November 19, 2005

Jefferson and Delaware researchers combine tiny nanotubes and antibodies to detect cancer

By coating the surfaces of tiny carbon nanotubes with monoclonal antibodies, biochemists and engineers at Jefferson Medical College and the University of Delaware have teamed up to detect cancer cells in a tiny drop of water The work is aimed at developing nanotube-based biosensors that can spot cancer cells circulating in the blood from a treated tumor that has returned or from a new cancer. The technique has limitations. "We don't know if we can detect more than one antigen at a time on a single cell," Dr. Wickstrom says. Ultimately, the researchers would like to design an assay that can detect cancer cells circulating in the human bloodstream on a hand-held device no bigger than a cell phone.

Researchers find pathways linking caloric restriction to aging process

Researchers at the University of Washington have found a genetic pathway linking nutrient response and the aging process, they report in the Nov. 18 issue of the journal Science. The UW researchers conducted a genome-wide screen of yeast cells to find which genes, and their corresponding proteins, affect lifespan. Two of the proteins, called Tor1 and Sch9, are signaling molecules that are linked to nutrient uptake in many different organisms. Their results suggest that the same proteins, or very similar ones, may be related to both nutrient response and the aging process in humans. After finding ten genes that regulate lifespan, the researchers tested two Tor1 and Sch9 to confirm their connection to caloric restriction. They saw lifespan increases in modified yeast cells that were about the same as a cell that had just the Tor1 mutation, indicating that the mutation was doing the same thing as caloric restriction.

Flipping a single molecule switch: advance towards molecular computers

Researchers from Penn State, Rice University, and the University of Oregon demonstrated that single-molecule switches can be tailored to respond in predictable and stable ways, depending on the direction of the electric field applied to them The research is the latest achievement in the team's ongoing studies of a family of stiff, stringy molecules known as as OPEs--oligo phenylene-ethynylenes--which the scientists have tailored in a number of ways to have a variety of physical, chemical, and electronic characteristics. The potential for using these OPE molecules as switches had been limited by their troublesome tendency to turn on and off at random, but Weiss and his colleagues recently discovered a way to reduce this random switching.

November 18, 2005

IBM creates LED from carbon nanotube with only electrical stimulation

IBM Corp. unveiled Thursday (Nov. 17) what is said is the world's first electroluminescent nanotube transistor and claimed it glows 1,000 times brighter than a light-emitting diode with as much as 10,000 times more photon flux.

By emitting thousands of photons in silicon with the same energy expenditure as one photon in gallium arsenide, IBM predicted that carbon nanotube transistors will lead to integrated optics on silicon chips. According to IBM, integrated optics on silicon chips could lower costs, accelerate electronics and mitigate the need for exotic semiconductors like gallium arsenide. Other research groups have reported light emission by carbon nanotubes stimulated to photoluminescence with a laser. IBM claims its technique uses only electrical stimulation to create an exciton density that is 100-fold larger than photoluminescence in nanotubes.

November 13, 2005

Preview of Molecular nanotech issues: Ordering DNA sequences

YOU might think it would be difficult for a terrorist to obtain genes from the smallpox virus, or a similarly vicious pathogen. Well, it's not. Armed with a fake email address, a would-be bioterrorist could probably order the building blocks of a deadly biological weapon online, and receive them by post within weeks.

That's the sobering reality uncovered by a New Scientist investigation into the bioterror risks posed by the booming business of gene synthesis. Dozens of biotech firms now offer to synthesise complete genes from the chemical components of DNA (See "A dollar a base pair"). Yet some are carrying out next to no checks on what they are being asked to make, or by whom. It raises the frightening prospect of terrorists mail-ordering genes for key bioweapon agents such as smallpox, and using them to engineer new and deadly pathogens.

These loose ordering procedures are even more of a problem when combined with the recent publication of the 1918 flu virus which was critized by Ray Kurzwell and Bill Joy

The combination of loose ordering procedures and loose informational procedures is a bad combination.

Enabling tool: New microscope allows scientists to track a functioning protein with atomic-level precision

A Stanford University research team has designed the first microscope sensitive enough to track the real-time motion of a single protein down to the level of its individual atoms. Writing in the Nov. 13 online issue of the journal Nature, the Stanford researchers explain how the new instrument allowed them to settle long-standing scientific debates about the way genes are copied from DNA--a biochemical process that's essential to life. They obtained measurements accurate to one angstrom, or one-tenth of a nanometer. A distance equivalent to the diameter of a single hydrogen atom, and about 10 times finer than any previous such measurement.

Block team focused on a crucial step in the central dogma [central dogma is that in living organisms, genetic information flows from DNA to RNA to proteins], a process known as "transcription," where each gene is copied from DNA onto RNA. Transcription begins when an enzyme called RNA polymerase (RNAP) latches onto the DNA ladder and pulls a small section apart lengthwise. The RNAP enzyme then builds a new, complementary strand of RNA by chemically copying each base in one of the exposed DNA strands. RNAP continues moving down the DNA strand until the gene is fully copied.

For the Nature experiment, Block and his colleagues used DNA and RNAP extracted from E. coli bacteria, which is remarkably similar to RNAP in more complex organisms, including humans. "RNAP is one of the most important enzymes in nature," Block says. "Without it there would be no RNA messages, no proteins and no life."

In addition to stabilizing the light, the researchers also had to improve the method for detecting force and displacement. Optical force clamps use tiny forces from an infrared laser beam to trap DNA and other molecules. In a conventional force clamp experiment, microscopic beads are attached near the opposite ends of a long DNA molecule--an arrangement that resembles a weight lifter's dumbbell. A single RNAP enzyme attached to the surface of one bead then moves along the DNA and churns out a complementary strand of RNA, drawing the ends of the dumbbell closer together as it advances. The two beads that form the dumbbell are usually held near the center two separate optical traps. But graduate student William Greenleaf discovered that if one of the two beads in the dumbbell was placed near the outer edge of its trap, the force on it would remain constant, allowing angstrom-level measurements to be made quickly and efficiently.

The development of an ultra-stable optical trapping system with angstrom resolution is "a major advance," says Charles Yanofsky, the Morris Herzstein Professor of Biological Sciences at Stanford and a pioneer of modern molecular genetics. The new device is like "adding movies to stills in understanding enzyme action," he says.

"This technical achievement will no doubt lead to new information about the molecular machinery that carries out basic cellular processes, particularly those related to replication, transcription and translation," adds Catherine Lewis, a program director in biophysics at the National Institute of General Medical Sciences (NIGMS).

"If I look in my crystal ball and see where this is going, I think this blows open the field of single-molecule biophysics," Block says. "We have achieved a resolution for a single molecule comparable to what a crystallographer typically achieves in a millimeter-sized crystal, which has 1,000 trillion molecules in it. Not only are we doing all this with one molecule at one-angstrom resolution, we're doing it in real time while the molecule is moving at room temperature in an aqueous solution."

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