This redwood, in Henry Cowell Redwoods State Park near Santa Cruz, might be genetically identical to some of its neighbors. Photo: kqedquest.

QUEST has an inordinate fondness for albino redwoods. It all started with the Science on the SPOT video Albino Redwoods, Ghosts of the Forest. Then there was a radio story, and a few blog posts. And last week QUEST revisited the research in two new Science on the SPOT videos about the ghosts of the forest. The video Revisiting Albino Redwoods, Cracking the Code focuses on QUEST blogger Barry Star and Stanford professor Ghia Euskirchen’s research on how the albinos are genetically different from “normal” coast redwoods. In Revisiting Albino Redwoods, Biological Mystery, Santa Cruz Professor Jarmila Pitterman wonders how albino redwoods’ total lack of chlorophyll affects their physiology and ecology. After producing all these videos, QUEST Producer Chris Bauer still had questions.

Chris saw three albino redwoods, arranged in a straight line, a short distance from one another. He wondered if these three redwoods, yards apart, might be genetically identical. Maybe they sprung from the same individual. To understand how this is even possible, you need to know about the numerous ways that redwoods can reproduce—some of which involve cloning themselves.

New redwood trees can come about in four ways: through seeds, cuttings, stump sprouts, and root sprouts.

QUEST on KQED Public Media.

Like all plants, redwoods can grow from seeds. Redwood seeds come from those tiny, inch-long redwood cones that fall from the branches in autumn. Each cone contains one to two dozen tiny seeds. These seeds were fertilized with redwood pollen; they are mix of genetic material from the parent that made the seed and the parent that made the pollen. However, redwood seeds have a notoriously low germination rate. Hardly any of them will grow into a plant. Which brings us to the next method of redwood tree generation: cuttings.

Redwood trees that you buy from a nursery probably began as cuttings—branches that were cut from a tree. To make a good redwood cutting, horticulturists will cut a branch from a young tree, or sapling, because cuttings from young trees tend to survive better. They treat the cutting with hormones to encourage growth, and plant the cutting in a special blend of soils. After a few months, about 25-35% of the cuttings have formed roots; the others do not survive. Once the cuttings have established, they can grow quite quickly—up to 7 feet in height in a single growing season. Regeneration from existing branches doesn’t just happen in the nursery—it happens in nature too. When a branch falls off a redwood tree, say in a storm, the branch can come in contact with the soil and develop roots. These provide the branch with nutrients and water, and before long the branch has grown into a tree. Trees grown from cuttings or from branches are genetically identical of the tree that donated the branch. (For the same reason, California’s vineyards are very low in genetic diversity; see this article in the New York Times.)

Stump sprouts on a coast redwood. Photo: kqedquest.

Many a majestic redwood tree began as a stump sprout. Stump sprouts are tiny growths from the base of existing trees. They can grow out of a healthy tree, or a tree that has been logged or damaged by fire. Redwoods have extensive underground root systems, which are impervious to trifling things like lumberjacks’ axes and fire. Trees that grow from stumps grow quickly and have a good chance of success, because the trees are automatically connected to a large root system. Multiple stump sprouts from a single trunk form what is called a fairy ring: a ring of trees, with a circular clearing in the middle, because the original tree breaks down. Stump sprouts are generally genetic clones of the original tree. However, the albino redwoods are stump sprouts with a mutation (or two, or three…). The genomic research happening Stanford will hopefully shed some light on how this mutation happens.

A fairy ring. The ring of trees has sprouted from the moss-covered trunk in the middle. Photo: Swiv.

Redwoods don’t just sprout from stumps; they can also sprout new growth from their roots. Redwood roots extend horizontally under the soil. Many redwoods live in flood-prone ecosystems, on the banks of rivers. When redwood forests become flooded, sediment piles up on the surface of the soil, burying the roots a bit deeper than they were before. Redwoods will grow another set of horizontal roots, a little closer to the surface. By digging deep into the ground and counting the horizontal layers of roots, people can tell how many floods a redwood has endured. When new growth sprouts from the surface roots, the original tree soon has a neighbor that is basically an identical twin. This is what Chris thinks is going on with the three albino redwoods, all in a row.

Hopefully Chris can test his hypothesis in a year or two, when the redwood genome is sequenced and we know what mutation (or mutations) cause albinism. Are the three neighboring albino redwoods mutants that sprung from genetically identical trees? Maybe that tree’s genotype is just a little different from that of an albino—and the mutation that causes albinism is very likely to occur. Or maybe the three albinos are a series of chlorophyll-free coincidences. We’ll have to wait patiently for the genome data. But, for a coast redwood that can live for 2,000 years, the wait won’t be long at all.

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Who ya gonna call? Stanford Genetics.

I know, I know…hokey title, hokey caption. But in many ways it's true.

Albino redwoods have been called the ghosts of the forest. And scientists from Stanford’s Department of Genetics are on the trail to figure out why these trees have white leaves instead of green.

This all started with a Science on the SPOT story about the albino redwoods by Chris Bauer right here on QUEST. In his accompanying blog post about these "ghost trees", he wondered aloud if any geneticists might be interested in trying to figure out what was going on genetically with these pale trees.

I was intrigued enough that I decided to ask the chair of the Department of Genetics, Dr. Mike Snyder, if he was interested in tackling the problem. By chance, he knew of a scientist in the department, Dr. Ghia Euskirchen, who was also interested in the redwood genome.

In the old days, figuring out what exactly was going on at the DNA level of something as complicated as a redwood would have cost way too much time and money to make a study like this worthwhile (if it was even possible at all). Nowadays things are simpler but still no walk in the park. Instead of elegant, time consuming experiments to pinpoint where the problem might be, scientists will use a more brute force method. They will simply sequence all of the DNA of albino and normal redwoods and compare them.

Sequencing is cheaper, simpler, and less time consuming than the old ways but this isn’t CSI. We’re not going to have answers right after this commercial break. It could still take a couple of years to figure this out. Or, if the biology doesn’t cooperate, even longer.

And the only reason we have a chance to do this so “quickly” is because redwoods can reproduce asexually. In other words, they can throw off clones of themselves.

It just so happens that occasionally, a few of these clones end up albino. What this means is that there shouldn’t be a whole lot of differences between the albino and wild type clones. This should make finding the change that caused the albinism relatively easy. That’s the hope anyway…

I am sure you’ve already started to think how weird it is that a clone ended up different from the original. After all, by definition, clones should be the same.

One letter change turns this watch into a cheap knock
off. The same thing may be going on with albino
redwoods but with DNA letters.In real life, though, clones are not the same as the original. They are more like subtle knock-offs. For example, cloned cats look similar but have different personalities. Same thing with garden variety human clones—identical twins.

So how does a clone end up different from the original? There are many possibilities, here are two:

1. The DNA is different. Even though a clone is really just a copy of the original, cells aren’t perfect at making copies of themselves. You try copying the 30 billion letters of redwood DNA and see how well you do! Most of these changes don’t matter but if one happens to hit and damage one of the hundreds of genes involved in making a redwood green, then you’ll get a white tree.

2. The DNA is used differently. All the cells in a redwood have the same DNA but a root is very different from a leaf. These differences come about because each cell uses its DNA differently. The environment can also affect which gene a cell chooses to turn on and to what level. This is often done with differences in something called methylation which scientists can detect. It may be that methylation has shut off a key gene involved in turning redwood leaves green.

Watch out for at least one more blog on this topic from me dealing with bits of DNA outside of the nucleus that may be involved. And for Chris’ upcoming story on how Stanford scientists are going about solving this albino mystery.

QUEST on KQED Public Media.

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Identical twins are more similar to one another than a clone
will be to the person cloned.

Of course, these cells aren't any less controversial than they were eight years ago. Researchers will still need to destroy embryos to get these cells (at least until they perfect iPS cells which would make this part of the debate moot). Anyone who considers an embryo made up of a few hundred cells to be alive will protest that embryo's destruction.

This is a legitimate argument based on when someone believes life begins. But some protests I heard were from people worried about embryonic stem cells being used to clone humans. What I can't figure out is why anyone would want to clone someone.

Cloning won't be like it is in the movies. Scientists won't take a cell from someone and make an exact copy of a person who is the same age and has the same memory.

Instead, a human will be cloned like any other mammal. First they'll remove the DNA-containing nucleus from an egg. Then they'll fuse that egg with a cell from the person they want to clone.

This "fertilized egg" will then have to grow and develop in a surrogate mother, be born, and then have to grow up. The clone won't have any of the original's memories.

In essence, a clone would be more like an identical twin who has been reared apart from his or her twin. Even though identical twins reared apart have a lot of similarities, they have a lot of differences, too. One article I saw put the amount of behavior/personality similarity due to genes at something around 50%.

And a clone will probably be more different than that. When the cell's nucleus is put into the egg, scientists erase a lot of the markings on the DNA that originally turned it into an adult cell. This "fertilized egg" is now a blank cell which can be shaped by both its genes AND its environment.

Identical twins develop in the same womb at the same time and so are exposed to the same sorts of environmental effects. A clone would not be. And these environmental factors can affect how we develop. They can even alter DNA and as a result, alter who we become.

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Maybe a clone of this guy will wander the Earth one day.A new study shows that scientists can clone a mouse that has been dead and frozen for 16 years. If they can apply what they've learned to a mammoth that has been dead and frozen for over 10,000 years, then maybe my kids can ride a mammoth one day. Or at least my grandkids can.

You Need More than DNA to Clone

Cloning isn't as simple as was shown in Jurassic Park. You can't take DNA and make a clone from it. Instead, you need an intact nucleus. And ideally, an intact nucleus in an intact cell.

The nucleus is where DNA is kept in our cells. The DNA is stored and packaged there in a way that only Mother Nature can do (for now). We can’t take our 6 feet of DNA and cram it into the tiny space of the nucleus.

Cloning 101.As I said, right now cloning uses intact cells. Here's how it works:

1) Take a cell from the animal to be cloned
2) Remove the nucleus from an egg (this is called an enucleated egg)
3) Fuse the two cells and let it divide a few times in a Petri dish
4) Implant the growing embryo into a surrogate mother
5) If everything goes well, a clone is born

This procedure requires living intact cells to be used. The problem with a frozen animal cell is that it is dead and ice crystals have torn it apart. It is not possible to fuse a beat up dead cell with an enucleated egg.

Cloning Using Frozen Cells

What the researchers in this new study did was change the protocol a bit. Instead of fusing two cells, they harvested nuclei from the frozen cells and injected them directly into the enucleated egg.

When they tried to clone the mouse that had been frozen for 16 years this way, it didn't work. But they managed to get 4 clones by adding an extra step. What they did was to make embryonic stem (ES) cells from the frozen mouse and use those cells to make a clone.

Basically they cloned the mouse but then instead of putting the embryo into a surrogate mother, they harvested its ES cells. Then they used the nuclei from these cells to create a clone in the usual way.

So we can now clone a long frozen mouse. The next step will be to try to clone an extinct animal like a mammoth.

Cloning a Mammoth is Trickier than a Mouse

Mammoth cloning will be no walk in the park. First off, we don’t have any mammoth eggs or cells to use. We'll have to use elephant ones. Hopefully, elephant eggs and/or cells will be compatible with a mammoth's nucleus. ( But there is some concern they they might not be compatible.)

Second, elephants are a lot harder to work with than mice. The experiments in this study used thousands of eggs to get a few clones. I don’t know enough about elephant biology but it seems like you'd need a lot of elephants to get that many eggs.

But this is definitely the first step in resurrecting long dead animals. For now we'll have to focus on the frozen ones. Maybe in the future researchers can figure out how to clone animals stored in formaldehyde. Or from pelts. Then we can start reviving species we humans have managed to kill off over the years.

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