In its own way, the axolotl salamander is a mighty beast. Chop off its leg, and the gilled creature will grow a new one. Freeze part of its heart, and the organ will form anew. Carve out half of its brain, and six months later, another half will have sprouted in its place. “You can do anything to it except kill it, and it will regenerate,” says Gerald Pao, a postdoctoral researcher at the Salk Institute for Biological Studies, in La Jolla, CA.
That extraordinary power of regeneration inspired Pao and his collaborator Wei Zhu, also at the Salk Institute, to probe the axolotl salamander’s DNA. Despite decades of research on the salamander, little is known about its genome. That began to change last year, when Pao and his collaborators won one billion bases’ worth of free sequencing from Roche Applied Science, based in Penzberg, Germany. Now that the data is in, scientists can finally begin the hunt for the genetic program that endows the animal with its unique capabilities.
While all animals can regenerate tissue to a certain extent–we can grow muscle, bone, and nerves, for example–salamanders and newts are the only vertebrates that can grow entire organs and replacement limbs as adults. When a leg is lost to injury, cells near the wound begin to dedifferentiate, losing the specialized characteristics that made them a muscle cell or bone cell. These cells then replicate and form a limb bud, or blastema, which goes on to grow a limb the same way that it forms during normal development.
Scientists have identified some of the molecular signals that play a key role in the process, but the genetic blueprint that underlies regeneration remains unknown. Researchers hope that by uncovering these molecular tricks, they can ultimately apply them to humans to regrow damaged heart or brain tissue, and maybe even grow new limbs.
In order to quickly identify sections of the salamander’s genome involved in regeneration, the scientists sequenced genes that were most highly expressed during limb-bud formation and growth. They found that at least 10,000 genes were transcribed during regeneration. Approximately 9,000 of those seem to have related human versions, but there appear to be a few thousand more that don’t resemble known genes. “We think many of them are genes that evolved uniquely in salamanders to help with this process,” says Randal Voss, a biologist at the University of Kentucky, who is working on the project.
The researchers now plan to make a gene chip designed to detect levels of some of these candidate genes, so that the scientists can determine at exactly what point during the regeneration process the genes are turned on. The team is also developing molecular tools that allow them to silence specific genes, which will enable them to pinpoint those that are crucial for proper regrowth.
Scientists also sequenced random chunks of the salamander genome. At about 30 billion bases and 10 times the size of the human genome, it is one of the largest among vertebrates. Most scientists expected that the extra DNA would be made up of junk DNA, long stretches of bases between genes. But initial findings were surprising. “Genes are on average 5 to 10 times larger than those in other vertebrates,” says Voss. “The region of the genome containing genes is estimated to be more than two gigabases, which is as big as some entire genomes.”
The extra DNA sequences sit within genes and are cut out during the translation from gene to protein. Much of this DNA comprises repetitive sequences not found in any other organisms to date, says Pao. However, it’s not yet clear whether these repetitive stretches help facilitate regeneration or play some other role in the salamander’s life cycle.
One of the key questions yet to be answered is whether the salamander has unique genetic properties that enable regeneration, or whether all animals have that innate capability. “If we come up with some totally unique gene only present in axolotl, that would make it really hard to replicate,” says David Gardiner, a biologist at the University of California, Irvine, who is also collaborating on the project. He prefers to think that regeneration comes from a fundamental abilitylying dormant in mammals, which could be reawakened with some simple genetic prodding.”Most of the tissue in our arm regenerates; it’s just the arm that doesn’t regenerate,” he says. “What’s missing is how you coordinate a response to get an integrated structure.”
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