The Data Management Group of the Universitat Politècnica de Catalunya (DAMA-UPC) has designed a system for exploring information on networks or graphs that can complement internet search engines and is of particular interest in areas related to social media, the internet, biomedicine, fraud detection, education and advanced bibliographic searches.
According to Josep Lluís Larriba, director of DAMA-UPC, the technology can be used to extract information from WikiLeaks from two perspectives: one, to obtain generic indicators that provide information on whether the data network has the features of a social network and whether communities of data are created that can provide relevant information; and two, to use the documents hosted on the website to analyze how a topic evolves over time, how a person or a group relates to different topics and how the documents themselves interrelate.
High-speed complex queries
The new DEX technology patented by the UPC can be used to explore large volumes of networked data. The system offers high-speed processing, configurable data entry from multiple sources, and the management of networks with billions of nodes and connections from a desktop PC.
Users can quickly and easily identify interrelated records by formulating queries based on simple values such as names and keywords. Until now, this was possible to a certain extent using database technology, but DEX extracts new information from interrelated data and improves the speed and the capacity to perform complex queries in large data networks.
The DAMA-UPC group, which sees huge potential for the technology in the field of social media and the internet, proposes using the DEX system to analyze data on WikiLeaks, the international media organization that publishes anonymous reports and leaked documents on its website.
From fraud detection to the evolution of cancer
In what was the first major application of DEX, the Notary Certification Agency (ANCERT) used the technology to detect fraud in real estate transactions and the Catalan Institute of Oncology is using it to study the evolution of cancer in Catalonia. The DAMA-UPC group is now looking into how DEX technology can be applied to pharmaceutical data analysis to explore developments in the use of medicines.
The group is also conducting research into how information spreads across the internet and at what speed, and why some news spreads faster than others. The project is developed in the framework of the Social Media project, a strategic industrial research project funded by the National Strategic Consortia for Technical Research (CENIT) program.
In the field of e-learning, the team is working on a project under the RecerCaixa grant program aimed at recommending and exploring audiovisual content for primary and secondary schools.
Exploring scientific information
In addition to the fields of health, fraud detection, education and the internet, the technology created by the DAMA-UPC group also offers benefits to the scientific world.
The group has designed BIBEX (www.dama.upc.edu/bibex), a unique prototype for the Spanish Ministry of Science and Innovation aimed at exploring scientific publications and relating specific literature published worldwide. BIBEX also offers other advantages: scientists can recommend scientific articles and find reviewers to evaluate scientific publications. In the future, BIBEX will offer a tool for businesses to find research groups that are working in common areas of interest.
Technology transfer Sparsity Technologies (www.sparsity-technologies.com) is a spin-off that was created in 2010 with the participation of the UPC to promote and market the technologies developed by the DAMA-UPC group.
If artificial devices could be combined with biological machines, laptops and other electronic devices could get a boost in operating efficiency.
Lawrence Livermore National Laboratory researchers have devised a versatile hybrid platform that uses lipid-coated nanowires to build prototype bionanoelectronic devices.
Mingling biological components in electronic circuits could enhance biosensing and diagnostic tools, advance neural prosthetics such as cochlear implants, and could even increase the efficiency of future computers.
While modern communication devices rely on electric fields and currents to carry the flow of information, biological systems are much more complex. They use an arsenal of membrane receptors, channels and pumps to control signal transduction that is unmatched by even the most powerful computers. For example, conversion of sound waves into nerve impulses is a very complicated process, yet the human ear has no trouble performing it.
“Electronic circuits that use these complex biological components could become much more efficient,” said Aleksandr Noy, the LLNL lead scientist on the project.
While earlier research has attempted to integrate biological systems with microelectronics, none have gotten to the point of seamless material-level incorporation.
“But with the creation of even smaller nanomaterials that are comparable to the size of biological molecules, we can integrate the systems at an even more localized level,” Noy said.
To create the bionanoelectronic platform the LLNL team turned to lipid membranes, which are ubiquitous in biological cells. These membranes form a stable, self-healing,and virtually impenetrable barrier to ions and small molecules.
“That's not to mention that these lipid membranes also can house an unlimited number of protein machines that perform a large number of critical recognition, transport and signal transduction functions in the cell,” said Nipun Misra, a UC Berkeley graduate student and a co-author on the paper.
Julio Martinez, a UC Davis graduate student and another co-author added: “Besides some preliminary work, using lipid membranes in nanoelectronic devices remains virtually untapped.”
The researchers incorporated lipid bilayer membranes into silicon nanowire transistors by covering the nanowire with a continuous lipid bilayer shell that forms a barrier between the nanowire surface and solution species.
“This 'shielded wire' configuration allows us to use membrane pores as the only pathway for the ions to reach the nanowire,” Noy said. “This is how we can use the nanowire device to monitor specific transport and also to control the membrane protein.”
The team showed that by changing the gate voltage of the device, they can open and close the membrane pore electronically.
University of Utah physicists stored information for 112 seconds in what may become the world's tiniest computer memory: magnetic "spins" in the centers or nuclei of atoms. Then the physicists retrieved and read the data electronically -- a big step toward using the new kind of memory for both faster conventional and superfast "quantum" computers.
"The length of spin memory we observed is more than adequate to create memories for computers," says Christoph Boehme (pronounced Boo-meh), an associate professor of physics and senior author of the new study, published Friday, Dec. 17 in the journal Science. "It's a completely new way of storing and reading information."
However, some big technical hurdles remain: the nuclear spin storage-and-read-out apparatus works only at 3.2 degrees Kelvin, or slightly above absolute zero -- the temperature at which atoms almost freeze to a standstill, and only can jiggle a little bit. And the apparatus must be surrounded by powerful magnetic fields roughly 200,000 times stronger than Earth's.
"Yes, you could immediately build a memory chip this way, but do you want a computer that has to be operated at 454 degrees below zero Fahrenheit and in a big national magnetic laboratory environment?" Boehme says. "First we want to learn how to do it at higher temperatures, which are more practical for a device, and without these strong magnetic fields to align the spins."
As for obtaining an electrical readout of data held within atomic nuclei, "nobody has done this before," he adds.
Two years ago, another group of scientists reported storing so-called quantum data for two seconds within atomic nuclei, but they did not read it electronically, as Boehme and colleagues did in the new study, which used classical data (0 or 1) rather than quantum data (0 and 1 simultaneously). The technique was developed in a 2006 study by Boehme, who showed it was feasible to read data stored in the net magnetic spin of 10,000 electrons in phosphorus atoms embedded in a silicon semiconductor.
The new study puts together nuclear storage of data with an electrical readout of that data, and "that's what's new," Boehme says.
The study was led by Boehme and first author Dane McCamey, a former research assistant professor of physics at the University of Utah and still an adjunct assistant professor. His main affiliation now is with the University of Sydney. Other co-authors were Hans van Tol of the National High Magnetic Field Laboratory in Tallahassee, Fla., and Gavin Morley of University College London.
The study was funded by the National High Magnetic Field Laboratory, the National Science Foundation, the Australian Research Council, Britain's Engineering and Physical Sciences Research Council and the Royal Commission for the Exhibition of 1851, a British funding agency led by Prince Philip.
Of Electronic and Spintronic Memories
Modern computers are electronic, meaning that information is processed and stored by flowing electricity in the form of electrons, which are negatively charged subatomic particles that orbit the nucleus of each atom. Transistors in computers are electrical switches that store data as "bits" in which "off" (no electrical charge) and "on" (charge is present) represent one bit of information: either 0 or 1.
Quantum computers -- a yet-unrealized goal -- would run on the odd principles of quantum mechanics, in which the smallest particles of light and matter can be in different places at the same time. In a quantum computer, one quantum bit or "qubit" could be both 0 and 1 at the same time. That means quantum computers theoretically could be billions of times faster than conventional computers.
McCamey says a memory made of silicon "doped" with phosphorus atoms could be used in both conventional electronic computers and in quantum computers in which data is stored not by "on" or "off" electrical charges, but by "up" or "down" magnetic spins in the nuclei of phosphorus atoms.
Externally applied electric fields would be used to read and process the data stored as "spins" -- just what McCamey, Boehme and colleagues did in their latest study. By demonstrating an ability to read data stored in nuclear spins, the physicists took a key step in linking spin to conventional electronics -- a field called spintronics.
Spin is an unfamiliar concept to comprehend. A simplified way to describe spin is to imagine that each particle -- like an electron or proton in an atom -- contains a tiny bar magnet, like a compass needle, that points either up or down to represent the particle's spin. Down and up can represent 0 and 1 in a spin-based quantum computer.
Boehme says the spins of atoms' nuclei are better for storing information than the spin of electrons. That's because electron spin orientations have short lifetimes because spins are easily changed by nearby electrons and the temperature within atoms.
In contrast, "the nucleus sits in the middle of an atom and its spin isn't messed with by what's going on in the clouds of electrons around the nucleus," McCamey says. "Nuclei experience nearly perfect solitude. That's why nuclei are a good place to store information magnetically. Nuclear spins where we store information have extremely long storage times before the information decays."
The average 112 second storage time in the new study may not seem long, but Boehme says the dynamic random access memory (DRAM) in a modern PC or laptop stores information for just milliseconds (thousandths of a second). The information must be repeatedly refreshed, which is how computer memory is maintained, he adds.
How to Store and Then Read Data in the Spins of Atomic Nuclei
For the experiments, McCamey, Boehme and colleagues used a thin, phosphorus-doped silicon wafer measuring 1 millimeter square, and placed electrical contacts on it. The device was inside a supercold container, and surrounded by intense magnetic fields. Wires connected the device to a current source and an oscilloscope to record data.
The physicists used powerful magnetic fields of 8.59 Tesla to align the spins of phosphorus electrons. That's 200,000 times stronger than Earth's magnetic field.
Then, pulses of near-terahertz electromagnetic waves were used to "write" up or down spins onto electrons orbiting phosphorus atoms. Next, FM-range radio waves were used to take the spin data stored in the electrons and write it onto the phosphorus nuclei.
Later, other pulses of near-terahertz waves were used to transfer the nuclear spin information back into the orbiting electrons, and trigger the readout process. The readout is produced because the electrons' spins are converted into variations in electrical current.
"We read the spin of the nuclei in the reverse of the way we write information," Boehme says. "We have a mechanism that turns electron spin into a current."
Summarizing the process, Boehme says, "We basically wrote 1 in atoms' nuclei. We have shown we can write and read [spin data in nuclei]," and shown that the information can be repeatedly read from the nuclei for an average of 112 seconds before all the phosphorus nuclei lose their spin information. In a much shorter time, the physicists read and reread the same nuclear spin data 2,000 times, showing the act of reading the spin data doesn't destroy it, making the memory reliable, Boehme says.
Reading out the data stored as spin involved reading the collective spins of a large number of nuclei and electrons, Boehme says. That will work for classical computers, but not for quantum computers, for which readouts must be able to discern the spins of single nuclei, he adds. Boehme hopes that can be achieved within a few years.
A nomogram, nomograph, or abac is a graphical calculating device, a two-dimensional diagram designed to allow the approximate graphical computation of a function: it uses a coordinate system other than Cartesian coordinates. Defining alternatively, a nomogram is a (two-dimensionally) plotted function with n parameters, from which, knowing n-1 parameters, the unknown one can be read, or fixing some parameters, the relationship between the unfixed ones can be studied. Like a slide rule, it is a graphical analog computation device; and, like the slide rule, its accuracy is limited by the precision with which physical markings can be drawn, reproduced, viewed, and aligned. Most nomograms are used in applications where an approximate answer is appropriate and useful. Otherwise, the nomogram may be used to check an answer obtained from an exact calculation method.
The slide rule is intended to be a general-purpose device. Nomograms are usually designed to perform a specific calculation, with tables of values effectively built in to the construction of the scales.
The weather satellite is a type of satellite that is primarily used to monitor the weather and climate of the Earth. Satellites can be either polar orbiting, seeing the same swath of the Earth every 12 hours, or geostationary, hovering over the same spot on Earth by orbiting over the equator while moving at the speed of the Earth's rotation.[1] These meteorological satellites, however, see more than clouds and cloud systems. City lights, fires, effects of pollution, auroras, sand and dust storms, snow cover, ice mapping, boundaries of ocean currents, energy flows, etc., and other types of environmental information are collected using weather satellites. Weather satellite images helped in monitoring the volcanic ash cloud from Mount St. Helens and activity from other volcanoes such as Mount Etna.[2] Smoke from fires in the western United States such as Colorado and Utah have also been monitored.
weather satellite using NASA's Chandra X-ray Observatory have found evidence of the youngest black hole known to exist in our cosmic neighborhood. The 30-year-old black hole provides a unique opportunity to watch this type of object develop from infancy.
Not even light can escape a black hole's grip, but gas falling into a black hole can heat up and become an intense source of X-rays, at temperatures up to 1,000 times hotter than the sun. Astronomers use the Chandra X-Ray Observatory -- a NASA satellite -- to map these X-ray sources and study their properties
Scientists have found evidence that a giant black hole has been jerked around twice, causing its spin axis to point in a different direction from before. This discovery, made with new data from NASA's Chandra X-ray Observatory, might explain several mysterious-looking objects found throughout the Universe.
One of the requirements to keep trends in computer technology on track -- to be ever faster, smaller, and more energy-efficient -- is faster writing and processing of data. In the Dec. 17 issue of the journal Science, physicists at the Technische Universitaet Muenchen (TUM) and the Universitaet zu Koeln report results that could point the way to a solution. TUM physicists set a lattice of magnetic vortices in a material in motion using electric curSetting a lattice of magnetic vortices in motion using electric current almost a million times weaker than in earlier studies, physicists observed the coupling between electric current and magnetic structure -- through measurements at the research neutron source FRM II in Garching, Germany.
While Peter Gruenberg and Albert Fert were awarded the Nobel Prize in 2007 for research that led to significantly faster reading of data, in the past few years scientists have been concentrating on how magnetic information can be directly written to media using electric current. So far, the problem with this kind of work has been the need for extremely high currents, whose side effects are nearly impossible to rein in, even in nanostructures.
A little over a year ago, Professor Christian Pfleiderer and his team at the Physics Department of the TUM discovered an entirely new magnetic structure in a crystal of manganese silicon -- a lattice of magnetic vortices. The experiments in Garching were spurred by the theoretical forecasts of Professor Achim Rosch at the Universitaet zu Koeln and Professor Rembert Duine from the Universiteit Utrecht. They were expecting new results in the field of so-called spintronics, nanoelectronic elements that use not only the electric charge of electrons to process information, but also their magnetic moment, or spin.
Christian Pfleiderer's team of scientists sent electric current through the manganese silicon. Using neutrons from FRM II, they were able to observe a twist in the magnetic vortex lattice, which they could not explain initially. More interesting than the twist was the newly discovered magnetic lattice.
In the next step, Christian Pfleiderer and his team made further measurements at the MIRA instrument of the neutron source FRM II in an attempt to determine why the lattice twisted when a current was applied. At first, the calculations of the theoreticians contradicted the results of the experiments in Garching. "The magnetic structure twists, because the direction of the electric current is deflected extremely efficiently by quantum mechanical effects," explains Christian Pfleiderer. When an electron flies through the magnetic vortex, the electron's spin reacts to the vortex (see animation). In this way the electric current exerts a force on the magnetic vortices, which eventually begin to flow.
After further measurements, the team of Christian Pfleiderer and Achim Rosch was able to establish that the newly discovered lattice of magnetic vortices displays properties that have been of interest in nanotechnology for quite some time. They are, among other things, relevant to the development of new data storage systems.
Notably, the magnetic vortices are very stable and at the same time very weakly anchored in the material, so that even the weakest of electric currents can lead to movement. This should allow data to be written and processed considerably faster and more efficiently in the future.
rent almost a million times weaker than in earlier studies.
In a new Cognitive Robotics Lab, students at Rensselaer are exploring how human thought outwits brute force computing in the real world. The lab's 20 programmable robots allow students to test the real-world performance of computer models that mimic human thought.
"The real world has a lot of inconsistency that humans handle almost without noticing -- for example, we walk on uneven terrain, we see in shifting light," said Professor Vladislav Daniel Veksler, who is currently teaching Cognitive Robotics. "With robots, we can see the problems humans face when navigating their environment."
Cognitive Robotics marries the study of cognitive science -- how the brain represents and transforms information -- with the challenges of a physical environment. Advances in cognitive robotics transfer to artificial intelligence, which seeks to develop more efficient computer systems patterned on the versatility of human thought.
Professor Bram Van Heuveln, who organized the lab, said cognitive scientists have developed a suite of elements -- perception/action, planning, reasoning, memory, decision-making -- that are believed to constitute human thought. When properly modeled and connected, those elements are capable of solving complex problems without the raw power required by precise mathematical computations.
"Suppose we wanted to build a robot to catch fly balls in an outfield. There are two approaches: one uses a lot of calculations -- Newton's law, mechanics, trigonometry, calculus -- to get the robot to be in the right spot at the right time," said Van Heuveln. "But that's not the way humans do it. We just keep moving toward the ball. It's a very simple solution that doesn't involve a lot of computation but it gets the job done."
Robotics are an ideal testing ground for that principle because robots act in the real world, and a correct cognitive solution will withstand the unexpected variables presented by the real world.
"The physical world can help us to drive science because it's different from any simulated world we could come up with -- the camera shakes, the motors slip, there's friction, the light changes," Veksler said. "This platform -- robotics -- allows us to see that you can't rely on calculations. You have to be adaptive."
The lab is open to all students at Rensselaer. In its first semester, the lab has largely attracted computer science and cognitive science students enrolled in a Cognitive Robotics course taught by Veksler, but Veksler and Van Heuveln hope it will attract more engineering and art students as word of the facility spreads.
"We want different students together in one space -- a place where we can bring the different disciplines and perspectives together," said Van Heuveln. "I would like students to use this space for independent research: they come up with the research project, they say 'let's look at this.'"
The lab is equipped with five "Create" robots -- essentially a Roomba robotic vacuum cleaner paired with a laptop; three hand-eye systems; one Chiara (which looks like a large metal crab); and 10 LEGO robots paired with the Sony Handy Board robotic controller.
On a recent day, Jacqui Brunelli and Benno Lee were working on their robot "cat" and "mouse" pair, which try to chase and evade each other respectively; Shane Reilly was improving the computer "vision" of his robotic arm; and Ben Ball was programming his robot to maintain a fixed distance from a pink object waved in front of its "eye."
"The thing that I've learned is that the sensor data isn't exact -- what it 'sees' constantly changes by a few pixels -- and to try to go by that isn't going to work," said Ball, a junior and student of computer science and physics.
Ball said he is trying to pattern his robot on a more human approach.
"We don't just look at an object and walk toward it. We check our position, adjusting our course," Ball said. "I need to devise an iterative approach where the robot looks at something, then moves, then looks again to check its results."
The work of the students, who program their robots with the Tekkotsu open-source software, could be applied in future projects, said Van Heuveln.
"As a cognitive scientist, I want this to be built on elements that are cognitively plausible and that are recyclable -- parts of cognition that I can apply to other solutions as well," said Van Heuveln. "To me, that's a heck of a lot more interesting than the computational solution."
In a generic domain, their early investigations clearly show how a more cognitive approach employing limited resources can easily outpace more powerful computers using a brute force approach, said Veksler.
"We look to humans not just because we want to simulate what we do, which is an interesting problem in itself, but also because we're smart," said Veksler. "Some of the things we have, like limited working memory -- which may seem like a bad thing -- are actually optimal for solving problems in our environment. If you remembered everything, how would you know what's important?"
A team of UCSF researchers has engineered E. coli with the key molecular circuitry that will enable genetic engineers to program cells to communicate and perform computations.
The work builds into cells the same logic gates found in electronic computers and creates a method to create circuits by "rewiring" communications between cells. This system can be harnessed to turn cells into miniature computers, according to findings reported in the journal Nature.
That, in turn, will enable cells to be programmed with more intricate functions for a variety of purposes, including agriculture and the production of pharmaceuticals, materials and industrial chemicals, according to Christopher A. Voigt, PhD, a synthetic biologist and associate professor in the UCSF School of Pharmacy's Department of Pharmaceutical Chemistry who is senior author of the paper.
The most common electronic computers are digital, he explained; that is, they apply logic operations to streams of 1's and 0's to produce more complex functions, ultimately producing the software with which most people are familiar. These logic operations are the basis for cellular computation, as well.
"We think of electronic currents as doing computation, but any substrate can act like a computer, including gears, pipes of water, and cells," Voigt said. "Here, we've taken a colony of bacteria that are receiving two chemical signals from their neighbors, and have created the same logic gates that form the basis of silicon computing."
Applying this to biology will enable researchers to move beyond trying to understand how the myriad parts of cells work at the molecular level, to actually use those cells to perform targeted functions, according to Mary Anne Koda-Kimble, dean of the UCSF School of Pharmacy.
"This field will be transformative in how we harness biology for biomedical advances," said Koda-Kimble, who championed Voigt's recruitment to lead this field at UCSF in 2003. "It's an amazing and exciting relationship to watch cellular systems and synthetic biology unfold before our eyes."
The Nature paper describes how the Voigt team built simple logic gates out of genes and inserted them into separate E. coli strains. The gate controls the release and sensing of a chemical signal, which allows the gates to be connected among bacteria much the way electrical gates would be on a circuit board.
"The purpose of programming cells is not to have them overtake electronic computers," explained Voigt, whom Scientist magazine named a "scientist to watch" in 2007 and whose work is included among the Scientist's Top 10 Innovations of 2009. "Rather, it is to be able to access all of the things that biology can do in a reliable, programmable way."
The research already has formed the basis of an industry partnership with Life Technologies, in Carlsbad, Cal., in which the genetic circuits and design algorithms developed at UCSF will be integrated into a professional software package as a tool for genetic engineers, much as computer-aided design is used in architecture and the development of advanced computer chips.
The automation of these complex operations and design choices will advance basic and applied research in synthetic biology. In the future, Voigt said the goal is to be able to program cells using a formal language that is similar to the programming languages currently used to write computer code.
The lead author of the paper is Alvin Tamsir, a student in the Biochemistry & Molecular Biology, Cell Biology, Developmental Biology, and Genetics (Tetrad) Graduate Program at UCSF. Jeffrey J. Tabor, PhD, in the UCSF School of Pharmacy, is a co-author.
The promise of quantum computing is that it will dramatically outshine traditional computers in tackling certain key problems: searching large databases, factoring large numbers, creating uncrackable codes and simulating the atomic structure of materials.
A quantum step in that direction, if you'll pardon the pun, has been taken by Stanford researchers who announced their success in a paper published in the journal Nature. Working in the Ginzton Laboratory, they've employed ultrafast lasers to set a new speed record for the time it takes to rotate the spin of an individual electron and confirm the spin's new position.
Why does that matter? Existing computers, from laptops to supercomputers, see data as bits of information. Each bit can be either a zero or a one. But a quantum bit can be both zero and one at the same time, a situation known as a superposition state. This allows quantum computers to act like a massively parallel computer in some circumstances, solving problems that are almost impossible for classic computers to handle.
Quantum computing can be accomplished using a property of electrons known as "spin." A single unit of quantum information is the qubit, and can be constructed from a single electron spin, which in this experiment was confined within a nano-sized semiconductor known as a quantum dot.
An electron spin may be described as up or down (a variation of the usual zero and one) and may be manipulated from one state to another. The faster these electrons can be switched, the more quickly numbers can be crunched in a quantum fashion, with its intrinsic advantages over traditional computing designs.
The qubit in the Stanford experiment was manipulated and measured about 100 times faster than with previous techniques, said one of the researchers, David Press, a graduate student in applied physics.
The experiments were conducted at a temperature of almost absolute zero, inside a strong magnetic field produced by a superconducting magnet. The researchers first hit the qubit with laser light of specific frequencies to define and measure the electron spin, all within a few nanoseconds. Then they rotated the spin with polarized light pulses in a few tens of picoseconds (a picosecond is one trillionth of a second). Finally, the spin state was read out with yet another optical pulse.
Similar experiments have been done before, but with radio-frequency pulses, which are slower than laser-light pulses. "The optics were quite tricky," Press said. The researchers had to find a single, specific photon emitted from the qubit in order confirm the spin state of the electron. That photon, however, was clouded in a sea of scattered photons from the lasers themselves.
"The big benefit is to make quantum computing faster," Press said. The experiment "pushed quantum dots up to speed with other qubit candidate systems to ultimately build a quantum computer."
Quantum computers are still years away. In the shorter term, Press said, researchers would like to build a system of tens or hundreds of qubits to simulate the operation of a larger quantum system.
The other authors of the Nature paper were Bingyang Zhang of the Ginzton Lab, and Thaddeus Ladd and Yoshihisa Yamamoto of the Ginzton Lab and the National Institute of Informatics in Tokyo.
Humans have long taken advantage of the huge variety of medicinal compounds produced by plants. Now MIT chemists have found a new way to expand plants' pharmaceutical repertoire by genetically engineering them to produce unnatural variants of their usual products.
The researchers, led by Associate Professor Sarah O'Connor, have added bacterial genes to the periwinkle plant, enabling it to attach halogens such as chlorine or bromine to a class of compounds called alkaloids that the plant normally produces. Many alkaloids have pharmaceutical properties, and halogens, which are often added to antibiotics and other drugs, can make medicines more effective or last longer in the body.
The team's primary target, an alkaloid called vinblastine, is commonly used to treat cancers such as Hodgkin's lymphoma. O'Connor sees vinblastine and other drugs made by plants as scaffolds that she can modify in a variety of ways to enhance their effectiveness.
"We're trying to use plant biosynthetic mechanisms to easily make a whole range of different iterations of natural products," she said. "If you tweak the structure of natural products, very often you get different or improved biological and pharmacological activity."
O'Connor, graduate student Weerawat Runguphan and former postdoctoral associate Xudong Qu describe their engineered periwinkle plants in the Nov. 3 online edition of Nature. The research was funded by the National Institutes of Health and the American Cancer Society.
Engineering new genes into plants has been done before: In the 1990s, scientists developed corn that could produce an insecticide called Bt, which comes from a bacterial gene. However, O'Connor's approach, known as metabolic engineering, goes beyond simply adding a gene that codes for a novel protein. Metabolic engineers tinker with the series of reactions that the host organisms use to build new molecules, adding genes for new enzymes that reshape these natural synthetic pathways. This can lead to a huge variety of end products.
Most metabolic engineers use bacteria as their host organism, in part because their genes are easier to manipulate. O'Connor's work with plants makes her a rare exception. She doesn't believe one approach is better than the other, but one factor that drew her to engineer plants is that most plant synthetic pathways have not been completely revealed. "You can't reconstitute a whole plant pathway in bacteria unless you have all the genes," she said.
In previous experiments, O'Connor and her students induced periwinkle root cells to create novel compounds by feeding them slightly altered versions of their usual starting materials. In the new study, they engineered the cells to express genes that code for enzymes that attach chlorine or bromine to vinblastine precursors and other alkaloids.
The two new genes came from bacteria that naturally produce halogenated compounds. It's much more rare for plants to generate such compounds on their own, said O'Connor. It is also possible, though very difficult, to synthesize halogenated alkaloids in a laboratory.
To make alkaloids, plants first convert an amino acid called tryptophan into tryptamine. After that initial step, about a dozen more reactions are required, and the plants can produce hundreds of different final products. In the new genetically engineered plants, a bacterial enzyme called halogenase attaches a chlorine (or bromine) atom to tryptamine. That halogen stays on the molecule throughout the synthesis.
In future work, the researchers hope to engineer full periwinkle plants to produce the novel compounds. They are also working on improving the overall yield of the synthesis, which is about 15 fold lower than the plant's yield of naturally occurring alkaloids. One way to do that is to introduce the halogen further along in the process, said O'Connor.
