Saturday, April 30, 2011

New 'nanobead' approach could revolutionize sensor technology

Researchers at Oregon State University have found a way to use magnetic "nanobeads" to help detect chemical and biological agents, with possible applications in everything from bioterrorism to medical diagnostics, environmental monitoring or even water and food safety.

When fully developed as a hand-held, portable sensor, like something you might see in a science fiction movie, it will provide a whole diagnostic laboratory on a single chip.

The research could revolutionize the size, speed and accuracy of chemical detection systems around the world.

New findings on this "microfluidic sensor" were recently reported in Sensors and Actuators B: Chemical, a professional journal, and the university is pursuing a patent on related technologies. The collaborative studies were led by Vincent Remcho, an OSU professor of chemistry, and Pallavi Dhagat, an assistant professor in the OSU School of Electrical Engineering and Computer Science.

The key, scientists say, is tapping into the capability of ferromagnetic iron oxide nanoparticles -extraordinarily tiny pieces of rust. The use of such particles in the new system can not only detect chemicals with sensitivity and selectivity, but they can be incorporated into a system of integrated circuits to instantly display the findings.

"The particles we're using are 1,000 times smaller than those now being used in common diagnostic tests, allowing a device to be portable and used in the field," said Remcho, who is also associate dean for research and graduate programs in the OSU College of Science.

"Just as important, however, is that these nanoparticles are made of iron," he said. "Because of that, we can use magnetism and electronics to make them also function as a signaling device, to give us immediate access to the information available."

According to Dhagat, this should result in a powerful sensing technology that is fast, accurate, inexpensive, mass-producible, and small enough to hold in your hand.

"This could completely change the world of chemical assays," Dhagat said.

Existing assays are often cumbersome and time consuming, using biochemical probes that require expensive equipment, expert personnel or a complex laboratory to detect or interpret.

In the new approach, tiny nanoparticles could be attached to these biochemical probes, tagging along to see what they find. When a chemical of interest is detected, a "ferromagnetic resonance" is used to relay the information electronically to a tiny computer and the information immediately displayed to the user. No special thin films or complex processing is required, but the detection capability is still extremely sensitive and accurate.

Essentially, the system might be used to detect almost anything of interest in air or water. And the use of what is ordinary, rusty iron should help address issues of safety in the resulting nanotechnology product.

Rapid detection of chemical toxins used in bioterrorism would be possible, including such concerns as anthrax, ricin or smallpox, where immediate, accurate and highly sensitive tests would be needed. Partly for that reason, the work has been supported by a four-year grant from the Army Research Laboratory, in collaboration with the Oregon Nanoscience and Microtechnologies Institute.

However, routine and improved monitoring of commercial water treatment and supplies could be pursued, along with other needs in environmental monitoring, cargo inspections, biomedical applications in research or medical care, pharmaceutical drug testing, or even more common uses in food safety.

Other OSU researchers working on this project include Tim Marr, a graduate student in electrical engineering, and Esha Chatterjee, a graduate chemistry student.

The concept has been proven in the latest study, scientists say, and work is continuing with microfluidics research to make the technology robust and durable for extended use in the field.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by Oregon State University.

Journal Reference:

Esha Chatterjee, Tim Marr, Pallavi Dhagat, Vincent T. Remcho. A microfluidic sensor based on ferromagnetic resonance induced in magnetic bead labels. Sensors and Actuators B: Chemical, 2011; DOI: 10.1016/j.snb.2011.02.012

Protein-devouring enzyme complex uses two different mechanisms to determine which targets to destroy

The proteasome is the garbage-disposal system of the cell, enzymatically clearing away unwanted proteins. Since this requires the recognition of individual targets within the crowded cellular environment, it is critically important that molecules ‘marked for death’ are appropriately flagged.

This signal, known as the degron, is composed of two components: an unstructured ‘initiation region’ within the target and a recognition tag. This tag typically consists of a chain of ubiquitin , but some proteins get steered to the proteasome with the help of ubiquitin-binding ‘adaptor’ proteins. “These two pathways work in parallel with and independently from each other, and converge at the initiation step,” explains Tomonao Inobe of the RIKEN Brain Science Institute in Wako, Japan.

By analyzing the efficiency with which different synthetic protein constructs get degraded by the proteasome, Inobe and colleagues in Andreas Matouschek’s laboratory at Northwestern University in Illinois, USA, have uncovered important structural details of the recognition mechanisms used by the proteasome to manage these distinct pathways. 

The team’s initial experiments showed that the minimum length for the initiation region is shorter in proteins tagged with ubiquitin alone (Ub4) than those tagged with an adaptor-derived ubiquitin-like (UbL) domain. Similarly, they found that Ub4–mediated degradation was most efficient when these sites were close together, and was impaired by the insertion of rigid ‘spacer’ protein segments between the two degron components. With UbL-tagged constructs, however, degradation was maximized when these components were moderately separated.

Based on their data, the researchers concluded that these physical constraints arise because Ub4- and UbL-tagged proteins bind to completely different sites on the proteasome; ubiquitin binds very near to the digestion machinery, requiring the initiation region to be close by (Fig. 1), while the UbL-binding site is considerably farther away, and thus accommodates greater separation. Inobe compares this to how an electrical plug must match its outlet. “The proteasome can recognize different plugs,” he says, “but each one has to have the correct specific arrangement of prongs.”

Inobe hopes to better characterize the functional role of this distance restriction in the future, but suggests that this mechanism may enable this protein complex to achieve both direct destruction of individual proteins and the targeted degradation of specific molecules nestled within larger complexes. “The spacing rules fit well with the way these tags are used physiologically and help explain how substrates are selected for degradation or manage to escape the process,” says Inobe.

More information: Inobe, T., et al. Defining the geometry of the two-component proteasome degron. Nature Chemical Biology 7, 161–167 (2011). http://www.nature. … bio.521.html

Provided by RIKEN (news : web)

'Going off the grid' helps some bacteria hide from antibiotics

Call them the Jason Bournes of the bacteria world. Going "off the grid," like rogue secret agents, some bacteria avoid antibiotic treatments by essentially shutting down and hiding until it's safe to come out again, says Thomas Wood, professor in the Artie McFerrin Department of Chemical Engineering at Texas A&M University.

This surreptitious and elaborate survival mechanism is explained in the online April edition of Nature Chemical Biology, which details the research of Wood and his post doctoral student Xiaoxue Wang along with colleagues Breann Brown, Wolfgang Peti and Rebecca Page of Brown University.

"Through our research, we're understanding that some go to 'sleep,' and that antibiotics only work on bacteria that are metabolically active," Wood explains. "You need actively growing bacteria to be susceptible to antibiotics. If the bacterium goes to sleep, the antibiotics, no matter what they do, are not effective because the bacterium is no longer doing the thing that the antibiotic is trying to shut down."

It's an alternative method for survival, Wood says, that starkly contrasts the widely studied genetically based approaches utilized by bacteria through which bacteria gain resistance to antibiotics as the result of mutations experienced throughout time. This mutation-free response, however, demonstrates that some bacteria need not mutate to survive external stressors, Wood says.

Instead, when triggered by an external stressor such as an antibiotic, a bacterial cell can render itself dormant by triggering an internal reaction that degrades the effectiveness of its own internal antitoxins, Wood explains. With its antitoxins damaged, the toxins present within the bacterial cell are left unchecked and damage the cell's metabolic processes so that it essentially shuts down, he adds.

It's self-inflicted damage but with a purpose.

"The cell normally doesn't want to hurt itself; it wants to grow as fast as possible," Wood states; the raison d'etre for a cell is to make another cell," Wood says. "However, most bacteria have this group of proteins, and if this group was active - if you got rid of the antitoxins - this group of toxins would either kill the cell or damage it."

Specifically, Wood and his colleagues found that when encountering oxidative stress, their bacterial initiated a process through which an antitoxin called MqsA was degraded, in turn allowing the toxin MqsR to degrade all of the cells' messenger RNA. This messenger RNA, Wood explains, plays a critical intermediate role in the cell's process of manufacturing proteins, so without it the cell can't make proteins. With the protein-manufacturing factory shut down, the bacterial cell goes dormant, and an antibiotic cannot "lock on" to the cell. When the stressor is removed, the bacterial cells eventually come back online and resume their normal activities, Wood says.

"It was the combination of the genetic studies at Texas A&M with our structural studies at Brown University that demonstrated that the proteins MqsR:MqsA form an entirely new family of toxin:antitoxin systems," Page says. "Remarkably, we have shown this system not only controls its own genes, but also many other genes in E. coli, including the gene that controls the response to oxidative stress."

This response mechanism, Wood emphasizes, does not replace the mutation-based approaches that have for years characterized cell behavior; it's merely another method in a multifaceted approach undertaken by bacteria to ensure survival.

"A small community of bacteria is in a sense hedging its bet against a threat to its survival by taking another approach," Wood says. "To the bacteria, this is always a numbers game. In one milliliter you can have a trillion , and they don't always do the same thing under stress.

"If we can determine that this 'going to sleep' is the dominant mechanism utilized by bacteria, then we can begin to figure out how to 'wake them up' so that they will be more susceptible to the antibiotic. This ideally would include simultaneously applying the antibiotic and a chemical that wakes up the bacteria. That's the goal - a more effective antibiotic."

Provided by Texas A&M University

Nanoscience may hold key to surgical recovery

New nano-systems developed in York may eventually help patients recover from surgery without the danger of allergic reactions to drugs.

Researchers from the University of York's Department of Chemistry have developed synthetic molecules capable of binding the chemical drug heparin, which they believe may provide an alternative to protamine.

During surgery patients are given heparin to thin the blood and prevent clotting. However, once surgery is finished, it is essential to remove the heparin and allow clotting so the patient can recover. Currently this is done with the drug protamine, a natural product extracted from shellfish which can cause serious side effects in some patients.

The synthetic molecules created in York are designed to self-assemble into nanometre-sized structures with similar dimensions to protamine and containing multiple heparin binding units.

The results of the early stage study, published in Angewandte Chemie, show that the new nano-systems are capable of binding heparin just as effectively as protamine.

Professor Dave Smith, from the Department of Chemistry, said: "Clearly there is lots of fundamental work still to be done before clinical application. However, we hope that this approach may eventually yield biocompatible and degradable heparin binders which will help surgical recovery without any of the side effects which can be caused by protamine."

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by University of York, via AlphaGalileo.

Journal Reference:

Ana C. Rodrigo, Anna Barnard, James Cooper, David K. Smith. Self-Assembling Ligands for Multivalent Nanoscale Heparin Binding. Angewandte Chemie International Edition, 2011; DOI: 10.1002/anie.201100019

Sweet chemistry: Carbohydrate adhesion gives stainless steel implants beneficial new functions

A new chemical bonding process can add new functions to stainless steel and make it a more useful material for implanted biomedical devices. Developed by an interdisciplinary team at the University of Alberta and Canada's National Institute for Nanotechnology, this new process was developed to address some of the problems associated with the introduction of stainless steel into the human body.

Implanted , such as cardiac stents, are implanted in over 2 million people every year, with the majority made from stainless steel. Stainless steel has many benefits - strength, generally stability, and the ability to maintain the required shape long after it has been implanted. But, it can also cause severe problems, including blood clotting if implanted in an artery, or an allergenic response due to release of such as nickel ions.

The University of Alberta campus is home to a highly multidisciplinary group of researchers, the CIHR Team in for Glyconanotechnology in Transplantation, that is looking to develop new synthetic that modify the body's before an . The ultimate goal is to allow cross-blood type organ transplants, meaning that blood types would not necessarily need to be matched between donor and recipient when an organ becomes available for transplantation. Developing new nanomaterials that engage and interact with the body's immune system are an important step in the process. In order to overcome the complex range of requirements and issues, the project team drew on expertise from three major areas: surface science chemistry and engineering, carbohydrate chemistry, and immunology and medicine.

For the transplantation goals of the project, sophisticated carbohydrate (sugar) molecules needed to be attached to the stainless steel surface to bring about the necessary interaction with the body's immune system. Its inherent stainless characteristic makes stainless steel a difficult material to augment with new functions, particularly with the controlled and close-to-perfect coverage needed for biomedical implants. The Edmonton-based team found that by first coating the surface of the stainless steel with a very thin layer (60 atoms deep) of glass silica using a technique available at the National Institute for Nanotechnology, called Atomic Layer Deposition (ALD), they could overcome the inherent non-reactivity of the stainless steel. The silica provide a well-defined "chemical handle" through which the carbohydrate molecules, prepared in the Alberta Ingenuity Centre for Carbohydrate Science, could be attached. Once the stainless steel had been controlled, the researchers demonstrated that the carbohydrate molecules covered the in a highly controlled way, and in the correct orientation to interact with the immune system.

"We are immensely pleased with this progress. We have every expectation that this set of steps creating novel tools for engagement will lead us closer to clinical application aimed at preparing patients for successful organ transplants." stated Dr. Lori West, Professor of Pediatrics, Surgery and Immunology, and Director of Heart Transplant Research at Univ. of Alberta.

Provided by National Institute for Nanotechnology

Laying bare the not-so-sweet tale of a sugar and its role in the spread of cancer

Cancer has a mighty big bag of tricks that it uses to evade the body's natural defense mechanisms and proliferate. Among those tricks is one that allows tumor cells to turn the intricate and extensive system of lymphatic vessels into something of a highway to metastasis. Yet research unveiled this week may aid in the development of therapeutics that will put the brakes on such cancer spread, and the researchers who completed the study say the findings may extend to other lymphatic disorders.

In the latest issue of the , the team at the VA San Diego Healthcare System and the University of California, San Diego, reports an important advance in the understanding of the molecular machinery needed for lymphatic cell growth.

"In many carcinomas, lymphatic vessels grow and remodel around and sometimes within tumors. This allows to go upstream to the ," explains assistant professor Mark Fuster, who led the study. Once tumor cells hitch a ride to the lymph nodes, the disease can be more difficult to fight. "We were trying to understand the mechanisms that turn on the growth of lymphatic vessel cells in the laboratory."

To better understand how tumors get lymphatic vessels to construct an entry ramp for , Fuster's team began by looking at a much-studied lymphatic stimulatory protein that is often over-produced by tumors. The protein migrates from the tumor to a layer of cells within lymphatic vessels known as the endothelium. The tumor-produced protein is officially known as C, or VEGF-C for short (pronounced "vej-eff-cee").

"The growth factor VEGF-C lands on a special receiving molecule, or receptor, on the surface of the lymphatic endothelial cells, sending a signal that says it's time for the endothelial cells to replicate and send offshoots," Fuster says. But the team was curious as to whether VEGF-C and its receptor were getting any help from nearby molecules to make that happen. "After all, if there were other players in the mix, that might mean there are other possible drug targets," Fuster explains.

The team focused on a glycan, or sugar, known as heparan sulfate. After some initial clues indicated that destroying the unique sugar on lymphatic endothelial cells would inhibit VEGF-C-dependent growth signaling, Fuster and his team dug in to figure out more about heparan sulfate's role.

"In a cell-based system, we tried to interfere with the components that are involved in making heparan sulfate in lymphatic . We tried inhibiting the production of the sugar and destroying it," Fuster says.

Xin Yin, a postdoctoral research fellow, and Scott Johns, a research associate in the laboratory, both lead authors on the paper, carried out a variety of studies to examine how silencing enzymes in the cell that are responsible for putting the sugar together might alter various cell-growth behaviors and affect VEGF-C's ability to activate its receptor.

"What we found was that giving the glycan-altered cells the VEGF-C resulted in a blunting of the normal growth rate or signaling for growth," Fuster says. "This work shows there may be a key role for heparan sulfate in the initiation of lymphatic vessel-growth responses."

In the setting of cancer, it is thus possible that the presence of heparan sulfate is important for tumor-spurred lymphatic vessel growth: This not only identifies a potential target for anti-cancer drugs, Fuster says, but it may also offer insights about how to stimulate lymphatic vascular growth in diseased parts of the body that, conversely, need for normal circulatory and immune functions.

Still, though, Fuster emphasizes that more work remains to be done, because how exactly heparan sulfate interacts with VEGF-C and its receptor remains unclear: "Identifying the importance of heparan sulfate in the growth of living lymphatic systems and identifying its possible importance in mediating the functions of multiple lymphatic growth factors simultaneously remain important considerations for ongoing and future research."

More information: Lymphatic Endothelial Heparan Sulfate Deficiency Results in Altered Growth Responses to Vascular Endothelial Growth Factor-C (VEGF-C), doi: 10.1074/jbc.M110.206664

Growth and remodeling of lymphatic vasculature occur during development and during various pathologic states. A major stimulus for this process is the unique lymphatic vascular endothelial growth factor-C (VEGF-C). Other endothelial growth factors, such as fibroblast growth factor-2 (FGF-2) or VEGF-A, may also contribute. Heparan sulfate is a linear sulfated polysaccharide that facilitates binding and action of some vascular growth factors such as FGF-2 and VEGF-A. However, a direct role for heparan sulfate in lymphatic endothelial growth and sprouting responses, including those mediated by VEGF-C, remains to be examined. We demonstrate that VEGF-C binds to heparan sulfate purified from primary lymphatic endothelia, and activation of lymphatic endothelial Erk1/2 in response to VEGF-C is reduced by interference with heparin or pretreatment of cells with heparinase, which destroys heparan sulfate. Such treatment also inhibited phosphorylation of the major VEGF-C receptor VEGFR-3 upon VEGF-C stimulation. Silencing lymphatic heparan sulfate chain biosynthesis inhibited VEGF-C-mediated Erk1/2 activation and abrogated VEGFR-3 receptor-dependent binding of VEGF-C to the lymphatic endothelial surface. These findings prompted targeting of lymphatic N-deacetylase/N-sulfotransferase-1 (Ndst1), a major sulfate-modifying heparan sulfate biosynthetic enzyme. VEGF-C-mediated Erk1/2 phosphorylation was inhibited in Ndst1-silenced lymphatic endothelia, and scratch-assay responses to VEGF-C and FGF-2 were reduced in Ndst1-deficient cells. In addition, lymphatic Ndst1 deficiency abrogated cell-based growth and proliferation responses to VEGF-C. In other studies, lymphatic endothelia cultured ex vivo from Ndst1 gene-targeted mice demonstrated reduced VEGF-C- and FGF-2-mediated sprouting in collagen matrix. Lymphatic heparan sulfate may represent a novel molecular target for therapeutic intervention.

Provided by American Society for Biochemistry and Molecular Biology

Breakthrough in the search for the holy grail for data storage

One of The University of Nottingham’s leading young scientists has created a new compound which could lead to a breakthrough in the search for high performance computing techniques.

Dr Steve Liddle, an expert in molecular depleted chemistry, has created a new molecule containing two Uranium atoms which, if kept at a very low temperature, will maintain its magnetism. This type of single-molecule magnet (SMM) has the potential to increase capacity by many hundreds, even thousands of times — as a result huge volumes of data could be stored in tiny places.

Dr Liddle, a Royal Society University Research Fellow and Reader in the School of Chemistry, has received numerous accolades for his ground breaking research. His latest discovery has just been published in the journal .

Dr Liddle said: “This work is exciting because it suggests a new way of generating SMM behaviour and it shines a light on poorly understood uranium phenomena. It could help point the way to making scientific advances with more technologically amenable metals such as the lanthanides. The challenge now is to see if we can build bigger clusters to improve the blocking temperatures and apply this more generally.

Computer hard discs are made up of magnetic material which record digital signals. The smaller you can make these tiny magnets the more information you can store.

Although it may have somewhat negative PR it seems depleted Uranium — a by-product from uranium enrichment and of no use in nuclear applications because the radioactive component has been removed — could now hold some of the key to their research. Dr Liddle has shown that by linking more than one uranium atom together via a bridging toluene molecule SMM behaviour is exhibited.

He said: “At this stage it is too early to say where this research might lead but single-molecule magnets have been the subject of intense study because of their potential applications to make a step change in data storage capacity and realise high performance computing techniques such as quantum information processing and spintronics.”

Dr Liddle said: “The inherent properties of uranium place it between popularly researched transition and lanthanide metals and this means it has the best of both worlds. It is therefore an attractive candidate for SMM chemistry, but this has never been realised in polymetallic systems which is necessary to make them work at room temperature.”

Dr Liddle is a regular contributor to the School of Chemistry’s award winning Periodic Table of Videos — The website, created by Brady Haran, the University’s film maker in residence, won the 2008 IChemE Petronas Award for excellence in education and training. This video is not supported by your browser at this time.

More information: A delocalized arene-bridged diuranium single-molecule magnet, Nature Chemistry (2011) doi:10.1038/nchem.1028

Single-molecule magnets (SMMs) are compounds that, below a blocking temperature, exhibit stable magnetization purely of molecular origin, and not caused by long-range ordering of magnetic moments in the bulk. They thus show promise for applications such as data storage of ultra-high density. The stability of the magnetization increases with increasing ground-state spin and magnetic anisotropy. Transition-metal SMMs typically possess high-spin ground states, but insufficient magnetic anisotropies. Lanthanide SMMs exhibit large magnetic anisotropies, but building high-spin ground states is difficult because they tend to form ionic bonds that limit magnetic exchange coupling. In contrast, the significant covalent bonding and large spin–orbit contributions associated with uranium are particularly attractive for the development of improved SMMs. Here we report a delocalized arene-bridged diuranium SMM. This study demonstrates that arene-bridged polyuranium clusters can exhibit SMM behaviour without relying on the superexchange coupling of spins. This approach may lead to increased blocking temperatures.

Provided by University of Nottingham (news : web)