, as doing so would have been too disruptive to the fragile plant community.


Saturday, November 26, 2016

Future of the Guinea Worm

Guinea worm (Dracunculus medinensis) is one of those parasites that nightmares are made of. Juvenile worms infect freshwater copepods, which invariably end up getting ingested [by humans] when drinking contaminated water. The adult female grows up to a few feet long. It migrates to the skin (usually in the lower leg) and induces an extremely painful blister about a year after infection. The blister is described like being set on fire. The pain is alleviated best by standing in water, which is exactly what the worm wants. When the blister is in water, the female worm releases hundreds or thousands of babies into the water.

Former US President Jimmy Carter has been leading an organization working to make the worm go extinct. As a disease organism, few people are going to lament its extinction. When I first learned about this organism, it was invariably described as infecting humans only. This would make the process of wiping it out so much simpler. Unfortunately, the story isn't quite so simple. The worm has other plans.

Figure 1 from paper.
Increasingly, dogs in Chad are being found with lower-leg lesions that have worms hanging out of them. Genetic analysis has shown it is the same species as the Guinea worm which infects people. Even if we prevent all human infections for long enough to interrupt the parasite's life cycle, it can still persist in other animals. It looks like it would take continuing diligence to keep it from erupting into an active human disease again.

Adapted from page.
Over the last several years, the number of infections observed in dogs has been going up and up, while human infections have been minimal. This pattern of yearly increases suggests the worms have been adapting to their new hosts.

The researchers did find evidence for human behavior that helped give the parasite the opportunity to make this transition. At the end of the dry season, the locals do a mass harvest of fish. The fish are processed and dried/smoked for later use. The guts and other undesirable bits are discarded for the dogs, chickens, etc. to deal with. The dogs are then getting infected by eating the fish guts. It also appears that uncooked/undercooked fish are responsible for the human cases of infection.

Adapted from Figure 9 of paper.
Historically, most human infections by this parasite were due to ingestion of water contaminated by infected copepods (an host to an earlier stage of the worm). With increasing knowledge about this mode of transmission, it became dramatically less useful of a pathway for the parasite. At the same time, any alternate pathway for the parasite to get into its main host would have been positively selected. Essentially, we've just seen a parasite go from a life-cycle with one intermediate host to a life-cycle with two intermediate hosts.

Many parasites are known to have complicated life-cycles passing through several intermediate hosts, but this is the first case I've come across that helps to illustrate how those complex life-cycles could have evolved.

Better control of the fish discards will help minimize the infection pathway through dogs, but it won't necessarily get rid of the problem. While adapting to their new hosts, the worms have had to evolve to better escape notice by the canine immune system. A consequence of this is that they will be better prepared to infect dogs later by other pathways, even if fish discards aren't available. Maybe dogs will start getting infected by ingesting infected copepods like humans used to. Maybe dogs will start getting infected by eating scavenged fish that died in the dry season. I can't predict what will happen exactly, but I understand the power of natural selection and very much believe the worm will find another way to survive even if we completely prevent transmission to humans in the near future.


Friday, November 18, 2016

Frosty Physalis

This has been a long and relatively warm fall season. There have been a few frosts, but most days the sun came out and it warmed up nicely. This is all over now that it is snowing. It might melt away and we might have some warmish days still, but after it has snowed I really can't convince myself that winter hasn't begun.

I grew a couple different types of tomatillos (Physalis ixocarpa) this year. I collected seeds for the first one from a medium-sized, dark purple fruit I got from a local CSA. The plants didn't thrive, but they did pretty good considering the lack of care I gave them. The plants have lots of purple pigment on the stems and the fruit husks, but the fruit themselves remain bright green on the plant. Once the fruit are picked and the husk is removed, the green fruit start developing intense purple pigment in response to light. The original fruit was purple all the way through, but no fruit this year have such a pigment pattern. I'm hoping the coloration of these plants indicates they are hybrids and so the darker color may turn up again in the F2 generation next year.

I collected seeds for the second type from a very large, green fruit I got at the grocery store. It didn't have a name associated with it, but it matches one of a few commercial varieties grown in Mexico. The plants did about as well as the other type. The fruit they grew weren't anywhere near as large as the original fruit, but they were much larger than the fruit from the other variety.

A couple days ago, I noticed the large-green variety had been killed back by one of the recent frosts... while the purple variety showed absolutely no damage. The above photos were taken at the same time and well illustrate the differences in frost-sensitivity.

Tomatillos are profligate outcrossers, due to the self-incompatibility mechanisms in their flowers. A consequence of this is that it is much harder to develop stable strains than it is with tomatoes and peppers, because you always have heterogeneity in at least the incompatability locus genes (and likely any nearby genes). The flip side of this is that it should be relatively easy to mix up the genetics of different strains that you happen to be growing next to each other.

I'd really like to develop a strain with the large fruit of the Mexican strain, but with the purple color and frost-resistance of the CSA strain. I expect I'll be able to find some hybrid seedlings with extra purple color among the masses I can grow out from the seeds in a few of the green fruit. These hybrids would have all of the alleles I'm interested in, though it would probably take several years to stabilize them in the homozygous condition.

A close relative of the tomatillo is the Cape Gooseberry (P. peruviana). I grew out this plant from a couple different seed sources. The plants ended up looking identical to each other early in the season, so I assumed they were essentially the same.

After I noticed the different frost-sensitivities of the tomatillo types, I checked on the Cape Gooseberry plants. Several plants were in perfect health (at left), while one was heavily damaged from frost (at right). The condition of the damaged plant indicates it was harmed by a more recent frost than the green tomatillo, suggesting that it has a greater resistance (even though it wasn't enough to matter).

There doesn't seem to be much trait diversity in these plants to do much breeding with. I'll probably only save seeds from the more frost resistant plants to grow next year.

If I had only grown the large-green tomatillo, I wouldn't have realized there was variation in frost resistance that could be bred with. This highlights the importance of collecting diverse germplasm when starting a breeding project. That I collected seeds from a local CSA and grocer shows it doesn't have to be a very difficult process.

If no or very limited genetic diversity is available, like in P. peruviana, it can take more dramatic efforts to collect sufficient germplasm. International travel or nurturing wide-flung collaborations may be necessary. I like the concept of mutation breeding, the use of chemical or radiological means to damage DNA of the plant to generate usefull diversity to breed with. Each approach has its own costs and difficulties, so the direction a breeder chooses will depend on what makes sense for them and the specific plant they're working with.


Tuesday, November 1, 2016

Aphids in Red

I've found myself very busy lately. The little free time I've had after work and on the weekends has been consumed with the process of repairing some windows in my old house as well as sundry other necessary tasks. The main consequence for this blog has been that I haven't found myself able to sit down in front of my computer for long enough to write a post.

I have no plans to end this blog, but I do expect that life will occasionally get in the way like it has lately. To get myself back into the swing of things, I'm probably going to have a few light posts while I work on some more intensive ones.

Earlier in the summer, my wife and I went camping with some friends. Early one of the mornings, I was wandering around looking for photographic subjects when I noticed a bright red color along the stems of some plants. On closer examination, I realized the red color was a mass of aphids.

Aphids may be the bane of many a gardener, but they illustrate some really interesting biology. Aphids have a very complicated life cycle. During most of the year they're all females and don't have sex. Instead they multiply through parthenogenesis. They're so efficient at this that new baby aphids are born (not hatched) already pregnant. Most of the new babies don't waste energy growing wings, instead every calorie is dedicated to growing the swarm. When food starts to run out or the aphids get too crowded some babies will grow wings and fly off to other plants and continue their parthenogenic ways. When the weather starts turning colder in fall, winged male babies are produced. The males then mate with females to produce eggs which can survive more extreme winters than the adults.

Aphids come in a whole range of colors, from pale white to yellow, green, red, or even black. These red ones are really interesting because their color is due to high levels of carotenoid pigments (lycopene and related compounds) that are normally only synthesized by plants and fungi. Since the plants the aphids feed on don't have high levels of these compounds, it was at first confusing as to where they would get them. I turned out that the aphids have the genes needed to produce carotenoids and they seem to have acquired them from a fungus via horizontal gene transfer.

The really bizarre thing about these aphids is that they seem to be using the carotenoids to harvest energy from light. It isn't exactly photosynthesis the way plants do it since they're not incorporating CO2 to build sugars, but they do seem to produce more ATP when they're in sunlight compared to when they're not. This ability might help them survive tough times when other tiny insects would perish, but it really isn't at all clear.