How dinosaurs put proteins into long-term storage

How does one prove that the protein isolated from a 68-million-year-old dinosaur bone is not a contamination from the intervening millenia or from the lab?

This is the task of a research team who say they have isolated peptides of the common structural protein, collagen, from bones of Tyrannosaurus rex and Brachylophosauraus canadensis.

Although the team had previously presented multiple lines of evidence supporting the veracity of the find, the fact that the age of the peptides far exceeds any previous predictions of how long a protein could resist degradation has generated controversy.

In their current work, the researchers used x-ray diffraction data collected utilizing the Bio-CAT 18-ID x-ray beamline at the U.S. Department of Energy Office of Science’s Advanced Photon Source at Argonne National Laboratory to generate a model of collagen structure on which to overlay the location of the putative dinosaur peptides.

The results provide support for a model in which the dinosaur peptides were protected from degradation due to their location within the collagen fibril. This is important evidence supporting the ancient origin of the peptides and the mechanism by which they were preserved. In addition, this new knowledge of collagen structure could be used in the design of highly stable collagenous scaffolds to promote bone and tissue regeneration in humans.

Collagen is a common structural protein found in animals. It makes up about 25% of the human body and is a major component of tendons, ligaments, skin, and bone. Collagen literally holds the body together and its high tensile strength is attributed to its fibrillar structure. Recent evidence has shown that the collagen fibril is made up of microfibrillar units. Three polypeptides wind into a triple helical structure to form a collagen molecule. Five collagen molecules twist around each other to make microfibrils which then pack next to each other to form larger characteristic collagen fibrils. The amino acid sequence of collagen is highly conserved, so it is possible to compare peptides from diverse and ancient species.

To explain the remarkable durability of dinosaur collagen, the researchers from Orthovita Inc., North Carolina State University, Montana State University, the University of Pennsylvania, the Beth Israel Deaconess Medical Center and Harvard Medical School, the Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology,The University of Manchester, Manchester, The University of York, York, and the Illinois Institute of Technology (IIT) hypothesized that areas of the protein deeply within the complex fibrillar structure might be preferentially protected from degradation.

To test this, they set out to create a model on which to map specific amino acid sequences along and within the collagen fibril to see where their dinosaur peptides matched up. This was achieved by using x-ray diffraction data from the rat tendon collagen I microfibril and fibril in situ collected at the Bio-CAT beamline to construct a model showing the orientation of the molecules of the triple helix within the microfibril.

According to research team leader Joseph Orgel of IIT, “The approach of our team over the last decade has been to study the structure of collagen in its context, as fibrils located within intact tissue samples. By far our most important work has been in developing the x-ray diffraction techniques and facilities [at BioCAT] to allow us to understand collagen structure in situ. Without this understanding, we would not have been able to perform the analysis undertaken in this recent work.”

Using this approach, the team was able identify the location of collagen sequences that are known to interact with other molecules and those which would be expected to be protected in the interior of the fibrillar structure. Sequencing and mapping of 11 dinosaur peptides that represented 8 sequences revealed that the dinosaur sequences were from regions of the protein that were partly protected by molecular packing. This localization could be responsible for protecting the peptides over the millenia.

Further comparison of the sequences to human collagen provided other clues to how these particular peptides might have been preserved. First, there were very few acidic residues found in five of the sequences, meaning their hydrophobic nature would limit their solubility and availability for degradation. Also, few of the peptides represented regions of collagen containing sites targeted by breakdown enzymes and none of them were from the most unstable region of the protein. These features provide hard biochemical evidence for why these particular peptides endured for such a long time.

Does this work satisfy the skeptics? Not yet, but having a new mechanism for how ancient proteins might be preserved is a dinosaur-sized step in the right direction.

More information: James D. San Antonio, et al., “Dinosaur Peptides Suggest Mechanisms of Protein Survival,” PLoS ONE 6(6), e20381 (June 2011). DOI:10.1371/journal.pone.0020381

Provided by Argonne National Laboratory (news : web)

Got flow cytometry? All you need is five bucks and a cell phone

Flow cytometry, a technique for counting and examining cells, bacteria and other microscopic particles, is used routinely in diagnosing disorders, infections and cancers and evaluating the progression of HIV and AIDS. But flow cytometers are big, bulky contraptions that cost tens of thousands of dollars, making them less than ideal for health care in the field or other settings where resources are limited.

Now imagine you could achieve the same results using a device that weighs about half an ounce and costs less than five dollars.

Researchers at the BioPhotonics Laboratory at the UCLA Henry Samueli School of Engineering and Applied Science have developed a compact, lightweight and cost-effective optofluidic platform that integrates imaging cytometry and florescent microscopy and can be attached to a cell phone. The resulting device can be used to rapidly image bodily fluids for cell counts or cell analysis.

The research, which was led by Aydogan Ozcan, a professor of electrical engineering and bioengineering and a member of the California NanoSystems Institute at UCLA, is currently available online in the journal Analytical Chemistry.

"In this work, we developed a cell phone–based imaging cytometry device with a very simple optical design, which is very cost-effective and easy to operate," said Hongying Zhu, a UCLA Engineering postdoctoral scholar at the BioPhotonics Lab and co-author of the research. "It has great potential to be used in resource-limited regions to help people there improve the quality of their health care."

The device is the latest advance by Ozcan's research team, which has developed a number of innovative, scaled-down, cell phone–based technologies that have the potential to transform global health care.

"We have more than 5 billion cell phone subscribers around the world today, and because of this, cell phones can now play a central role in telemedicine applications," Ozcan said. "Our research group has already created a very nice set of tools, including cell phone microscopes, that can potentially replace most of the advanced instruments used currently in laboratories."

How it works

Ozcan's group integrated compact optical attachments to create the optofluidic fluorescent cytometry platform. The platform, which weighs only 18 grams, includes:
1 simple lens (less than $3)
1 plastic color filter (less than $1)
2 LEDs (less than 30 cents each)
Simple batteries The microfluidic assembly is placed just above a separate, inexpensive lens that is put in contact with the cell phone's existing camera unit. This way, the entire cross-section of the microfluidic device can be mapped onto the phone's CMOS sensor-chip. The sample fluid is delivered continuously through a disposable microfluidic channel via a syringe pump.

The device is illuminated from the side by the LEDs using a simple butt-coupling technique. The excitation light is then guided within the cross-section of the device, uniformly exciting the specimens in the imaging fluid. The optofluidic pumping scheme also allows for the use of an inexpensive plastic absorption filter to create the dark-field background needed for fluorescent imaging.

In addition, video post-processing and contour-detection and tracking algorithms are used to count and label the cells or particles passing through the microfluidic chip.

In order to demonstrate proof-of-concept for the new platform, the team used the device to measure the density of white blood cells in human whole-blood samples, as white blood cell density is routinely tested to diagnosis various diseases and infections, including leukemia, HIV and bone marrow deficiencies.

"For the next step, we'd like to explore other potential applications of this device," Zhu said. "For example, we also want to utilize this device to count potential waterborne parasites for water-quality monitoring."

"We'd like to translate our devices for testing in the field and start using them in places they're supposed to be used," Ozcan said. "So I think the next stage for several of our technologies, including this one, is to deploy and test them in extremely poor-resource countries."

Provided by University of California - Los Angeles

Startling new truth about sugar

Flying in the face of years of scientific belief, University of Illinois researchers have demonstrated that sugar doesn't melt, it decomposes.

"This discovery is important to food scientists and candy lovers because it will give them yummier caramel flavors and more tantalizing textures. It even gives the pharmaceutical industry a way to improve excipients, the proverbial spoonful of sugar that helps your medicine go down," said Shelly J. Schmidt, a University of Illinois professor of food chemistry.

In a presentation to the Institute of Food Technologists about the importance of the new discovery, Schmidt told the food scientists they could use the new findings to manipulate sugars and improve their products' flavor and consistency.

"Certain flavor compounds give you a nice caramel flavor, whereas others give you a burnt or bitter taste. Food scientists will now be able to make more of the desirable flavors because they won't have to heat to a 'melting' temperature but can instead hold sugar over a low temperature for a longer period of time," she said.

Candy makers will be able to use a predictable time-temperature relationship, as the dairy industry does in milk pasteurization, to achieve better results, she said.

Schmidt and graduate student Joo Won Lee didn't intend to turn an established rule of food science on its head. But they began to suspect that something was amiss when they couldn't get a constant melting point for sucrose in the work that they were doing.

"In the literature, the melting point for sucrose varies widely, but scientists have always blamed these differences on impurities and instrumentation differences. However, there are certain things you'd expect to see if those factors were causing the variations, and we weren't seeing them," Schmidt said.

The scientists determined that the melting point of sugar was heating-rate dependent.

"We saw different results depending on how quickly we heated the sucrose. That led us to believe that molecules were beginning to break down as part of a kinetic process," she said.

Schmidt said a true or thermodynamic melting material, which melts at a consistent, repeatable temperature, retains its chemical identity when transitioning from the solid to the liquid state. She and Lee used high-performance liquid chromatography to see if sucrose was sucrose both before and after "melting." It wasn't.

"As soon as we detected melting, decomposition components of sucrose started showing up," she said.

To distinguish "melting" caused by decomposition from thermodynamic melting, the researchers have coined a new name -- "apparent melting." Schmidt and her colleagues have shown that glucose and fructose are also apparent melting materials.

Another of Schmidt's doctoral students is investigating which other food and pharmaceutical materials are apparent melters. She says the list is growing every day.

Having disposed of one food science mystery, Schmidt plans to devote time to others. For instance, staling intrigues her. "We could ship a lot more food around the world if we could stabilize it, keep it from getting stale," she said.

Or there's hydrate formation, which can make drink mixes clumpy if they're open for a while. "We've observed the results -- clumping under conditions of low relative humidity -- but we really don't know why it happens," she noted.

Schmidt said that new instruments are making it possible to probe some of the processes scientists have taken for granted in a way they couldn't do before.

Four studies describing Schmidt's research have been published in recent issues of the Journal of Agricultural and Food Chemistry. Co-authors of the first, third, and fourth articles are Joo Won Lee of the U of I and Leonard C. Thomas of DSC Solutions. Joo Won Lee, John Jerrell, Hao Feng, and Keith Cadwallader, all of the U of I, and Leonard C. Thomas of DSC Solutions co-authored the second article.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by University of Illinois College of Agricultural, Consumer and Environmental Sciences. The original article was written by Phyllis Picklesimer.

Journal Reference:

Joo Won Lee, Leonard C. Thomas, Shelly J. Schmidt. Can the Thermodynamic Melting Temperature of Sucrose, Glucose, and Fructose Be Measured Using Rapid-Scanning Differential Scanning Calorimetry (DSC)? Journal of Agricultural and Food Chemistry, 2011; 59 (7): 3306 DOI: 10.1021/jf104852u

Self-healing, self-cooling, metamaterials: Vascular composites enable dynamic structural materials

Taking their cue from biological circulatory systems, University of Illinois researchers have developed vascularized structural composites, creating materials that are lightweight and strong with potential for self-healing, self-cooling, metamaterials and more.

"We can make a material now that's truly multifunctional by simply circulating fluids that do different things within the same material system," said Scott White, the Willet Professor of aerospace engineering who led the group. "We have a vascularized structural material that can do almost anything."

Composite materials are a combination of two or more materials that harness the properties of both. Composites are valued as structural materials because they can be lightweight and strong. Many composites are fiber-reinforced, made of a network of woven fibers embedded in resin -- for example, graphite, fiberglass or Kevlar.

The Illinois team, part of the Autonomous Materials Systems Laboratory in the Beckman Institute for Advanced Science and Technology, developed a method of making fiber-reinforced composites with tiny channels for liquid or gas transport. The channels could wind through the material in one long line or branch out to form a network of capillaries, much like the vascular network in a tree.

"Trees are incredible structural materials, but they're dynamic too," said co-author Jeffrey Moore, the Murchison-Mallory professor of chemistry and a professor of materials science and engineering. "They can pump fluids, transfer mass and energy from the roots to the leaves. This is the first step to making synthetic materials that have that kind of functionality."

The key to the method, published in the journal Advanced Materials, is the use of sacrificial fibers. The team treated commercially available fibers so that they would degrade at high temperatures. The sacrificial fibers are no different from normal fibers during weaving and composite fabrication. But when the temperature is raised further, the treated fibers vaporize -- leaving tiny channels in their place -- without affecting the structural composite material itself.

"There have been vascular materials fabricated previously, including things that we've done, but this paper demonstrated that you can approach the manufacturing with a concept that is vastly superior in terms of scalability and commercial viability," White said.

In the paper, the researchers demonstrate four classes of application by circulating different fluids through a vascular composite: temperature regulation, chemistry, conductivity and electromagnetism. They regulate temperature by circulating coolant or a hot fluid. To demonstrate a chemical reaction, they injected chemicals into different vascular branches that merged, mixing the chemicals to produce a luminescent reaction. They made the structure electrically active by using conductive liquid, and changed its electromagnetic signature with ferrofluids -- a key property for stealth applications.

Next, the researchers hope to develop interconnected networks with membranes between neighboring channels to control transport between channels. Such networks would enable many chemical and energy applications, such as self-healing polymers or fuel cells.

"This is not just another microfluidic device," said co-author Nancy Sottos, the Willett professor of materials science and engineering and a professor of aerospace engineering. "It's not just a widget on a chip. It's a structural material that's capable of many functions that mimic biological systems. That's a big jump."

This work was supported by the Air Force Office of Scientific Research.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by University of Illinois at Urbana-Champaign.

Journal Reference:

Aaron P. Esser-Kahn, Piyush R. Thakre, Hefei Dong, Jason F. Patrick, Vitalii K. Vlasko-Vlasov, Nancy R. Sottos, Jeffrey S. Moore, Scott R. White. Three-Dimensional Microvascular Fiber-Reinforced Composites. Advanced Materials, 2011; DOI: 10.1002/adma.201100933

Chemists make first molecular binding measurement of radon

ScienceDaily (July 29, 2011) — Even in trace quantities, the radioactive gas radon is very dangerous; it is second only to cigarette smoking as a cause of lung cancer deaths in the United States. The expense and precautions necessary to study it safely have limited research into its properties.Now, University of Pennsylvania chemists have for the first time measured how well radon binds to a molecule, paving the way for future research on it and other noble gasses.

The research was led by associate professor Ivan J. Dmochowski, along with undergraduate Vagelos Scholar David R. Jacobson and graduate students Najat S. Khan and Yubin Bai of the Department of Chemistry in Penn's School of Arts and Sciences. Because radon is so difficult to generate and handle safely, the Penn team collaborated with researchers at the National Institute of Standards and Technology who have experience in that area.

Their work was published in the journal Proceedings of the National Academy of Sciences.

Dmochowski's research group has long studied how xenon, a gas chemically similar to radon, interacts with the organic molecule cryptophane. With its cage-like structure, different kinds of cryptophane excel at binding even the non-reactive noble gasses, of which xenon and radon are both members.

"We predicted that radon would bind slightly better than xenon, as xenon under-fills the cavity in the cryptophane, and radon is a little bit larger," Dmochowski said. "There is an attractive force between the noble gas atom and the cage, and, if you optimize that interaction by matching the size of the atom and the cage's volume, you can increase the affinity."

"Other researchers made previous measurements of radon's interaction with bulk materials, like charcoal or ice," Jacobson said. "But this is the first measurement of radon binding to a discrete molecule."

The team didn't measure individual radon atoms but rather a solution of radon and a new water-soluble cryptophane. The cryptophane was synthesized for the first time in their lab, but acquiring an appreciable amount of radon was a bigger challenge. Jacobson made several trips to the NIST facility in Maryland, where the experiment was conducted using NIST's standard method for safely generating and working with the element.

At the core of the method are capsules of another radioactive element, radium, which were developed by NIST researcher and co-author Ronald Collé. The team placed the capsules into sealed vials of water.As the radium decayed, the gaseous radon leached out. After a period of a few days, the researchers were left with a precise amount of radon dissolved in the water that was then carefully transferred into a series of sealed vials containing different amounts of cryptophane.

"Some of the radon eventually evaporates out of the liquid phase inside the sealed vessels," Jacobson said. "We showed that the amount that's left behind in the liquid phase is more when there's more cryptophane to hold it within the liquid."

Less free radon gas indicates that the element was binding to the cryptophane. To measure exactly how much radon was bound, the team used a process known as liquid scintillation.

"Because radon is radioactive, we can take the liquid and inject it into a cocktail that fluoresces when something undergoes radioactive decay," Jacobson said. "We then put that into a machine that counts the number of fluorescence incidents."

From that measurement, the team was able to determine radon's "affinity constant," a measure of how much radon was bound to cryptophane at a given temperature.

The principles behind making this determination could be used on different binding targets.

"Now that we have a robust method for measuring radon binding to discrete entities, we could apply it to things like proteins found in the lungs," Dmochowski said. "If you know radon's affinity for those proteins, you have a better idea of the concentration and timescale over which it will be dangerous."

Better radon-binders could be also used to extract the dangerous element from groundwater, for example, and the same principle could be used to harvest xenon from the atmosphere. Xenon is relatively safe and has a wide range of medical and industrial uses.

Dmochowski's group is interested in using xenon for making better MRI contrast agents, but the gas is also used in plasma televisions, lasers and ion propulsion systems for deep space satellites.

In addition to Dmochowski, Jacobson, Khan, Bai and Collé, Ryan Fitzgerald and Lizbeth Laureano-Pérez of NIST contributed to the research. Their work was supported by the Department of Defense, the National Institutes of Health and the National Science Foundation.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of Pennsylvania.

Journal Reference:

D. R. Jacobson, N. S. Khan, R. Colle, R. Fitzgerald, L. Laureano-Perez, Y. Bai, I. J. Dmochowski. Measurement of radon and xenon binding to a cryptophane molecular host. Proceedings of the National Academy of Sciences, 2011; 108 (27): 10969 DOI: 10.1073/pnas.1105227108

Note: If no author is given, the source is cited instead.

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