5 replies to this topic

[Cyto]

Crystallographers take note: A synchrotron light source for your home lab

A new technological development promises to shed light--synchrotron light, that is--on structural genomics. Crystallographers will soon be able to perform state-of-the-art protein structure determination in their own laboratory with a new miniature synchrotron light source capable of producing high-intensity, tunable, near-monochromatic X-rays. This tabletop device, the Compact Light Source, will soon bring high-flux, high-quality X-rays directly to the university or industrial laboratory--and one day to the hospital or clinic.

Today at the Keystone Symposia on Structural Genomics in Snowbird, Utah, Ronald Ruth, Ph.D., president of Lyncean Technologies, Inc., announced the construction of a tabletop synchrotron light source that will be tested early in 2005. The prototype development is supported by the Protein Structure Initiative of the National Institute of General Medical Sciences (NIGMS) and is based on licensed technology from Stanford Linear Accelerator Center (SLAC).

Unlike the city-block-sized synchrotron radiation sources, the Compact Light Source fits within the footprint of a large desk. The reduction in scale by a factor of 200 is caused by using a laser beam instead of the "undulator" magnets of the large synchrotrons. Making electrons rapidly undulate, or wiggle, causes them to emit a pencil beam of nearly monochromatic X-rays.

"The Compact Light Source will boost scientific productivity by providing high-quality X-ray beams right at the fingertips of researchers in all fields of X-ray science," Ruth said, "but looking ahead, some of the most exciting applications for our source are in health care. New medical imaging techniques that provide exquisite detail of soft tissue are being developed at synchrotron beamlines today. The Compact Light Source will bring these out of the laboratory and into the hospital."

[manofsan]

Hey, I remember this -- it was called Surfatron technology in the article I read.

The idea is to use a laser to excite the electrons in a plasma, and to give them an abbreviated oscillation right around the peak area of their energy state. So instead of rolling the ball all the way up each mountain peak and all the way down into each valley, you just move back and forth across a small zone around the peak. This abbreviated oscillation can be done at higher frequency.

So do a google on "surfatron" and read up -- it's really cool stuff!

[manofsan]

Oh yeah, and I wonder if that ELVES software that someone posted about wouldn't also be compatible with this desktop crystallography revolution. Can you imagine what would happen if one of these Craig Venter types started using this stuff to totally document the Human Proteome?

I read that when Dr Venter first saw the automated sequencing machine, that's when the lightbulb first went on in his head, and he realized the thing could be used to churn thru the entire human genome. And so that's what led him to found Celera, and embark on his own Human Genome Project.

So I'd wonder if a setup like this tabletop crystallography device hooked up to ELVES couldn't do the same for the entire proteome?

I'm imagining a cyberpunk type of future, with underground groups doing their own genemods to themselves, using all this desktop biotech equipment. Sort of like how the shift from mainframes to PCs gave rise to the hacker/cyberpunk culture. There's actually a cool scifi anthology novel by Paul DiFilippo in this vein, called Ribofunk. I really liked the stories and found them to be very cool.

Hehe, then everytime you find a useful protein you want to try out on someone, then just insert its genecode into a biopump graft with a Membrane Translocation Sequence added on to facilitate uptake, and you're in business.

Btw, has anyone considered hooking up Leptin to a Membrane Translocation Sequence, to have it penetrate the cells better? Just a thought.

[Cyto]

I'm posting this here because some time, maybe this summer, we can organize Biotech tools into one catchy post. Overall it is very important to have these advancements coming about now.

Wet scans

The "scanning electron microscope" (SEM) has been a basic research tool for fifty years, and for those fifty years, scientists have been looking for better ways to observe biological samples under its beam. The problem is that the viewing chamber of the SEM must contain a vacuum (in which liquid water in tissues "boils" away). To overcome this difficulty, scientists have had to resort to all sorts of complicated procedures, including coating the specimens with an ultra-fine layer of gold, quick-freezing samples in special deep-freezes, or treating them with drying solvents.
Now, scientists at the Weizmann Institute of Science have found a way to view samples of biological materials in their natural, "wet" state. Their secret lies in the production of a very thin but tough polymer capsule to enclose the sample, allowing it to withstand the force of the vacuum. Says Dr. Ory Zik, who worked on the capsule with Professor Elisha Moses of the Physics of Complex Systems Department: "The material for the capsule is a result of advances in the area of semiconductors. We came across it while researching ways to apply automation techniques used in the semiconductor industry to the life sciences' scanning electron microscopes."

The capsule's polymer is unique in that it is allows the electrons with which a SEM works to pass through unobstructed, giving scientists a clear view of what lies within, without the use of tricky, tissue-distorting procedures. Researchers hope the new method will advance the studies of biological materials, such as the lipids that make up fat, which are easily destroyed by the old sample preparation methods.

[Cyto]

Hopkins scientists overcome main obstacle to making tons of short, drug-like proteins

Two Johns Hopkins scientists have figured out a simple way to make millions upon millions of drug-like peptides quickly and efficiently, overcoming a major hurdle to creating and screening huge "libraries" of these super-short proteins for use in drug development.
"Our work dramatically increases the complexity of peptide libraries that can be created and the speed with which they can be made and processed," says Chuck Merryman, Ph.D., a postdoctoral fellow who developed the new technique. "In an afternoon, we'll be able to make literally millions of millions of different peptides with medicinal potential."

Usually less than 40 building blocks long, peptides act as important messengers and hormones in the body. But because their building blocks, called amino acids, are quickly recycled, peptides made from the 20 naturally occurring amino acids don't last long enough to be useful as medicines. However, adding a tiny methyl group to each amino acid gives the resulting peptide "drug-like" stability.

Writing in the April 19 issue of Chemistry & Biology, the Hopkins scientists reveal that using a simple chemical reaction, first reported in the early 1980s, allows them to convert en masse the naturally occurring amino acids to ones that form more stable peptides.

The tricky part, Merryman says, was figuring out how to do the conversion while the amino acids were attached to transfer RNA, a carrier molecule required for the biological production of peptides. The advance makes it possible to build upwards of 10,000,000,000,000 -- that's 1 with 13 zeros behind it -- stabilized, 10-block-long peptides at once.

"The idea of creating large peptide libraries and testing them for medicinal uses has been around a long time, but until now it's just not been very practical," says Merryman.

A key aspect of all scientists' efforts to create libraries of drug-like peptides is "biology in a dish" -- harnessing the same machinery cells use to read genetic instructions and assemble correct proteins. Since at least the 1970s, scientists have known that this machinery, called the ribosome, also can string together a wide variety of artificial amino acids, as long as the fake building block is tied to transfer RNA that the ribosome can use to "decode" genetic information.

[Cyto]

ORNL’s nanobiosensor technology gives new access to living cell’s molecular processes

Researchers at the Department of Energy's Oak Ridge National Laboratory have developed a nanoscale technology for investigating biomolecular processes in single living cells. The new technology enables researchers to monitor and study cellular signaling networks, including the first observation of programmed cell death in a single live cell.

The "nanobiosensor" allows scientists to physically probe inside a living cell without destroying it. As scientists adopt a systems approach to studying biomolecular processes, the nanobiosensor provides a valuable tool for intracellular studies that have applications ranging from medicine to national security to energy production.

ORNL Corporate Fellow and Life Sciences Division researcher Tuan Vo-Dinh leads a team of researchers who are developing the nanoscale technology. "This research illustrates the integrated ‘nano-bio-info' approach to investigating and understanding these complex cell systems," Vo-Dinh said. "There is a need to explore uncharted territory inside a live cell and analyze the molecular processes. This minimally invasive nanotechnology opens the door to explore the inner world of single cells".

ORNL's work was most recently published in the Journal of the American Chemical Society and has appeared in a feature article of the journal Nature. Members of Vo-Dinh's research team include postdoctoral researchers Paul M. Kasili, Joon Myong Song and research staff biochemist Guy Griffin.

The group's nanobiosensor is a tiny fiber-optic probe that has been drawn to a tip of only 40 nanometers (nm) across—a billionth of a meter and 1,000 times smaller than a human hair. The probe is small enough to be inserted into a cell.

Immobilized at the nanotip is a bioreceptor molecule, such as an antibody, DNA or enzyme that can bind to target molecules of interest inside the cell. Video microscopy experiments reveal the minimally invasive nature of the nanoprobe in that it can be inserted into a cell and withdrawn without destroying it.

Because the 40-nm diameter of the fiber-optic probe is much narrower than the 400-nm wavelength of light, only target molecules bound to the bioreceptors at the tip are exposed to and excited by the evanescent field of a laser signal.

"We detect only the molecules that we target, without all the other background ‘noise' from the myriad other species inside the cell. Only nanoscale fiber-optics technology can provide this capability," said Vo-Dinh.

ORNL's technology gives molecular biologists an important systems biology approach of studying complex systems through the nano-bio-info route. Conventional analytical methods—electron microscopy or introducing dyes, for example—have the disadvantage of being lethal to the cell.

"The information obtained from conventional measurements is an average of thousands or millions of cells," said Vo-Dinh. "When you destroy cells to study them, you can't obtain the dynamic information from the whole live cell system. You get only pieces of information. Nanosensor technology provides a means to preserve a cell and study it over time within the entire cell system."

The ability to work with living cells opens a new path to obtaining basic information critical to understanding the cell's molecular processes. Researchers have a new tool for understanding how toxic agents are transported into cells and how biological pathogens trigger biological responses in the cell.

Vo-Dinh's team recently detected the biochemical components of a cell-signaling pathway, apoptosis. Apoptosis is a key process in an organism's ability to prevent disease such as cancer. This programmed cell-death mechanism causes cells to self-destruct before they can multiply and introduce disease to the organism.

"When a cell in our body receives insults such as toxins or inflammation and is damaged, it kills itself. This is nature's way to limit and stop propagation of many diseases such as cancer," said Vo-Dinh. "For the first time we've seen apoptosis occur within a single living cell."

Apoptosis triggers a host of tell-tale enzyme called caspases. Vo-Dinh's team introduced a light-activated anti-cancer drug into cancer cells. They then inserted the fiberoptic nanoprobe with a biomarker specific for caspase-9 attached to its tip. The presence of caspase-9 caused cleavage of the biomarker from the tip of the nanobiosensor. Changes in the intensity of the biomarker's fluorescence revealed that the light-activated anti-cancer drug had triggered the cell-death machinery.

"The nanobiosensor has many other applications for looking at how cells react when they are treated with a drug or invaded by a biological pathogen. This has important implications ranging from drug therapy development to national security, environmental protection and a better understanding of molecular biology at a systems level," said Vo-Dinh. "This area of research is truly at the nexus of nanotechnology, biology and information technology."