Mapping malaria, deriving stem cells from unfertilized eggs, and sequencing DNA on a stick
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A study of malaria genomes reveals the pathogen’s hidden diversity
A research team from the Harvard School of Public Health and the Broad Institute has mapped the genomes of more than 50 different samples of the malaria parasite from around the world, revealing a surprising amount of genetic diversity in this deadly organism.
Malaria kills nearly two million people worldwide every year, mostly children in Africa, and the parasite is growing increasingly resistant to antimalarial drugs. The diversity map gives researchers a valuable tool to get a handle on the 60 percent of malaria genes whose functions are not yet known. It also provides insight on how the organism can rapidly change to evade natural immune defenses and drugs.
The researchers, led by Dyann Wirth, a professor at the Harvard School of Public Health and co-director of the Broad Institute Initiative on Infectious Disease, completely sequenced two Plasmodium falciparum isolates, from Central America and Asia, and compared them to the first malaria genome sequenced in 2002. Working with colleagues in Senegal, the researchers then did a less detailed analysis of dozens of additional isolates from around the world.
In all, they found nearly 50,000 differences in the DNA sequence between the various samples, about twice as many as they expected. They discovered an additional 37,000 spots where DNA was inserted or deleted, generating even more diversity.
Their study revealed that the genes for cell surface proteins, which are recognized by the immune system, showed the highest diversity. And by comparing the genomes of parasites exposed to different antimalarial drugs, they confirmed the location of genes that enable resistance to chloroquine, a common antimalarial. They also discovered a new region that appeared to carry resistance genes for another drug, pyrimethamine.
The work was published online this week in Nature Genetics, along with two other large-scale studies of the P. falciparum genome by other groups. They used similar data to trace the evolution of the parasite worldwide and to select promising new vaccine targets. Pat McCaffrey
Mouse eggs yield transplantable stem cells
Local researchers have reported a new method for producing and transplanting mouse embryonic stem cells that, if proven to work in humans, could lead to the production of genetically compatible tissue for the repair of diseased tissues.
But men shouldn’t get their hopes up—the technique starts with unfertilized eggs, so even if it does work in humans, the approach would only be an option for women. And the researchers have not yet proven that the derived cells, which lack important contributions from sperm, would function like normal embryonic stem cells, or that they would be safe to transplant into humans.
The researchers, led by George Daley at Children’s Hospital Boston, showed they could use unfertilized eggs from mice to produce embryonic stem cells that genetically match the egg donor. They stimulated the eggs, which had half of the maternal chromosomes, to begin development without the addition of paternal chromosomes from sperm.
During this process, called parthenogenesis, the maternal chromosomes were essentially duplicated, giving the resulting stem cells the complete set of chromosomes. The researchers were able to isolate stem cells, grow them into mature tissues, and transplant them back into mice with no sign of immune rejection.
The derived stem cells were not completely genetically identical to the egg donor, so it was possible that the immune system would treat them as foreign. But they turned out to be close enough. Further analysis of the stem cells showed that many carried the full complement of genes coding for key proteins that protect cells from immune rejection.
The authors caution that the cells are not normal and more studies will be needed to assure their safety. They are now trying to replicate their results with human eggs.
The paper appeared online this week in Science. Pat McCaffrey
Next-generation DNA sequencing with carbon nanotubes
Wrap a strand of DNA around a nanometer-sized hollow tube of carbon and you’ve got a system for ultrafast DNA sequencing, suggests a new study from Harvard.
With today’s technology, DNA sequencing is time consuming and expensive, partly because the DNA of interest must be copied millions of times in order to be sequenced. One faster and cheaper approach could be to directly read the sequence from a single DNA strand—say, by threading the DNA through a tiny pore outfitted with sensors. So far, though, no such method has made it into biology labs.
Now, Efthimios Kaxiras and colleagues at Harvard and at the University of Ioannina in Greece have proposed another way to do this kind of direct sequencing, using existing scanning microscopes. Single-stranded DNA will naturally wrap itself around carbon nanotubes—rolled-up sheets of carbon just one atom thick—while leaving the DNA bases A, G, C, and T exposed. A powerful scanning tunneling microscope could then read off the individual bases one at a time, Kaxiras’s team says.
A scanning tunneling microscope (STM) has an extremely sharp metal tip that shoots electrons into a sample, enabling it to measure the local density of electrons in a part of a molecule—thus deducing its chemical structure—with a resolution of two angstroms, the width of a couple of hydrogen atoms.
Carbon nanotubes would not only hold the DNA steady in front of the microscope but, because they are conductive, would also ease the flow of electrons from the microscope to the DNA.
Based on computer simulations of the interactions between DNA and carbon nanotubes, Kaxiras’s team concluded that the sequencing plan should work, since each base should look sufficiently different to the STM. The researchers estimate that this method could theoretically sequence perhaps 10,000 bases per second, several orders of magnitude faster than today’s methods. The limitation would be how quickly the researchers can move the DNA strand past the STM tip without breaking it.
The study appeared online last week in Nano Letters. Mason Inman
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