Thursday, March 24, 2011

Molecular-level analysis of organic particles put in perspective


When it comes to air pollution, further development and integration of complementary analytical methods are needed to understand the effect of atmospheric particles, according to scientists at Pacific Northwest National Laboratory and University of California, Irvine. Dr. Julia Laskin and Dr. Alexander Laskin at PNNL and Prof. Sergey Nizkorodov at UCI share this other insights into the state of organic aerosol chemistry in Physical Chemistry Chemical Physics, March 2011. Artwork from the article graces the cover.

Air pollution by emissions related to energy production and the transportation fleet presents economic and environmental consequences. Understanding and mitigating these consequences requires answering challenging questions about the chemically complex particles emitted by these sources. By reporting on the state of the science and discussing future needs, the Laskins and Nizkorodov are providing other scientists with a solid, foundational reference.

High-resolution provides researchers with the ability to characterize organic matter in aerosols and water samples. In the review article, the scientists discuss all studies published to date using high-resolution mass spectrometry to characterize aerosols and cloud water samples.

The authors also discuss new ionization techniques necessary to advance analysis of aerosol samples using high-resolution mass spectrometers, overcoming previous sample preparation limitations. One example is nanoDESI or Nanospray Desorption Electrospray Ionization. This approach provides a highly sensitive analysis of complex analytes, enabling a molecular-level understanding of the particles.

The authors also cover data analysis and visualization tools to aid in sorting through the hundreds of features on each mass spectrum. Using various tools and careful analysis, scientists are attaining solid information about the molecular composition and fundamental chemistry of particles. For example, researchers in 2010 found that N-heteroatom organic compounds produced through atmospheric aging of aerosols can contribute to the absorption of the visible light by pollutants.

More information: Nizkorodov SA, et al. 2011. "Molecular Chemistry of Organic Aerosols Through the Application of High Resolution Mass Spectrometry." Physical Chemistry Chemical Physics 13(9):3612-3629. DOI: 10.1039/c0cp02032j

Provided by Pacific Northwest National Laboratory (news : web)

Magnetic chameleons: New displays that change color under the influence of magnets

 Chinese researchers have created microscopic capsules that change color when a magnetic field is applied. When the capsules are collected into an array, magnetic fields can be used to create colored patterns on an extremely small scale.

Many animals use tiny physical changes at their skin or surface to alter their . Chameleons do this by pumping slightly different amount of dye into the surface of their skins. Other animals, such as some beetles, fish and birds, have special arrays of light-reflecting cells that are moved apart very slightly by the injection or removal of a fluid, or by tiny stretching of their skin. These nanometer changes in spacing are enough to change the of light that is reflected and hence the color that we see.

Scientists have been able to replicate this effect to some extent using regular clusters of tiny spheres known as colloidal crystals. The spacing between the centres of the spheres determines the wavelength of that is reflected and, hence the color of the crystal. Simple actions such as adding fluid (as described above) or swelling the size of the particles have been used to change the color.

If the spheres used are magnetic, then a can be used to control the spacing between them, and, of course, the color. This phenomenon has been shown previously, but stable systems were not created and the color seen was very dependent on viewing angle.

Now, as described in the journal , Zhongze Gu and coworkers at the Southeast University in Nanjing have created stable droplets of particles whose color can be tuned through a wide range and which does not depend on where the viewer stands.

Their breakthrough was to encapsulate clusters of magnetic spheres in a liquid within tiny, transparent resin beads. The beads are highly uniform and could be used as individual pixels in a display. Applying different magnetic fields causes the spheres within the capsules to move further apart or closer together, resulting in different colors. The picture shows the effect of applying different magnetic fields.

Another clever idea of Gu and his team was to use automated technology to create the capsules. Uniform sizes and composition are required if such materials are to be used as displays, and this was achieved by using microfluidic techniques, where reactions occur continuously as ingredients travel along the narrow channels of a very small-scale reactor. Tuning the flow rates of various reactants easily controls the capsules’ size, shell thickness and shape.

The scientists are proud of their work and imagine that it could be adapted to be used with electronic magnetic fields, using the full potential of the tiny scale of the microcapsules and leading to “more complex and interesting patterns.”

More information: C. Zhu, W. Y. Xu, L. S. Chen, W. D. Zhang, H. Xu, and Z. Z. Gu, “Magnetochromatic Microcapsule Array for Display”, Adv. Funct. Mater. 2011; DOI: 10.1002:adfm.201002296

Provided by Wiley (news : web)

New blood analysis chip could lead to disease diagnosis in minutes

A major milestone in microfluidics could soon lead to stand-alone, self-powered chips that can diagnose diseases within minutes. The device, developed by an international team of researchers from the University of California, Berkeley, Dublin City University in Ireland and Universidad de Valparaíso Chile, is able to process whole blood samples without the use of external tubing and extra components.

The researchers have dubbed the device SIMBAS, which stands for Self-powered Integrated Microfluidic Analysis System. SIMBAS appeared as the cover story March 7 in the peer-reviewed journal Lab on a Chip.

“The dream of a true has been around for a while, but most systems developed thus far have not been truly autonomous,” said Ivan Dimov, UC Berkeley post-doctoral researcher in bioengineering and co-lead author of the study. “By the time you add tubing and sample prep setup components required to make previous chips function, they lose their characteristic of being small, portable and cheap. In our device, there are no external connections or tubing required, so this can truly become a point-of-care system.”

Dimov works in the lab of the study’s principal investigator, Luke Lee, UC Berkeley professor of bioengineering and co-director of the Berkeley Sensor and Actuator Center.

“This is a very important development for global healthcare diagnostics,” said Lee. “Field workers would be able to use this device to detect diseases such as HIV or tuberculosis in a matter of minutes. The fact that we reduced the complexity of the biochip and used plastic components makes it much easier to manufacture in high volume at low cost. Our goal is to address global health care needs with diagnostic devices that are functional, cheap and truly portable.”

For the new SIMBAS biochip, the researchers took advantage of the laws of microscale physics to speed up processes that may take hours or days in a traditional lab. They note, for example, that the sediment in red wine that usually takes days to years to settle can occur in mere seconds on the microscale.

The SIMBAS biochip uses trenches patterned underneath microfluidic channels that are about the width of a human hair. When whole blood is dropped onto the chip’s inlets, the relatively heavy red and white blood cells settle down into the trenches, separating from the clear blood plasma. The blood moves through the chip in a process called degas-driven flow.

For degas-driven flow, air molecules inside the porous polymeric device are removed by placing the device in a vacuum-sealed package. When the seal is broken, the device is brought to atmospheric conditions, and air molecules are reabsorbed into the device material. This generates a pressure difference, which drives the blood fluid flow in the chip.

In experiments, the researchers were able to capture more than 99 percent of the blood cells in the trenches and selectively separate plasma using this method.

“This prep work of separating the blood components for analysis is done with gravity, so samples are naturally absorbed and propelled into the chip without the need for external power,” said Dimov.

The team demonstrated the proof-of-concept of SIMBAS by placing into the chip’s inlet a 5-microliter sample of whole blood that contained biotin (vitamin B7) at a concentration of about 1 part per 40 billion.

“That can be roughly thought of as finding a fine grain of sand in a 1700-gallon sand pile,” said Dimov.

The biodetectors in the SIMBAS chip provided a readout of the biotin levels in 10 minutes.

“Imagine if you had something as cheap and as easy to use as a pregnancy test, but that could quickly diagnose HIV and TB,” said Benjamin Ross, a UC Berkeley graduate student in bioengineering and study co-author. “That would be a real game-changer. It could save millions of lives.”

“The SIMBAS platform may create an effective molecular diagnostic biochip platform for cancer, cardiac disease, sepsis and other diseases in developed countries as well,” said Lee.

Provided by University of California - Berkeley (news : web)

Researchers use light to move molecules

Using a light-triggered chemical tool, Johns Hopkins scientists report that they have refined a means of moving individual molecules around inside living cells and sending them to exact locations at precise times.

This new tool, they say, gives scientists greater command than ever in manipulating single , allowing them to see how molecules in certain cell locations can influence cell behavior and to determine whether cells will grow, die, move or divide. A report on the work was published online December 13 in the .

Studying how just one signaling molecule communicates in various parts of a living cell has posed a challenge for scientists investigating how different interactions influence cell behavior, such as the decision to move, change shape or divide.

"By using one magical chemical set off by light, we modified our previous technique for moving molecules around and gained much more control," says Takanari Inoue, Ph.D., assistant professor of and member of the Center for in the Institute for Basic Biomedical Sciences. "The advantage of using light is that it is very controllable, and by confining the light, we can manipulate communication of molecules in only a tiny region of the cell," he says.

Specifically, the Hopkins team designed a way to initiate and spatially restrict the to a small portion of the cell by attaching a light-triggered chemical to a bulky molecule, the bond between which would break when researchers shined a defined beam of on it. This enabled the chemical to enter the cell and force two different and specific proteins in that cell to mingle when they otherwise wouldn't. Normally, these proteins would have nothing to do with each other without the presence of the light-triggered chemical, but researchers decided to take advantage of this mingling to explore how certain proteins in a cell behave when transported to precise locations.

Next, researchers modified the two mingling proteins by attaching special molecules to them — one sent one of the proteins to the edge of the cell and another caused ripples to form on the edge of the cell — so that if ripples form on the edge of the cell, they would know that the proteins were interacting there.

The researchers put both modified proteins inside human skin cells and bathed the cells in the light-triggered chemical tool. Then, they shone a tiny UV beam directed on approximately ten percent of the edge of a skin cell. Ripples appeared only on the region of the cell near where the light was beamed, demonstrating that the tool could limit cell activity to a precise location in the cell.

The tool can be used in larger cells, Inoue says, to monitor as little as one percent of a specific molecule if the beam intensity is varied. That in turn could reveal in even more detail the secret affairs of proteins in cellular cubbyholes.

"With this technique, we can get a finer understanding of cell function on the molecular level," says Inoue. "Our technique allows us to monitor whatever molecule we choose in whichever tiny space we choose so that we can understand how a molecule functions in a specific part of a live cell."

More information: http://pubs.acs.or … urnal/jacsat

Provided by Johns Hopkins Medical Institutions

New clues for asthma treatment

 New information that could help in the fight against asthma has been obtained by an international collaboration of scientists utilizing the U.S. Department of Energy’s Advanced Photon Source at Argonne National Laboratory. Their results, which were recently published in the journal Nature, show how an important human transmembrane protein functions at a molecular level. The findings are significant in that the particular human transmembrane protein known as ß2-adrenergic receptor, a G protein-coupled receptor (GPCR), is the focus of a series of drugs for the treatment of asthma. This new research on its structure and function has the potential of leading to the development of improved drug therapies.

There are over 750 human GPCRs distributed throughout the body with representatives in almost every cell type. They function in myriad ways enabling us to interact with our environment, and with one another through the sense of sight and smell. They also play key roles in heart and lung function, in how we respond to hormones and neurotransmitters and by extension how they influence mood and behavior, and are involved in immunity and inflammation. It is apparent, therefore, why a full suite of properly functioning GPCRs is integral to human health and wellbeing. About a third of drugs on the market today target GPCRs.

The research, by investigators from the Stanford University School of Medicine, Trinity College Dublin, the University of Limerick, Friedrich Alexander University, D. E. Shaw Research, the University of Michigan Medical School, and the University of Wisconsin-Madison set out to understand how one of these GPCRs, the ß2-adrenergic receptor, works at a molecular level. The receptor is long enough to comfortably span the 5-nanometer width of the cell’s outer protective membrane. In this way, one end of the receptor can sense what is happening outside the cell and transmit the information it collects there to the cell’s interior for appropriate action. The fight-or-flight hormone adrenaline mediates its activity by way of the ß2-adrenergic receptor. When the receptor binds adrenaline shot into the blood by the adrenal gland it snaps into action by binding with its cognate G-protein located inside the cell. This interaction triggers a series of reactions within and between cells that are part of the body’s response to adrenaline. These include vasodilation and constriction, smooth muscle relaxation, hearth muscle contraction, and mobilization of energy reserves in the liver and muscle. The ß2-adrenergic receptor is an important pharmaceutical paradigm for the larger family of GPCRs, some of which are targeted by beta blockers.

Martin Caffrey, Trinity College Professor of Membrane Structural and Functional Biology in the Schools of Medicine and Biochemistry & Immunology explained: “New and improved drugs are always in demand. But to design them in a rational way we need to know how the receptor, in this case the ß2-adrenergic receptor, is put together in a structural sense and how this structure enables it to function as a receptor and a communicator of information.

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“By structure we refer to the arrangement in three-dimensions of the receptor’s constituent atoms, amino acids, and the ligands it binds. We would also like to know how this structure changes when adrenaline nudges the receptor and how this facilitates downstream signaling.

“The only way to get such detailed information for a complicated membrane protein like the ß2-adrenergic receptor is to use macromolecular crystallography, which requires a well-ordered crystal of the receptor. The crystals must then be irradiated with x-ray photons in a way that can be used to decipher the receptor’s structure.

“One of the big challenges in this protracted and involved process is to coax the protein into the regular and ordered lattice of a crystal,” said Caffrey. “This is particularly difficult in the case of GPCRs because they continually flit about structurally in the plane of the membrane and, at any one moment, can be seen to exist in a number of different conformations or shapes. The particular conformation assumed, in turn, dictates the receptor’s biological activity. To get a collection of receptor molecules to crystallize, ideally they should all assume the one stance or conformation.”

Brian Kobilka, Professor of Molecular and Cellular Physiology at Stanford University, who led this research project, devised a strategy for locking the into what amounts to a single conformation by covalently or irreversibly splicing an adrenaline look-alike molecule into the binding site of the receptor. So stabilized and rendered uniform, the receptor was successfully crystallized and its structure solved.

The study featured the use of a novel, high-throughput method and instrumentation, developed by the Trinity team members that crystallized the stabilized ß2-adrenergic receptor. Custom-designed robots dispensed nanoliter volumes of a highly viscous, protein-laden lipidic liquid crystal or mesophase into home-built, multi-well glass sandwich plates for crystallization screening. The mesophase mimics the lipid bilayer membrane in which the receptor resides in the cell. When treated appropriately it undergoes a transition to a second mesophase in which receptor molecules preferentially cluster, arrange themselves regularly in two- and then three-dimensional arrays, and eventually form crystals. The crystals typically are very small, just a tenth to a hundredth of a millimeter in size, and are extremely fragile. They were harvested carefully from the toothpaste-textured mesophase, cryo-cooled in liquid nitrogen, and then shipped in special dewars from the laboratory at Trinity to the General Medicine and Cancer Institutes Collaborative Access Team facility on x-ray beamline 23-ID at the Advanced Photon Source. There, the team used state-of-the-art technologies to center the crystal in the x-ray beam and collect diffraction data, which, upon processing and modeling by researchers at Stanford, generated the structure reported in Nature.

More information: Daniel M. Rosenbaum, et al., “Structure and function of an irreversible agonist-ß2 adrenoceptor complex,” Nature 469, 236 (13 January 2011)

Provided by Argonne National Laboratory (news : web)

Mutant proteins weigh in: Researchers 'see' binding with DNA through quartz crystal microbalance

 Rice University scientists have demonstrated a new way to see and quickly measure DNA/protein binding, a discovery that prompted one journal reviewer to write, "This study has made my day."

"I've never had that happen," said co-author Kathleen Matthews, Rice's Stewart Memorial Professor of Biochemistry and Cell Biology and former dean of the Wiess School of Natural Sciences.

Sibani Lisa Biswal, an assistant professor in chemical and biomolecular engineering, led the study with Matthews that made novel use of a quartz crystal microbalance (QCM) to dynamically measure the binding activity of wild-type and mutant proteins. The process let them monitor what happened in real time when DNA was first introduced to and then removed from attached to the microbalance.

The study published this week in the American Chemical Society journal is of interest to researchers who work in biological and chemical sensing. Co-authors include Jia Xu, a Welch postdoctoral fellow in biochemistry and cell biology, and Kai-Wei Liu, a graduate student in chemical and biomolecular engineering.

There's nothing new about QCM, a device Biswal said probably exists at most research universities. "It's mainly used for chemical and biomolecular sensing," she said. "QCM works by measuring the resonance frequency of a quartz crystal. When you apply current, it resonates, and we translate that through electronic measurements into a frequency. When you add something to the surface of the crystal, the frequency changes. That's what we're looking for."

The sensitivity is so fine that she can see the difference in a when a attaches itself to the protein. "When you apply sufficient mass to the , it's going to change its resonance frequency," Biswal said. "The change in mass is proportional to the change in frequency."

The researchers chose to look at an Escherichia coli protein, a lactose repressor called LacI, primarily because Matthews has the wild-type protein and multiple variants. "She has studied LacI for a long time," Biswal said. "It's a well-characterized system, and we wanted to use something we know about."

The team compared two types of LacI via QCM. The first, wild-type LacI, was used as a control because it bonds strongly to the gold-coated QCM surface using its DNA-binding domain, which spreads out like a mold and is then unable to bind DNA.

The second was a mutant form of LacI, engineered with a sulfur-based amino acid introduced far from the protein's DNA binding site. Unlike the wild-type, this mutant LacI puts down tight roots at the site of the mutation and stands like a tree, waving in the liquid breeze. "The mutation will actually orient the protein, so we can immobilize it onto a solid support," Biswal said.

Experimenting on both types, the researchers flowed liquid containing DNA and then IPTG, an inducer that releases the DNA, over the proteins bound to the QCM. In the process that took between 90 minutes and two hours, the wild-type Lacl, adsorbed by the gold surface, largely ignored the offerings.

But the mutant LacI responded with a clear change in the signal as it first grabbed passing DNA and then released it when IPTG was introduced to the stream.

"It's dynamic," Matthew said of the process. "We're flowing very small volumes of liquid over the sensor. We start with a buffer, then add the protein. When the protein binds, we can see how much goes on the surface of the crystal. Then we add the DNA and we can see that binding process with the mutant (for the wild-type, nothing happens) and then we add the IPTG and see the release."

As a bonus, the QCM technique also provides information about the viscoelastic properties of bound proteins. "It's nice that we can measure dissipation," Biswal said. "When we turn off the current, we can watch how the resonance decays -- and that tells us things like the elasticity of the material on top of the quartz."

Biswal, thinking about that reviewer, noted he had studied proteins on surfaces for the past 25 years and was delighted that one could study how mutations to a protein would change its binding properties and functionalities.

"People who develop biosensors need to be able to attach proteins onto surfaces," she said. "Our work indicates that you can't just immobilize proteins nonspecifically onto a surface. You actually do need to make some type of mutation to make sure the binding site is accessible. This platform allows us to easily screen and study what type of mutations are needed."

More information: Read the abstract at http://pubs.acs.or … 21/la200056h

Provided by Rice University (news : web)

Scientists discover recycling method to advance fuel cell practicality

The use of hydrogen as a practical, widespread alternative fuel to gasoline took another step today as researchers from Los Alamos National Laboratory and The University of Alabama announce a method for recycling a hydrogen fuel source.

The scientists demonstrate that a lightweight material, , can be a feasible material for storing on vehicles, according to an article publishing in the March 18 issue of Science. In the upcoming article, researchers describe an efficient method of adding hydrogen back into the material once the is spent.

“This is a critical step if we want to use hydrogen as a fuel for the transportation industry,” said Dr. David Dixon, the Robert Ramsay Chair of Chemistry at The University of Alabama and one of the article’s co-authors.

In this approach, ammonia borane in a fuel tank produces hydrogen which, when combined with oxygen in the vehicle’s , releases energy. That energy is then converted to electricity that powers an electric motor. Water is the only emission.

After hydrogen is released from the ammonia borane, a residue, which the researchers refer to as “spent fuel,” remains.

“The spent fuel stays in the car, and we need to add hydrogen back to it in order to use it again,” Dixon says. “What this paper describes is an efficient way to add the hydrogen back to make the ammonia borane again. And it can be done in a single reactor.”

Practical, efficient and affordable storage of hydrogen has been one of the challenges in making the powering of electrical motors via hydrogen fuel cells a viable alternative to traditional gasoline powered engines. Benefits of hydrogen fuel cell technology include cleaner air and less dependence on foreign oil.

Today’s announcement of a successful “fuel regeneration process,” as the scientists call it, overcomes one key hurdle.

The experimental work was done at Los Alamos and the computer modeling work was done in Dixon’s University of Alabama lab. UA co-authors with Dixon are Edward “Ted” B. Garner III, a University graduate student from Florence; J. Pierce Robinson, a UA undergraduate from Atmore; and Dr. Monica Vasiliu, a UA alumna from Romania who is working with Dixon as a post-doctoral researcher.

The article’s lead author is Dr. Andrew D. Sutton of Los Alamos National Laboratory. Other Los Alamos co-authors are Drs. Anthony K. Burrell, John C. Gordon, Tessui Nakagawa and Kevin C. Ott.

While there has been much progress toward making the widespread use of hydrogen fuel cell technology practical, Dixon said other challenges remain.

“The basic three steps – the initial synthesis, the controlled release of hydrogen, and the regeneration of fuel – are actually in pretty good shape. The next piece is to get a cheap source of hydrogen that doesn’t come from coal or fossil fuels.

“The biggest hurdle which we, and everybody else in the world, are looking at is ‘how do I use solar energy efficiently to split water in order to make hydrogen and oxygen.’”

Provided by University of Alabama