Thursday, November 24, 2011

New biosensor benefits from melding of carbon nanotubes, DNA

 Purdue University scientists have developed a method for stacking synthetic DNA and carbon nanotubes onto a biosensor electrode, a development that may lead to more accurate measurements for research related to diabetes and other diseases.

Standard sensors employ metal electrodes coated with enzymes that react with compounds and produce an electrical signal that can be measured. But the inefficiency of those sensors leads to imperfect measurements.

Carbon nanotubes, cylindrically shaped carbon molecules known to have excellent thermal and electrical properties, have been seen as a possibility for improving sensor performance. The problem is that the materials are not fully compatible with water, which limits their application in biological fluids.

Marshall Porterfield, a professor of agricultural and biological engineering and biomedical engineering, and Jong Hyun Choi, an assistant professor of mechanical engineering, have found a solution. Their findings, reported in the journal The Analyst, describe a sensor that essentially builds itself.

"In the future, we will be able to create a DNA sequence that is complementary to the carbon nanotubes and is compatible with specific biosensor enzymes for the many different compounds we want to measure," Porterfield said. "It will be a self-assembling platform for biosensors at the biomolecular level."

Choi developed a synthetic DNA that will attach to the surface of the carbon nanotubes and make them more water-soluble.

"Once the carbon nanotubes are in a solution, you only have to place the electrode into the solution and charge it. The carbon nanotubes will then coat the surface," Choi said.

The electrode coated with carbon nanotubes will attract the enzymes to finish the sensor's assembly.

The sensor described in the findings was designed for glucose. But Porterfield said it could be easily adapted for various compounds.

"You could mass produce these sensors for diabetes, for example, for insulin management for diabetic patients," Porterfield said.

Porterfield said it may one day be possible to develop other sensors using this technology that could lead to more personalized medicines that could test in real time the effectiveness of drugs on their targets as with cancer patients.

Porterfield said he would continue to develop biosensors to detect different compounds.

The National Institutes of Health and the Office of Naval Research funded the research.

Story Source:

The above story is reprinted from materials provided by Purdue University. The original article was written by Brian Wallheimer.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Jin Shi, Tae-Gon Cha, Jonathan C. Claussen, Alfred R. Diggs, Jong Hyun Choi, D. Marshall Porterfield. Microbiosensors based on DNA modified single-walled carbon nanotube and Pt black nanocomposites. The Analyst, 2011; 136 (23): 4916 DOI: 10.1039/c1an15179g

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Critical step to opening elusive class of compounds to drug discovery

Taxanes are a family of compounds that includes one of the most important cancer drugs ever discovered, Taxol®, among other cancer treatments. But the difficulty producing these complex molecules in the lab has hampered or blocked exploration of the family for further drug leads. Now, a group of Scripps Research Institute scientists has successfully achieved a major step toward the goal of synthetically producing Taxol® and other complex taxanes on a quest to harness chemical reactions that could enable research on previously unavailable potential drugs.

The project, led by Scripps Research chemist Phil Baran, is described Nov. 6, 2011 in an advance, online issue of the journal Nature Chemistry.

Taxol®, the trade name for a chemical called paclitaxel first discovered in 1967 in the bark of a yew tree, is a highly successful drug used to treat ovarian, breast, lung, liver, and other cancer types. No less than seven different research groups have designed several ways to produce Taxol® synthetically, beginning in the 1990s with a team led by K.C. Nicolaou, chair of the Scripps Research Department of Chemistry.

While each synthesis was a significant accomplishment, each has also been exceedingly complex and inefficient. Using all these methods collectively, researchers have produced less than 30 milligrams of synthetic Taxol®. Producing other chemicals from the same promising taxanes chemical group is nearly as challenging, vastly limiting access to them for research.

Building Ferraris

Finding an efficient way to produce Taxol® in sizable quantity in the laboratory remains one of the most sought-after and elusive goals in organic chemistry. If accomplished, it would open the door to producing countless other taxanes that are not accessible from nature. Past methods were devised using conventional schemes where researchers plot a linear path of increasingly complex molecules leading to a target compound. Creating each increasingly complex molecule along that line is an inefficient process that often requires numerous extra steps to prevent unwanted reactions or to correct other chemical complications. "It's like trying to convert a Toyota Corolla into a Ferrari instead of just building a Ferrari," said Baran.

To build the Ferrari, Baran and his team are taking a different route. In 2009, the researchers showed that by using an unconventional scheme they could produce a simpler relative of Taxol® called eudesmane. They analyzed this target and then created what Baran calls a retrosynthesis pyramid. This is a diagram with the target compound at the top and lower levels filled with molecules that could theoretically be modified to reach the level above them. Such a pyramid reveals not a set linear path, but a variety of path options open to chemical exploration.

With taxanes and related compounds there are two main phases in production, the cyclase phase and oxidase phase. Working up the bottom half of the pyramid involves mostly well-understood chemistry. During this cyclase phase, researchers construct a chemical scaffolding that Baran likens to a Christmas tree to which ornaments must then be attached. The ornaments are primarily reactive oxygen molecules and this "decoration," or oxidation, phase is the most challenging.

The eudesmane synthesis was something like decorating the Charlie Brown Christmas tree, while a completed Taxol® production could be compared to the lighting of the famous multi-story Rockefeller Center tree.

In the new paper, Baran's group reports erecting that Rockefeller tree and adding the first few ornaments -- a molecule called taxadiene. "It's a Herculean task," said Baran of Taxol® synthesis, "What we're doing here is merely part one."

A conventional taxadiene synthesis is inefficient and involves 26 steps to produce. The Baran group's method involves just 10 steps to produce many times what has been previously synthesized -- more than sufficient for planned research to find a way to efficiently produce Taxol®.

Innovation Leads to Access

The taxadiene synthesis is more than just a midway stop on the way to Taxol®. The researchers chose this molecule intentionally because, like a Christmas tree that can be decorated in any number of ways, this molecule can be modified to create a wide range of taxanes of varying complexities.

This is key, because at its heart the research isn't only about finding a better way to produce Taxol®, even though the group is working toward that goal. The current commercial Taxol® production method, which involves culturing cells from the yew tree, is more economical than any new synthesis is likely to be.

Instead, Baran and his team are aiming to understand the processes used in nature to produce the compound, which are many times more efficient than those used by scientists to date. "It's my opinion that when there's a huge discrepancy between the efficiency of nature and humans, in the space between, there's innovation."

More specifically, Baran believes that while developing an efficient synthesis for Taxol®, they will gain a fundamentally improved understanding of the chemistry involved and develop more widely applicable techniques. Such innovation could allow production of a whole range of taxanes currently inaccessible for drug discovery research either because the quantities researchers can produce are vanishingly small, or because they can't produce them at all. Control of the taxane oxidation process therefore offers the potential for discovering new and important drugs, perhaps even one or more that is better at fighting specific cancers than Taxol®.

Establishing the remaining steps between taxadiene and Taxol® or other more complex taxanes remains a challenging task that Baran estimates will take years. "Nature has a choreography in the way she decorates the tree," he said. "It's a precise dance she has worked out over millennia. We have to figure out a way to bring that efficiency to the laboratory setting."

This research was supported by the National Institutes of Health, the Fulbright Scholar Program, the National Sciences and Engineering Research Council of Canada, and Bristol-Myers Squibb.

In addition to Baran, authors on the paper were co-first authors Abraham Mendoza and Yoshihiro Ishihara, both of Scripps Research.

Story Source:

The above story is reprinted from materials provided by Scripps Research Institute.

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Journal Reference:

Abraham Mendoza, Yoshihiro Ishihara, Phil S. Baran. Scalable enantioselective total synthesis of taxanes. Nature Chemistry, 2011; DOI: 10.1038/nchem.1196

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Chemists reveal the force within you: New method for visualizing mechanical forces on cell surface

A new method for visualizing mechanical forces on the surface of a cell, reported in Nature Methods, provides the first detailed view of those forces, as they occur in real-time.

"Now we're able to measure something that's never been measured before: The force that one molecule applies to another molecule across the entire surface of a living cell, and as this cell moves and goes about its normal processes," says Khalid Salaita, assistant professor of biomolecular chemistry at Emory University. "And we can visualize these forces in a time-lapsed movie."

Salaita developed the florescent-sensor technique with chemistry graduate students Daniel Stabley and Carol Jurchenko, and undergraduate senior Stephen Marshall.

"Cells are constantly tugging and pushing on their surroundings, and they can even communicate with one another using mechanics," Salaita says. "One way that cells use forces is evident from the characteristic architecture of tissue, like a lung or a heart. If we want to really understand cells and how they work, we have to understand cell mechanics at a molecular level. The first step is to measure the tension applied to specific receptors on the cell surface."

The researchers demonstrated their technique on the epidermal growth factor receptor (EGFR), one of the most studied cellular signaling pathways. They mapped the mechanical strain exerted by EGFR during the early stages of endocytosis, when the protein receptor of a cell takes in a ligand, or binding molecule. The results showed that the cell does not passively absorb the ligand, but physically pulls it inside during the process. Their experiments provide the first direct evidence that force is exerted during endocytosis.

Mapping such forces may help to diagnose and treat diseases related to cellular mechanics. Cancer cells, for instance, move differently from normal cells, and it is unclear whether that difference is a cause or an effect of the disease.

"It's known that if EGFR is over-active, that can lead to cancer," Salaita says. "And one of the ways that EGFR is activated is by binding its ligand and taking it in. So if we can understand how tugging on EGFR force changes the pathway, and whether it plays a role in cancer, it might be possible to design drugs that target this pulling process."

Several methods have been developed in recent years to try to study the mechanics of cellular forces, but they have major limitations.

One genetic engineering approach requires splitting open and modifying proteins of a cell. This invasive technique may change the behavior of the cell, skewing the results.

The technique developed at Emory is non-invasive, does not modify the cell, and can be done with a standard fluorescence microscope. A flexible polymer is chemically modified at both ends. One end gets a fluorescence-based turn-on sensor that will bind to a receptor on the cell surface. The other end is chemically anchored to a microscope slide and a molecule that quenches fluorescence.

"Once a force is applied to the polymer, it stretches out," Salaita explains. "And as it extends, the distance from the quencher increases and the fluorescent signal turns on and grows brighter. We can determine the force being exerted by measuring the amount of fluorescent light emitted."

The forces of any individual protein or molecule on the cell surface can be measured using the technique, at far higher spatial and temporal resolutions than was previously possible.

Many mysteries beyond the biology and chemistry of cells may be explained through measuring cellular forces. How does a cancer cell crawl when a tumor spreads? What are the forces involved in cell division and immune response? What are the mechanics that allow groups of cardiac cells to beat in unison?

"Our method can be applied to nearly any receptor, opening the door to rapidly studying chemical and mechanical interactions across the thousands of membrane-bound receptors on the surface of virtually any cell type," Salaita says. "We hope that measuring cellular forces could then become part of the standard repertoire of biochemical techniques that scientists use to study living systems."

Story Source:

The above story is reprinted from materials provided by Emory University. The original article was written by Carol Clark.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Daniel R Stabley, Carol Jurchenko, Stephen S Marshall, Khalid S Salaita. Visualizing mechanical tension across membrane receptors with a fluorescent sensor. Nature Methods, 2011; DOI: 10.1038/nmeth.1747

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Exploring the last white spot on Earth: New X-ray facility

 Scientists will soon be exploring matter at temperatures and pressures so extreme that the conditions can only be produced for microseconds using powerful pulsed lasers. Matter in such states is present in Earth's liquid iron core, 2500 kilometres beneath the surface, and also in elusive "warm dense matter" inside large planets like Jupiter. A new X-ray beamline ID24 at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France, allows a new level of exploration of the last white spot on our globe: the centre of Earth.

We know surprisingly little about the interior of Earth. The pressure at the centre can be calculated accurately from the propagation of earthquake waves; it is about three and a half million times atmospheric pressure. The temperature at the centre of Earth, however, is unknown, but is thought to be roughly as hot as the surface of the sun.

ID24, which was inaugurated on November 10, opens new fields of science, being able to observe many rapid processes, like in a time-lapse film sequence, whether laser-heating of iron to 10,000 degrees, charge reactions in new batteries or catalysts cleaning pollutants. It is the first of eight new beamlines to be built within the ESRF Upgrade Programme, a 180 million Euro investment over eight years, to maintain the world-leading role of the ESRF. ID24 extends the existing capabilities at the ESRF in X-ray absorption spectroscopy to sample volumes twenty times smaller and time resolutions one thousand times better than in the past.

"Scientists can use several other synchrotrons notably in Japan and the U.S for fast X-ray absorption spectroscopy, but it is the microsecond time resolution for single shot acquisition coupled to the micrometre sized spot that makes ID24 unique worldwide," says Sakura Pascarelli, scientist in charge of ID24. "The rebuilt ID24 sets the ESRF apart, and even before the first users have arrived, I am being asked to share our technology."

Earth's interior is literally inaccessible and today it is easier to reach Mars than to visit even the base of Earth's thin crust. Scientists can however reproduce the extreme pressure and temperature of a planet's interior in the laboratory, using diamond anvil cells to squeeze a material and once under pressure, heat it with short, intense laser pulses. However, these samples are not bigger than the size of a speck of dust and remain stable under high temperatures only for very short time, measured in microseconds.

Thanks to new technologies employed at ID24, scientists can now study what happens at extreme conditions, for example when materials undergo a fast chemical reaction or at what temperature a mineral will melt in the interior of a planet. Germanium micro strip detectors enable measurements to be made sequentially and very rapidly (a million per second) in order not to miss any detail. A stable, microscopic X-ray beam means that measurements can also be made in two dimensions by scanning across a sample to obtain a map instead of only at a single point. A powerful infrared spectrometer complements the X-ray detectors for the study of chemical reactions under industrial processing conditions.

Today, geologists want to know whether a chemical reaction exists between Earth's mostly liquid core and the rocky mantle surrounding it. They would like to know the melting temperature of materials other than iron that might be present in Earth's core in order to make better models for how the core -- which produces Earth's magnetic field -- works and to understand why the magnetic field changes over time and why periodically in Earth's history it has disappeared and reversed.

We know even less about warm dense matter believed to exist in the core of larger planets, for example Jupiter, which should be even hotter and denser. It can be produced in the laboratory using extremely powerful laser shock pulses compressing and heating a sample. The dream of revealing the secrets of the electronic and local structure in this state of matter with X-rays is now becoming reality, as ID24 allows sample volumes 10000 times smaller than those at the high power laser facilities to be studied, making these experiments possible at the synchrotron using table top lasers.

The ID24 beamline works like an active probe rather than a passive detector, firing an intense beam of X-rays at a sample. The technique used is called X-ray absorption spectroscopy and it involves the element specific absorption of X-rays by the atoms in a material. From this data not only the abundance of an element can be deducted but also its chemical states and which other atoms, or elements, are in their immediate neighbourhood, and even how far apart they are. In short, a complete picture is obtained of the sample at the atomic scale.

ID24 has just successfully completed first tests with X-ray beams. Testing will continue over the coming weeks, and the beamline will be open for users from around the world as of May 2012. The date for the inauguration on 10 November 2011 was chosen to coincide with the autumn meeting of the ESRF's Science Advisory Committee of external experts who played a key role in selecting the science case for ID24 and the other Upgrade Beamlines.

"ID24 opens unchartered territories of scientific exploration, as will the seven other beamlines of the ESRF Upgrade Programme. The economic crisis has hit our budgets hard, and it is not obvious to deliver new opportunities for research and industrial innovation under these circumstances," says Harald Reichert, ESRF Director of Research. "I wish to congratulate the project team for extraordinary achievements, and I look forward to seeing some extraordinary new science."

Story Source:

The above story is reprinted from materials provided by European Synchrotron Radiation Facility.

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No extraordinary effects from microwave and mobile phone heating: Study quantifies effects of electric field-induced versus conventional heating

The effect of microwave heating and cell phone radiation on sample material is no different than a temperature increase, according to scientists from the Department of Chemistry and Biochemistry, Arizona State University, in Tempe, as published in a recent issue of the The European Physical Journal B.

Abidah Khalife, Ullas Pathak and Ranko Richert attempted for the first time to systematically quantify the difference between microwave-induced heating and conventional heating using a hotplate or an oil-bath, with thin liquid glycerol samples. The authors measured molecular mobility and reactivity changes induced by electric fields in these samples, which can be gauged by what is known as configurational temperature.

By conducting experiments at varying field frequencies and sample thicknesses, they realised that thin samples exposed to low-frequency electric field heating can have a considerably higher mobility and reactivity than samples exposed to standard heating, even if they are at the exact same sample temperature. They also found that at frequencies exceeding several megahertz and for samples thicker than one millimetre, the type of heating used does not have a significant impact on the level of molecular mobility and reactivity, which is mainly dependent on the sample temperature. In effect, the configurational temperatures will only be marginally higher than the real measurable temperature.

Previous studies were mostly fundamental in nature and did not establish a connection between microwaves and mobile phone heating effects. These findings imply that for heating with microwave or cell phone radiation operating in the gigahertz frequency range, no other effect than a temperature increase should be expected.

Since the results are based on averaged temperatures, future work will be required to quantify local overheating, which can, for example, occur in biological tissue subjected to a microwave field, and better assess the risks linked to using both microwaves and mobile phones.

Story Source:

The above story is reprinted from materials provided by Springer Science+Business Media.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

A. Khalife, U. Pathak, R. Richert. Heating liquid dielectrics by time dependent fields. The European Physical Journal B, 2011; 83 (4): 429 DOI: 10.1140/epjb/e2011-20599-5

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