Researchers at Boston University, and colleagues, have developed a silicon nanopore-based method that promises to make future genome sequencing faster and cheaper by dramatically reducing the amount of DNA required, thus eliminating the expensive, time-consuming, and error-prone step of DNA amplification. The technique uses electrical fields to feed long strands of DNA through four-nanometer-wide pores, much like threading a needle. The method uses sensitive electrical current measurements to detect single DNA molecules as they pass through the nanopores. “The current study shows that we can detect a much smaller amount of DNA sample than previously reported,” said senior author Dr. Amit Meller. “When people start to implement genome sequencing or genome profiling using nanopores, they could use our nanopore capture approach to greatly reduce the number of copies used in those measurements,” said Dr. Meller. The group harnessed electric fields around the opening of the nanopore to attract long, negatively charged DNA strands and to slide them through the nanopore, where the DNA sequence can be detected. In doing this work, the researchers made the counterintuitive discovery that the longer the DNA strand, the more quickly it found the pore opening. “That’s really surprising,” Dr. Meller said. “You’d expect that if you have a longer ‘spaghetti,’ then finding the end would be much harder. At the same time, this discovery means that the nanopore system is optimized for the detection of long DNA strands–tens of thousands of basepairs, or even more. This could dramatically speed future genomic sequencing by allowing analysis of a long DNA strand in one swipe, rather than having to assemble results from many short snippets.” Dr. Meller added, “DNA amplification technologies limit DNA molecule length to under a thousand basepairs.
Year: 2009
Peptide from Ancient Organism May Thwart Multi-Resistant Pathogens
A discovery made while investigating the ancient multicellular organism Hydra magnipapillata has revealed a new antimicrobial peptide that shows significant activity against a variety of bacteria, including multi-resistant human strains such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Once commonly thought of as a hospital-acquired infection, MRSA has now spread to the community (now known as community-acquired or CA-MRSA) and is infecting previously healthy young people who have not been recently hospitalized or undergone a medical procedure. Past research has proven that ancient organisms are well equipped at preventing infectious pathogens from entering the body and given the desperate need for new drug targets, further exploration of these organisms is warranted. MRSA has already developed resistance to CA-MRSA human antimicrobial peptides and prior studies have shown antibacterial immune responses in the simple metazoan Hydra magnipapillata to include bactericidal peptides with novel structural features and modes of action. In the current study, researchers identified the antimicrobial peptide arminin 1a from Hydra and found that it exhibited significant and wide-spread activity against bacteria including MRSA and enterococci, a common cause of hospital-acquired infections that is also drug-resistant. Further observations revealed that bacteria are killed when the bacterial cell wall is disrupted and that the antibacterial activity of arminin 1a is not affected by exposure to salt in human blood. Finally, researchers determined that arminin 1a does not share any ancestry with any known antimicrobial peptides.
Sexual Trickery by Orchids Promotes Efficient Pollination
New research has explained why orchids sometimes employ a seemingly limiting approach to attracting insect pollinators. While most flowering plants reward pollinators with tasty nectar, many orchid species turn to trickery. Some use what’s called food deception. They produce flowers that look or smell as if they offer food, but actually offer no edible reward. Other orchids use sexual deception. They produce flowers that look or smell like female insects, usually bees or wasps. Males are drawn to the sexy flowers and attempt to mate with them. In doing so, they accidentally collect pollen on their bodies, which fertilizes the next orchid they visit. From an evolutionary perspective, the sexual strategy is a bit puzzling. Orchids that offer nectar or mimic food can attract a wide variety of food-seeking pollinators—bees, wasps, flies, ants, and so on. But sexual displays are only attractive to the males of a single species—a flower that looks like a female wasp is only going to attract male wasps, not other insects. So in appealing to sex, these orchids limit their potential pollinators, which would seem to be a reproductive disadvantage. The scientists, however, showed that populations of sexually deceptive orchids had higher “pollen transport efficiency” than the species with multiple pollinators. In other words, a higher percentage of the pollen that was taken from sexually deceptive orchids actually made it to another orchid of the same species. The orchids with multiple pollinators had more pollen taken from their flowers, but more of that pollen was lost—dropped to the ground or deposited in flowers of the wrong species. This research was published in the January 2010 issue of The American Naturalist.
Natural Human Proteins Prevent H1N1 and Other Virus Infections
Scientists have discovered a family of human proteins that prevent or slow H1N1 influenza particles, as well as certain other viruses, from infecting human cells at the earliest stage of the virus life cycle. The anti-viral action happens sometime after the virus attaches itself to the cell and before it delivers its pathogenic cargo into the cell. The researchers believe that their findings may lead to better ways to treat influenza and other viral infections. The protein family, called interferon-inducible transmembrane proteins (IFITM), was first discovered 25 years ago as products of one of the thousands of genes turned on by interferon. Since then, not much else has been discovered about the IFITM family. Versions of the IFITM genes are found in the genomes of many creatures, from fish to chickens to mice to people, suggesting that the antiviral mechanism has been working successfully for millions of years in protecting organisms from viral infections. In the current study, the surprisingly versatile antiviral proteins were found to protect cells against several devastating human viruses—not only the current influenza A strains including H1N1 and strains going back to the 1930s, but also the West Nile virus and dengue virus. While IFITM proteins did not protect against HIV or the hepatitis C virus, experiments suggested they may defend against other viruses, including the yellow fever virus. The report was published online on December 17 in Cell. [Press release 1] [Press release 2] [Cell article]
Next-Gen DNA Sequencing Illuminates Mutations in Lung Cancer
Aided by powerful next-generation DNA sequencing technology, researchers have identified nearly 23,000 mutations in a patient’s small cell lung cancer. The mutations were identified by comparing the entire genetic sequence of the cancer against that of normal DNA from the same patient. In the process, the researchers also identified a new gene (CHD7) associated with lung cancer. The number of mutations found in the study suggests that a person may develop one mutation for every 15 cigarettes smoked, said Dr. John Minna, director of the Nancy B. and Jake L. Hamon Center for Therapeutic Oncology Research at the University of Texas Southwestern and one of the authors of the new study. The researchers said the findings illustrate the power of advanced technology to provide important new information about human cancer, including the effect of cancer-causing chemicals on the body and the identification of potential new therapeutic targets. “Cancer is driven by acquired mutations in genes, and we are at a point where it soon will be possible to actually know every mutation in the tumors of each of our patients,” Dr. Minna said. “The key will be to use this information to find new ways to help prevent cancers, diagnose them earlier, and to select treatments that might be specific for each patient’s tumor. While these findings are the first step, they have lighted our path to clearly point us in the right direction. In addition, they provide the first detailed analysis of a human cance–lung cancer–that is closely linked to smoking.” Furthermore, Dr. Minna said, “The data demonstrate the power of whole-genome sequencing to untangle the complex mutational signatures found in cancers induced by cigarette smoke.
New Antifreeze Molecule Found in Alaska Beetle
Scientists have identified a novel antifreeze molecule in a freeze-tolerant Alaska beetle able to survive temperatures below minus 100 degrees Fahrenheit. Unlike all previously described biological antifreezes that contain protein, this new molecule, called xylomannan, has little or no protein. It is composed of a sugar and a fatty acid and may exist in new places within the cells of organisms. “The most exciting part of this discovery is that this molecule is a whole new kind of antifreeze that may work in a different location of the cell and in a different way,” said Dr. Brian Barnes, director of the University of Alaska Fairbanks Institute of Arctic Biology and one of five scientists who participated in the Alaska Upis ceramboides beetle project. A possible advantage of this novel molecule comes from it having the same fatty acid that cell membranes do. This similarity, said Dr. Barnes, may allow the molecule to become part of a cell membrane and protect the cell from internal ice crystal formation. Antifreeze molecules made of proteins may not fit into cell membranes. This report was featured as one of the cover articles in the December 1 issue of PNAS. [Press release] [PNAS abstract]
Corn Genome Sequence Is Detailed
A four-year, multi-institutional effort culminated today in publication of a landmark series of papers in the journal Science, revealing in unprecedented detail the DNA sequence of maize (Zea mays). Maize, or corn, as it is commonly called by North American consumers, is one of the world’s most important plants and the most valuable agricultural crop grown in the United States, representing $47 billion in annual value. The sequence spans 2.3 billion DNA base-pairs and contains some 32,500 genes, or about one-third more than the human genome, according to the team that assembled it over the last four years. This version of the maize genome–taken from a variant called B73–is important, in part, because it is regarded by the scientific and agricultural communities as a “reference” version. It represents a significant filling-in of gaps in a draft maize sequence announced a year and a half ago, but more importantly, comes with what amounts to a detailed reference manual, a set of comprehensive annotations. “What’s important about the maize project,” said Dr. W. Richard McCombie, a Cold Spring Harbor Laboratory (CSHL) professor, a co-principal investigator on the maize genome project, and a pioneer in genome sequencing efforts, “is that it provides a reference DNA sequence for the most important agricultural crop in the U.S., making it much easier for people to look at the many variants of different strains or ‘accessions’ of maize.” New sequencing technologies, just now becoming commercially viable, will now be used to “analyze other maize strains by comparing them to this one–albeit at dramatically lower costs and accelerated speeds,” Dr. McCombie noted. Another of the co-project leaders from CSHL, Professor Robert Martienssen, put the maize sequencing project into historical perspective.
Stanford Mouse Study Suggests Possible Help for Down Syndrome
New findings from researchers at the Stanford University School of Medicine and Lucile Packard Children’s Hospital, and colleagues, shed light on the neural basis of memory defects in Down syndrome and suggest a new strategy for treating the defects with medication. The study, which was conducted in mice, is the first to show that boosting norepinephrine signaling in the brains of mice, which have been genetically engineered to mimic Down syndrome, improves their cognition. Norepinephrine is a neurotransmitter that nerve cells use to communicate. The scientists said that their findings raise the possibility that restoring norepinephrine-mediated neurotransmission could reverse cognitive dysfunction in Down syndrome. “If you intervene early enough, you will be able to help kids with Down syndrome to collect and modulate information,” said Dr. Ahmad Salehi, the first author of the study. “Theoretically, that could lead to an improvement in cognitive functions in these kids.” The results give “a ray of hope and optimism for the Down syndrome community for the future,” said Dr. Melanie Manning, director of the Center for Down Syndrome at Lucile Packard Children’s Hospital. Dr. Manning was not a part of the research team. “It’s very exciting,” she said. “We still have a long way to go, but these are very interesting results.” This report was featured as the cover story of the November 18 issue of Science Translational Medicine. [Press release] [Science Translational Medicine abstract]
Female Mountain Goats May Be Conflicted over Mate Choice
Mountain goats are no exception to the general rule among mammals that larger males sire more and healthier offspring. But University of Alberta researcher Dr. David Coltman and colleagues have recently found a genetic quirk that might make female mountain goats think twice about their prospective mates. The larger males pass their physical attributes and mating success to their male heirs. But Dr. Coltman’s data shows the daughters of these larger males are routinely smaller and less fit than females produced by physically more modest fathers. Life on the side of a mountain favors bigger, healthier animals, both male and female. Dr. Coltman’s research shows that this anomaly could have implications for female mate choice, because a female that mates with a large, dominant male can expect to have larger sons, but smaller and less fit daughters. The research also poses the question of why female offspring sired by the dominant male would be compromised. Another question the study raises is: what if any consideration does the size of their daughters have for would-be mothers? Could this be a factor weighed by a sexually mature female when courted by males that come in a variety of sizes? This study was featured as the cover story of the November 22 issue of the Proceedings of the Royal Society B. [Press release] [PRS abstract]
Nano “Fly Paper” Captures Metastatic Cancer Cells for Testing
Just as fly paper captures insects, an innovative new device with nano-sized features developed by researchers at UCLA is able to capture cancer cells in the blood that have broken off from a tumor. These cells, known as circulating tumor cells, or CTCs, can provide critical information for examining and diagnosing cancer metastasis, determining patient prognosis, and monitoring the effectiveness of therapies. The current gold standard for examining the disease status of tumors is an analysis of metastatic solid biopsy samples, but in the early stages of metastasis, it is often difficult to identify a biopsy site. By capturing CTCs, doctors can essentially perform a “liquid” biopsy, allowing for early detection and diagnosis, as well as improved treatment monitoring. To date, several methods have been developed to track these cells, but the UCLA team’s novel “fly paper” approach may be faster and cheaper than others, and it appears to capture far more CTCs. The UCLA team developed a 1-by-2-centimeter silicon chip that is covered with densely packed nanopillars and looks like a shag carpet. To test cell-capture performance, researchers incubated the nanopillar chip in a culture medium with breast cancer cells. As a control, they performed a parallel experiment with a cell-capture method that uses a chip with a flat surface. Both structures were coated with anti-EpCAM, an antibody that can help recognize and capture tumor cells. The researchers found that the cell-capture yields for the UCLA nanopillar chip were significantly higher; the device captured 45 to 65 percent of the cancer cells in the medium, compared with only 4 to 14 percent for the flat device. The time required for CTC detection using CellSearch, a technology currently approved by the U.S.