// Twitter Cards // Prexisting Head The Biologist Is In: April 2016

Tuesday, April 26, 2016

Growing Bur Oak Trees (Quercus macrocarpa)

Oak trees (Quercus spp.) have a long history of being used as a food source. Acorns are produced in large amounts by older trees, usually in alternating years. This fruiting strategy, called "masting", helps to prevent the population of seed predators from overwhelming the tree and killing every acorn every year.

1. Bur Oak (Q. macrocarpa)
acorn cap.
I've made an occasional habit of tasting acorns over the years. They routinely have the strongly bitter taste of tannic acid, but occasionally I find one that doesn't taste so bad. When I was in Texas for my oldest brother's funeral (November 2014), I found a nice Bur Oak (Q. macrocarpa) tree on a walk. The tree had a few acorns (in huge caps) on its branches, but the ground beneath was littered with them in various conditions. I broke open one intact looking acorn with my shoe. I noted the nut-meat looked in moist and in good shape, so I picked up one of the pieces and tasted it. The juice tasted distinctly sweet, with no bitter aftertaste.

I was astounded by this and collected a large handful of the best looking acorns I could find. I then continued with my walk. Back at my parents' house, I put the acorns in a resealable plastic bag and put them with my things. When I returned home to Minnesota, I added some moisture to the bag and put it into a basement micro-fridge I've dedicated for botanical specimen storage.

2. Bur Oak acorn; partially
dissected and sprouting.
(USA quarter for scale.)
A year and some four months later (March 2016), I decided to try growing the acorns. Winter here was wrapping up and I was already growing a Chestnut (Castanea spp.) tree in my basement. I took the acorns out of the fridge to examine them. I had previously extracted one nut-meat from its shell and found it had begun to mold. I discarded this one and opened up a few others. Each acorn with an intact shell survived storage without molding.

3. Germinating acorn.
I left the acorns (shelled, partially shelled, and intact) in a dark, but room-temperature spot and waited. By late in March, I noticed a small swelling forming on one acorn (images 2 & 3). At first I wasn't sure if I was actually seeing a change in the acorn, but once I was sure that I was, I removed the remaining membrane layer from around the germinating acorn embryo to get a better view of it.

4. Germinating naked acorns.
I had fully extracted two of the acorn nut-meats during my examination for mold. Once I noted the one acorn germinating, I took a look at these two. Both were obviously germinating too. One (image 4, left) had split in two, revealing the anatomy of the embryonic oak tree and its two cotyledons. To stabilize the baby tree, and partly mimic the acorn shell I had removed, I secured the cotyledons together with some small cable-ties. I secured the other naked acorn in the same way.

5. Stem growth.
Three of the germinating acorns are planted into air-pruning planters (just like the Chestnut trees). The acorns produced a stout taproot which extended to the bottom of the planter well before the stem had grown an inch or unfolded its first leaf. After stalling for a while at less than an inch tall, the stem started elongating rapidly.

6. Air-pruning in process.
The taproots were too thick to pass through the screen material, so the either terminated on impact or grew sideways for a bit before catching on the screen and terminating (or as in image 6, growing through the screen anyway). Many side roots then grew, soon after poking through the bottom of the planter.

As long as the large and tasty nut remains attached to the seedling, it will be a strong incentive to squirrel predation. I suspect I'll have to keep the baby trees in protective custody until at least summer of 2017. One tree will probably go into the back corner of my yard. (There are some very large Buckthorn specimens there to clear out first.) The others will probably go to my wife's family farm, joining a pair of the chestnut trees to form the start of a nut orchard.

7. Bur Oak range, source, and me.
This species of Oak is native to a large swath of the central part of this country (figure 7). The specimens at the extreme southern part of the range tend to produce larger acorns than those at more northern locations. It seems that this gradient is in part due to the history of glaciation on this continent and the improved ability of individuals with smaller acorns to travel north into areas where it was previously extirpated, though the details have not been fully worked out.

If these very southern trees manage to survive the cooler climate here in Minnesota, they should start producing their first acorns in somewhere from 10 to 35 years (depending on who you talk to). Hopefully I'll still be around (at somewhere between 48 and the ripe old age of 73) to collect some acorns and make a few meals of them. For the purposes of the ongoing domestication of the tree as a food source, I hope I'll also be able to convince the young'uns around at that time to plant some acorns from the best of my trees so as to grow their own.


Tuesday, April 19, 2016

Mutation Breeding 2

1. Spare microwave.
In a recent post, I talked about how ultraviolet light could be a useful mutatgen. It damages DNA effectively, is easy to generate, is easy to keep contained, and there's no cleanup required. This post is going to be something of a departure from what I typically post, as this is just a short little story of how I built a device to try and mutate seeds with germicidal-UV light, starting with a spare microwave oven.

2. Dangerous bits.
It took a little work to get into the guts of the microwave. The outer shell was held in place with security screws, intended to keep the unwary away from some very dangerous components. The large transformer and capacitor on the bottom together increase the voltage supplied by the wall current from 120 V to something like 4 kV. This higher voltage is then fed into the magnetron (at the top), which generates microwaves. These parts are able and quite willing to kill you if power is running through them. If you don't have years of experience with electronic components, don't mess with the guts of a microwave.

3. Neutered and running.
Once the microwave was neutered, I had to make sure the other aspects of the device were still working. when the "microwave" is running, theory says the two lines running to the dangerous parts should essentially be wall current. This is dangerous, but much more in the realm of the familiar (to anyone who has rewired a lamp, installed a fluorescent ballast, or many other minor tasks). When it isn't running, there shouldn't be anything running through these lines. My multimeter showed otherwise. When running, it is straight wall current at 120 VAC. When it isn't running, but plugged in, there is roughly 7 VAC running through it.

4. Rewired for UV.
After unplugging the device and making sure there was no unexpected voltage remaining in the system, I installed the ballasts and receptacles need for a pair of fluorescent light bulbs. Germicidal-UV bulbs are similar to regular fluorescent bulbs, they all use a small amount of ionized mercury to produce copious amounts of UV. Regular bulbs are lined with phosphors to convert the UV into visible light and are made with UV-absorbing glass to minimize the amount of UV that escapes. Germicidal-UV bulbs don't have any phosphors and are made from UV-transparent glass to maximize the UV that "escapes".

5. Door disassembled.
The front door of a microwave includes a metal layer gridded with holes. The holes are small enough that quanta of microwave energy just can't fit through them. Ultraviolet, on the other hand, can get through the holes just fine. To remedy this, I decided to replace the clear front plastic panel with a piece of opaque orange acrylic.

6. The ultraviolet oven.
Now that everything is put back together, I have an ultraviolet oven. I don't have a direct photo of the bulbs in action. I didn't feel like focusing intense ultraviolet light onto my retina. The final photo at left shows some intense UV bouncing through the exhaust port at left. The opaque acrylic front lets you see when the bulbs light up, but should be blocking sufficient UV to make the machine not be hazardous. I need to find something that strongly fluoresces in UV-C for testing purposes. Inside the oven, or adjacent to the exhaust, the object should fluoresce. In front of the door, the object should remain dark. If the door is passing much UV-C, I'll have to reassess the safety protocols I'll have to keep in mind while using the device.

The next step would then be to start experimenting with mutagenizing batches of seeds. To maximize the number of mutant plants which get produced, the basic idea is to dose the seeds at a high enough level to reduce germination by roughly 50%. It will probably take several mutations to actually kill a seed, so dosing them at this level will ensure that most of the seeds that germinate and survive will also be carrying mutations.

What sort of exposure can my new ultraviolet oven produce? Some really rough calculations indicate that seeds held within an inch of the bulbs for about five minutes would be approximately the same exposure that seeds on the space-station received over a year in direct sunlight. Seeds protected from UV, but otherwise exposed to space, showed higher survival. A few minutes in the ultraviolet oven should have a significant impact of germination, at least with smaller seeds.

Another thing to be tested is the effect on seeds that are dry vs. ones that have been soaked in water overnight. Plant embryos that have woken up and are metabolically active will be more able to repair DNA damaged by UV (a necessary part of converting damaged DNA into new mutations), compared to those that are completely asleep in dry seeds.

After I dose a few different batches of seeds, it will take another couple weeks to determine what impact on their germination was had. I'll probably do some really high doses, just to make sure I am likely to cover the range from no-impact to strong-impact. Once I get a basic idea of the range of doses that are interesting, I'll do more test exposures at intermediate levels to better resolve the dosage-response curve. All of this will take me several weeks further, so the next posting on this topic will probably be a while.


Tuesday, April 12, 2016

Growing Chestnut Trees (Castanea spp.)

A couple of years ago, a member of a forum I frequent offered to send some Chestnut (Castanea spp.) tree seeds to interested parties. He has been breeding Chestnut trees over the last decade and was interested in sharing the results of his work. I expressed interest and soon after a small box arrived, packed with seeds from a few different sources. The box was far larger and held far more seeds than I expected the individual was going to send me.

The seeds were collected from a range of different Chestnut trees:
  • Chinese seedling (C. mollissima)
  • Miller's Hope (C. mollissima)
  • Szego (seedling of Linden; mostly C. mollissima/C. crenata)
  • Gillet (seedling from Colossal; C. sativa/C. crenata)
  • Kaibutsu (seedling from Colossal; C. sativa/C. crenata)
  • Silverleaf (C. sativa/C. crenata)
  • Double Sweet
  • Patterson
Most of them have a mixed ancestry, but all have been selected for high production of large edible nuts. From a long-term view, growing these varieties is entirely about the ongoing domestication of chestnuts as a food source, i.e., improving food security through increasing the diversity of our food plants.

American chestnut range vs. me.
Growing these chestnuts has nothing to do with resurrecting the American chestnut (C. dentata), which is something I consider a very important goal. The American chestnut, in the pre-blight era, dominated the Eastern Woodlands and provided food for a thriving ecosystem (and economy) that has been only a shadow of its former self. Go over to www.acf.org to read more about what they're doing to restore this tree to the dominant role it used to have. Because I live well outside the native range for the American chestnut, I'm not worried about interfering with the their restoration by growing closely related trees that can cross successfully with the American chestnut.

From a short-term view, I'm interested in growing chestnuts simply because I want to grow a new food source. I like having a hand in producing the food I eat and I'm interested in the process of domesticating plants to be better foodstuffs for the future. There really is nothing like planting a tree, that will probably outlive me, for having a future perspective.

When I received the package of chestnut seeds, I had just moved into a new house and didn't have the resources on hand to build the rodent-proof growing area I would need to keep baby Chestnut trees alive. They rely on the nutrients found in the seed for the first year, which is a long time to be exposed to hungry squirrels that like to pull up newly-sprouted nut trees to get at the buried nut. (I learned this when one pulled up a baby Black Walnut tree I was tending, ate the previously-buried nut, then left the uprooted seedling beside its pot.) I had read that Chestnut tree seeds could stay viable for a few years if kept chilled, so I planted a handful of the seeds and kept the others in the fridge. My idea was that by next spring I'd be able to build them some proper protection.

1. Radicle extending.
One of the first batch of seeds germinated and started growing. After it was a few inches tall, the growth point died. A few new branches formed below that point, but their growth points soon died. This pattern repeated a few times before the whole plant died. It had never produced a single leaf, but had branched several times while trying to.

2. Hypocotyl beginning to extend.
I spent some time thinking about what went wrong with that seedling. On the idea that it was getting too much water and developed a fungal infection of some sort, I decided to build a potting system that would allow the seedlings to drain much better. I built a set of primitive air-pruning pots and a raised wire-mesh platform so they could drain. In addition to the better drainage, these pots should help encourage the development of a healthier root system (so the seedling will better survive transplant later in the season).

3. New leaves.
Of this second batch of seeds, only one (a seed from the variety "Kaibutsu") has woken up so far. It is growing happily and is just opening its second set of leaves. The remainder of the seeds seem to have either succumbed to a mold, or are still waiting to wake up. There are reports of chestnut seeds derived from hybrid origin (as most of these are) having reduced germination, but I would need to test a similar batch of seeds as a control. Without that control, I'm left with hoping more decide to germinate, that the elongated winter they experienced didn't kill off the remaining seeds.

4. LED lighting.
When this seedling started waking up, I put it near the front door where I could keep a close watch on it to make sure it didn't dry out. After it grew a couple inches, the drive to find light became the stronger factor guiding its growth and it began tilting towards the nearby window. To help keep the seedling from becoming permanently crooked, I built a rack that holds an LED floodlight directly over it. The base of the structure is a platform extending forward underneath the tray holding the plants, so it has very little risk of falling over. This setup should keep the seedling growing straight until it is time for it to go outside.

5. New lighting and further growth.
After a few more leaves had grown, it became apparent the lighting setup I built was too bright for the seedling. Leaves closer to the light were looking sunburned, while those further away were colored lightly brownish from photo-protective pigments. I think the new fixture produces more light overall, but it is spread over a larger area and so the peak intensity is lower. (This new fixture can also provide light for other plants, like those carrots.)

6. Roots.
The home-made air-pruning pot seems to be doing its job. There are little roots poking out all over the bottom of the container. The roots start out whitish, but then turn a dark brown as the tip dies and dries out. At some point soon, I'll have to transplant the seedling to a larger air-pruning pot. This will allow it to become larger/stronger as well as giving us the time to figure out where it should go into the ground and how to protect it from deer and other hazards. I might be able to make such a planter the same way I made this one, but I suspect I'll have to go with a bit more robust commercial offering.


Tuesday, April 5, 2016

Some Seeds for 2016

I wrote this earlier in the season, but it is only appearing now because I had several other posts already in the queue ahead of it. This happens from time to time when my writing gets ahead of the calendar, but usually my postings don't refer to a specific time frame and so nobody notices.

One can garden all year-round if they live in the warmer parts of the world. I'm stuck in the depths of a (really mild) Minnesota winter, but I don't have a greenhouse. I can still do some very limited gardening.

I just (17Feb2016) planted a whole mess of seeds into containers that are going to go outside and stay outside tomorrow. Tomorrow is expected to reach some 40F (and then 50F the day after), but we'll probably have some well below freezing in what is left of our winter. So... what am I thinking?

Lots of seeds spend winter outside. Many even require a lengthly cold and wet (from being under snow) winter experience to reliably germinate on schedule in spring. This requirement can be provided at any time of the year using a fridge (called cold stratification), but the winter here provides an easier way to do it...

So, I planted:
All in all, I planted some 600 seeds. I suspect most are viable and will start growing when the weather warms up. Some of them are a bit more uncertain. The Tulipa seeds were probably stored for far longer than they like. Rubus seeds are sometiems described as hard to grow (requiring acid treatment to improve germination). The Arisaema triphyllum seeds are very old, but previous testing had shown them to have very good germination.

The seeds represent various different goals and projects. I'm not going to go into detail about them, however, until I have living plants to help illustrate my ideas. In general, I'm hoping the plants will be interesting.