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 protein and a proteasome recognition tag. This tag typically consists of a chain of ubiquitin molecules, 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 bacteria 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 cells 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 bacterial cells, 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 biomedical devices, 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 metal ions 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 nanomaterials that modify the body's immune response before an organ transplant. 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 stainless steel 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 immune system 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 Journal of Biological Chemistry, 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 tumor cells to go upstream to the lymph nodes," 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 cancerous cells, 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 vascular endothelial growth factor 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 endothelial cells. 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 lymphatic vessels 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

Abstract
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 uranium 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 data storage 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 Nature Chemistry.

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 — periodicvideos.com. 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

Abstract
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)

Early warning system for Alzheimer's disease

 Scientists at the University of Strathclyde in Glasgow are developing a technique based on a new discovery which could pave the way towards detecting Alzheimer's disease in its earliest stages - and could help to develop urgently-needed treatments.

The technique uses the ratio of detected fluorescence signals to indicate that clusters of peptide associated with the disease are beginning to gather and to have an impact on the brain.

Current techniques are not able to see the peptide joining together until more advanced stages but a research paper from Strathclyde describes an approach which could not only give indications of the condition far sooner than is currently possible but could also screen patients without the need for needles or wires.

Alzheimer's disease, the most common form of dementia, currently affects around 450,000 people in the UK alone and currently has no cure.

Dr Olaf Rolinski, of the University of Strathclyde's Department of Physics, led the research. He said: "Alzheimer's Disease has a devastating impact on people around the world and their families but one of the reasons it is still incurable is that little is known about how and why the peptide that contributes to the disease aggregates in its initial stages.

"When irradiated with light, the intrinsic fluorescence given off by the peptide is like a communication from a spy. We took samples of the peptide and discovered that, where they were in the type of aggregation linked to Alzheimer's, they produced fluorescence light signals which could be picked up with our technique much earlier than in more conventional experiments, such as those that use the addition of a dye .

"This approach could help us understand better the role of these peptides in the onset of Alzheimer's and discover ways in which the disease could be stopped in its tracks early on. We now want to take the research further so that it can be used in the development of drugs to treat Alzheimer's."

More information: The research paper, by Dr Rolinski and colleagues Professor David Birch and research student Mariana Amaro, has been published in Physical Chemistry Chemical Physics.

Provided by University of Strathclyde

Tropical blueberries are extreme super fruits

The first analysis of the healthful antioxidant content of blueberries that grow wild in Mexico, Central and South America concludes that some of these fruits have even more healthful antioxidants than the blueberries — already renowned as "super fruits" — sold throughout the United States. These extreme super fruits could provide even more protection against heart disease, cancer and other conditions, the report suggests. It appears in ACS' Journal of Agricultural and Food Chemistry.

Edward Kennelly and colleagues note that although there are over 600 species of blueberries and blueberry-like fruits growing in Mexico, Central and South America (the so-called "neotropics"), very little research has been done on them. U.S.-grown blueberries are already famous for their antioxidants, which help the body get rid of harmful free radicals. So, the researchers decided to find out how neotropical blueberries stacked up against a grocery-store variety.

They found that two types of neotropical blueberries were extreme super fruits — they had significantly more antioxidants than a type of blueberry commonly sold in U.S. supermarkets stores. The researchers say that these neotropical blueberries "have the potential to be even more highly promising edible fruits."

More information: “Edible Neotropical Blueberries: Antioxidant and Compositional Fingerprint Analysis” Journal of Agricultural and Food Chemistry.

Provided by American Chemical Society (news : web)

Water molecules characterize the structure of DNA genetic material

Water molecules surround the genetic material DNA in a very specific way. Scientists at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) have discovered that, on the one hand, the texture of this hydration shell depends on the water content and, on the other hand, actually influences the structure of the genetic substance itself. These findings are not only important in understanding the biological function of DNA; they could also be used for the construction of new DNA-based materials.

The DNA's double helix never occurs in isolation; instead, its entire surface is always covered by water molecules which attach themselves with the help of hydrogen bonds. But the DNA does not bind all molecules the same way. "We've been able to verify that some of the water is bound stronger whereas other molecules are less so," notes Dr. Karim Fahmy, Head of the Biophysics Division at the Institute of Radiochemistry. This is, however, only true if the water content is low. When the water sheath swells, these differences are adjusted and all hydrogen bonds become equally strong. This, in turn, changes the geometry of the DNA strand: The backbone of the double helix, which consists of sugar and phosphate groups, bends slightly. "The precise DNA structure depends on the specific amount of water surrounding the molecule," summarizes Dr. Fahmy.

Analyses of the genetic material were conducted at the HZDR by the doctoral candidate Hassan Khesbak. The DNA, which came from salmon testes, was initially prepared in thin films and then wetted with ultrafine doses of water within a few seconds. With the help of infrared spectroscopy, Hassan Khesbak was able to verify that the strength of hydrogen bonds varies and that water molecules exhibit different rest periods in such configurations. Oscillations of the water bonds in the hydration shell of the double helix can be excited by infrared light. The higher the frequency of the oscillation, the looser the hydrogen bond. It became apparent that the sugar components and the base pairs create particularly strong bonds with the water sheath while the bonds between the water and the phosphate groups are weaker. The results were published just recently in the Journal of the American Chemical Society.

"DNA is, thus, a responsive material," explains Karim Fahmy. "By this, we refer to materials which react dynamically to varying conditions. The double helix structure, the strength of the hydrogen bonds, and even the DNA volume tend to change with higher water contents." Already today, genetic material is an extraordinarily versatile and interesting molecule for so-called DNA nanotechnology. Because with DNA it is possible to realize highly ordered structures with new optical, electronic, and mechanical properties at tiny dimensions which are also of interest for the HZDR. The bound water sheath is not just an integral part of such structures. It can also assume a precise switching function because the results indicate that increasing the hydration shell by only two water molecules per phosphate group may cause the DNA structure to "fold" instantly. Such water dependent switching processes might be able to control, for example, the release of active agents from DNA-based materials.

It does not come as a complete surprise that the water sheath of the genetic material is also of great relevance to the natural biological function of DNA. Because every biomolecule which is bound to the DNA has to first displace the water sheath. The Dresden scientists have analyzed this process for the peptide indolicidin. This antimicrobial protein is less structured and very flexible. That it still "identifies" the double helix so precisely is due to the fact that highly structured water molecules are released when it coalesces with the genetic material. The water sheath's restructuring, which is actually an energetic advantage, increases the binding of the active agent. Such details are really important for the development of DNA-binding drugs, for example, in cancer therapy because they can be ascertained with the method developed at the HZDR.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by Helmholtz Association of German Research Centres, via EurekAlert!, a service of AAAS.

Journal Reference:

Hassan Khesbak, Olesya Savchuk, Satoru Tsushima, Karim Fahmy. The Role of Water H-Bond Imbalances in B-DNA Substate Transitions and Peptide Recognition Revealed by Time-Resolved FTIR Spectroscopy. Journal of the American Chemical Society, 2011; 133 (15): 5834 DOI: 10.1021/ja108863v

Fine chemical processes safer and more efficient with new type of reactor

Researcher Marco Meeuwse of Eindhoven University of Technology (TU/e) has developed a unique chemical reactor, the 'spinning disc reactor'. This is a cylinder containing a rotor that increases the safety and efficiency of chemical production processes involving gases, liquids and solids through its very high mass transfer rate. This new reactor is particularly beneficial for the pharmaceutical and fine chemical industries.

The idea of the 'spinning disc reactor' came from Meeuwse's co-supervisor dr.ir. John van der Schaaf. Around five years ago he had seen a research project in which a liquid was sprayed onto a rotating disc and driven outwards by centrifugal force.

Assistant professor Van der Schaaf thought that combining the rotating disc with a nearby wall would create high shear stress and rapid turbulence, leading to high efficiency. He asked doctoral candidate Meeuwse to investigate whether this was true. Now, four years later, he can say without hesitation that the newly developed reactor does exactly what was expected of it. "In fact it does even more," says Meeuwse. "We were sure it would perform better than the conventional reactors, but we didn't expect it to be so much better."

Gas is fed into the reactor through the floor of the cylinder, with the rotating disc located just above it. The gas bubbles are effectively sheared off by the high-speed flow of rotating liquid through which they pass. "The higher the rotational speed, the smaller the bubbles and the larger the surface area," explains Meeuwse. "That translates into a higher rate of reaction and mass transfer. That was confirmed every time by analyses of the images of the gas-liquid flow and the mass transfer measurements."

Meeuwse was able to scale-up the principle by using a series of rotating discs. Three discs with a diameter of 13 cm were mounted on a shared spindle in a cylinder. "If each unit does the same thing, the total mass transfer of the three discs in series should also be three times as great. Our measurements clearly showed that this reasoning was true, providing the proof that we can scale the system up." An extra benefit of the reactor is that it is safer, because it is much smaller than conventional reactors. This is a big advantage in processes using hazardous substances.

Further development of the reactor is currently in full swing, and a number of related PhD projects are in progress at TU/e. A major equipment manufacturer has become involved, and several chemical and pharmaceutical companies have also shown interest, Meeuwse explains. "We know that this reactor is better than the conventional types. We have measured improvements by factors ranging from two to ten, but we haven't yet been able to identify the full potential of the new concept."

Is there a big market for this new type of reactor? "It is definitely usable for processes in which conversion and selectivity are important factors, such as in the pharmaceutical industry," says Meeuwse. "The raw materials for medicines are very costly, so the less you need to purify the products afterwards, and the less waste you throw away, the more rewarding it will be to use our reactor. In terms of volume it may not be a big market, but on the other hand the processes concerned have a high added value."

Story Source:

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

Diamond light illuminates process of silver decay in Catalonian altarpieces

 

Scientists from the Technical University of Catalonia in Barcelona have teamed up with Diamond Light Source to use a brilliant infrared microbeam to understand at the microscopic scale molecular processes affecting the decay or preservation of polychrome carved wood adorning churches and altarpieces depicting saints.

Celebrated on 23rd April each year, St George is not only the patron saint of England, but also the autonomous region of Catalonia and many other countries. His image, and those of other saints, adorns a number of medieval altarpieces in Catalonia around Europe. But many of these sacred artifacts are badly damaged due to the corrosive effects of air on organic-based glues or varnish that hold or cover the thin silver or gold foils used for the Saints’ aureola – the radiant cloud that surrounds the depicted sacred person.

The results of the group’s work published in the journal Analytical and Bioanalytical Chemistry demonstrate that, under different atmospheric conditions, various geographic areas and different climates, the microscopic alteration compounds formed on precious metal lustres are due to atmospheric corrosion but mainly depend on the state of conservation of the organic protective coating.

Dr. Nati Salvado, from the Technical University of Catalonia and lead researcher on the project, explains: “The conservation state of the silver foil is found to be directly related to the silver-atmosphere contact extent. When protected by a paint layer or a well-preserved resin coating, the silver foil can be found in a good conservation state. On the contrary, if the protective layer appears partly or fully absent leaving the silver surface, either directly or through the cracks, exposed to the atmosphere, the silver alteration products are all that is left.” 

Microscopic samples of silver decorations from various 15th Century artworks in different states of conservation were examined at Diamond.  These include the valuable altarpieces of St George, St Lucia, St Joan and others, some on display in major collections such as the Museu Nacional d’art de Catalunya in Barcelona.

Dr. Salvado said: “We are studying different artworks from the period of the old Crown of Aragon in order to determine the similarities and differences in the painting technique between painters and their relations with other painters in Europe. It is a very interesting historical period because it corresponds to the transition from Gothic to Renaissance style and technique. The artworks were preserved in various geographic areas with different climates, and the corrosion products enable us to assess the effect of the environmental conditions on the corrosion of silver foils.”

More information: ‘SR-XRD and SR-FTIR study of the alteration of silver foils in medieval paintings.' Nati Salvadó, et al. Analytical and Bioanalytical Chemistry, Volume 399, Number 9, 3041-3052. http://dx.doi.org/ … 6-010-4365-5

Provided by Diamond Light Source

Get a whiff of this: Low-cost sensor can diagnose bacterial infections

Bacterial infections really stink. And that could be the key to a fast diagnosis.

Researchers have demonstrated a quick, simple method to identify infectious bacteria by smell using a low-cost array of printed pigments as a chemical sensor. Led by University of Illinois chemistry professor Ken Suslick, the team published its results in the Journal of the American Chemical Society.

Hospitals have used blood cultures as the standard for identifying blood-borne bacterial infections for more than a century. While there have been some improvements in automating the process, the overall method has remained largely constant. Blood samples are incubated in vials for 24 to 48 hours, when a carbon dioxide sensor in the vials will signal the presence of bacteria. But after a culture is positive, doctors still need to identify which species and strain of bacteria is in the vial, a process that takes up to another day.

"The major problem with the clinical blood culturing is that it takes too long," said Suslick, the Marvin T. Schmidt professor of chemistry, who also is a professor of materials science and engineering and a member of the Beckman Institute for Advanced Science and Technology. "In 72 hours they may have diagnosed the problem, but the patient may already have died of sepsis."

While there has been some interest in using sophisticated spectroscopy or genetic methods for clinical diagnosis, Suslick's group focused on another distinctive characteristic: smell. Many experienced microbiologists can identify bacteria based on their aroma. Bacteria emit a complex mixture of chemicals as by-products of their metabolism. Each species of bacteria produces its own unique blend of gases, and even differing strains of the same species will have an aromatic "fingerprint."

An expert in chemical sensing, Suslick previously developed an artificial "nose" that can detect and identify poisonous gases, toxins and explosives in the air.

"Our approach to this problem has been to think of bacteria as simply micron-sized chemical factories whose exhaust is not regulated by the EPA," Suslick said. "Our technology is now well-proven for detecting and distinguishing among different chemical odorants, so applying it to bacteria was not much of a stretch."

An array developed by University of Illinois researchers demonstrated on 10 common infectious bacteria. The color changes of the sensor array show what kind of bacteria is growing and even if they are antibiotic resistant. Credit: K. S. Suslick

The artificial nose is an array of 36 cross-reactive pigment dots that change color when they sense chemicals in the air. The researchers spread blood samples on Petri dishes of a standard growth gel, attached an array to the inside of the lid of each dish, then inverted the dishes onto an ordinary flatbed scanner. Every 30 minutes, they scanned the arrays and recorded the color changes in each dot. The pattern of color change over time is unique to each bacterium.

"The progression of the pattern change is part of the diagnosis of which bacteria it is," Suslick said. "It's like time-lapse photography. You're not looking just at a single frame, you're looking at the motion of the frames over time."

In only a few hours, the array not only confirms the presence of bacteria, but identifies a specific species and strain. It even can recognize antibiotic resistance – a key factor in treatment decisions.

In the paper, the researchers showed that they could identify 10 of the most common disease-causing bacteria, including the hard-to-kill hospital infection methicillin-resistant Staphylococcus aureus (MRSA), with 98.8 percent accuracy. However, Suslick believes the array could be used to diagnose a much wider variety of infections.

"We don't have an upper limit. We haven't yet found any bacteria that we can't detect and distinguish from other bacteria," he said. "We picked out a sampling of human pathogenic bacteria as a starting point."

Given their broad sensitivity, the chemical-sensing arrays also could enable breath diagnosis for a number of conditions. Medical researchers at other institutions have already performed studies using Suslick's arrays to diagnose sinus infections and to screen for lung cancer.

Next, the team is working on integrating the arrays with vials of liquid growth medium, which is a faster culturing agent and more common in clinical practice than Petri dishes. They have also improved the pigments to be more stable, more sensitive and easier to print. The device company iSense, which Suslick co-founded, is commercializing the array technology for clinical use.

More information: "Rapid Identification of Bacteria with a Disposable Colorimetric Sensing Array," http://pubs.acs.or … 21/ja201634d

Abstract
Rapid identification of both species and even specific strains of human pathogenic bacteria grown on standard agar has been achieved from the volatiles they produce using a disposable colorimetric sensor array in a Petri dish imaged with an inexpensive scanner. All 10 strains of bacteria tested, including Enterococcus faecalis and Staphylococcus aureus and their antibiotic-resistant forms, were identified with 98.8% accuracy within 10 h, a clinically important time frame. Furthermore, the colorimetric sensor arrays also proved useful as a simple research tool for the study of bacterial metabolism and as an easy method for the optimization of bacterial production of fine chemicals or other fermentation processes.

Provided by University of Illinois at Urbana-Champaign (news : web)

Researchers find fat turns into soap in sewers, contributes to overflows

Researchers from North Carolina State University have discovered how fat, oil and grease (FOG) can create hardened deposits in sewer lines: it turns into soap! The hardened deposits, which can look like stalactites, contribute to sewer overflows.

"We found that FOG deposits in sewage collection systems are created by chemical reactions that turn the fatty acids from FOG into, basically, a huge lump of soap," says Dr. Joel Ducoste, a professor of civil, construction and environmental engineering at NC State and co-author of a paper describing the research. Collection systems are the pipes and pumping stations that carry wastewater from homes and businesses to sewage-treatment facilities.

These hardened FOG deposits reduce the flow of wastewater in the pipes, contributing to sewer overflows – which can cause environmental and public-health problems and lead to costly fines and repairs.

The research team used a technique called Fourier Transform Infrared (FTIR) spectroscopy to determine what the FOG deposits were made of at the molecular level. FTIR spectroscopy shoots a sample material with infrared light at various wavelengths. Different molecular bonds vibrate in response to different wavelengths. By measuring which infrared wavelengths created vibrations in their FOG samples, researchers were able to determine each sample's molecular composition.

Using this technique, researchers confirmed that the hardened deposits were made of calcium-based fatty acid salts – or soap.

"FOG itself cannot create these deposits," Ducoste says. "The FOG must first be broken down into its constituent parts: glycerol and free fatty acids. These free fatty acids – specifically, saturated fatty acids – can react with calcium in the sewage collection system to form the hardened deposits.

"Until this point we did not know how these deposits were forming — it was just a hypothesis," Ducoste says. "Now we know what's going on with these really hard deposits."

The researchers are now focused on determining where the calcium in the collection system is coming from, and how quickly these deposits actually form. Once they've resolved those questions, Ducoste says, they will be able to create numerical models to predict where a sewage system may have "hot spots" that are particularly susceptible to these blockages.

Ultimately, Ducoste says, "if we know how – and how quickly – these deposits form, it may provide scientific data to support policy decisions related to preventing sewer overflows."

More information: “Evidence for Fat, Oil, and Grease (FOG) Deposit Formation Mechanisms in Sewer Lines”
Authors: Xia He, Mahbuba Iasmin, Lisa O. Dean, Simon E. Lappi, Joel J. Ducoste, and Francis L. de los Reyes, III, North Carolina State University
Published: forthcoming, Environmental Science & Technology

Abstract
The presence of hardened and insoluble fats, oil, and grease (FOG) deposits in sewer lines is a major cause of line blockages leading to sanitary sewer overflows (SSOs). Despite the central role that FOG deposits play in SSOs, little is known about the mechanisms of FOG deposit formation in sanitary sewers. In this study, FOG deposits were formed under laboratory conditions from the reaction between free fatty acids and calcium chloride. The calcium and fatty acid profile analysis showed that the laboratory-produced FOG deposit displayed similar characteristics to FOG deposits collected from sanitary sewer lines. Results of FTIR analysis showed that the FOG deposits are metallic salts of fatty acid as revealed by comparisons with FOG deposits collected from sewer lines and pure calcium soaps. Based on the data, we propose that the formation of FOG deposits occurs from the aggregation of excess calcium compressing the double layer of free fatty acid micelles and a saponification reaction between aggregated calcium and free fatty acids.

Provided by North Carolina State University (news : web)

Water molecules characterize the structure of DNA genetic material

 

Water molecules surround the genetic material DNA in a very specific way. German scientists at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) have discovered that, on the one hand, the texture of this hydration shell depends on the water content and, on the other hand, actually influences the structure of the genetic substance itself. These findings are not only important in understanding the biological function of DNA; they could also be used for the construction of new DNA-based materials.

The DNA's double helix never occurs in isolation; instead, its entire surface is always covered by water molecules which attach themselves with the help of hydrogen bonds. But the DNA does not bind all molecules the same way. "We've been able to verify that some of the water is bound stronger whereas other molecules are less so," notes Dr. Karim Fahmy, Head of the Biophysics Division at the Institute of Radiochemistry. This is, however, only true if the water content is low. When the water sheath swells, these differences are adjusted and all hydrogen bonds become equally strong. This, in turn, changes the geometry of the DNA strand: The backbone of the double helix, which consists of sugar and phosphate groups, bends slightly. "The precise DNA structure depends on the specific amount of water surrounding the molecule," summarizes Dr. Fahmy.

Analyses of the genetic material were conducted at the HZDR by the doctoral candidate Hassan Khesbak. The DNA, which came from salmon testes, was initially prepared in thin films and then wetted with ultrafine doses of water within a few seconds. With the help of infrared spectroscopy, Hassan Khesbak was able to verify that the strength of hydrogen bonds varies and that water molecules exhibit different rest periods in such configurations. Oscillations of the water bonds in the hydration shell of the double helix can be excited by infrared light. The higher the frequency of the oscillation, the looser the hydrogen bond. It became apparent that the sugar components and the base pairs create particularly strong bonds with the water sheath while the bonds between the water and the phosphate groups are weaker. The results were published just recently in the professional magazine Journal of the American Chemical Society.

"DNA is, thus, a responsive material," explains Karim Fahmy. "By this, we refer to materials which react dynamically to varying conditions. The double helix structure, the strength of the hydrogen bonds, and even the DNA volume tend to change with higher water contents." Already today, genetic material is an extraordinarily versatile and interesting molecule for so-called DNA nanotechnology. Because with DNA it is possible to realize highly ordered structures with new optical, electronic, and mechanical properties at tiny dimensions which are also of interest for the HZDR. The bound water sheath is not just an integral part of such structures. It can also assume a precise switching function because the results indicate that increasing the hydration shell by only two water molecules per phosphate group may cause the DNA structure to "fold" instantly. Such water dependent switching processes might be able to control, for example, the release of active agents from DNA-based materials.

It does not come as a complete surprise that the water sheath of the genetic material is also of great relevance to the natural biological function of DNA. Because every biomolecule which is bound to the DNA has to first displace the water sheath. The Dresden scientists have analyzed this process for the peptide indolicidin. This antimicrobial protein is less structured and very flexible. That it still "identifies" the double helix so precisely is due to the fact that highly structured water molecules are released when it coalesces with the genetic material. The water sheath's restructuring, which is actually an energetic advantage, increases the binding of the active agent. Such details are really important for the development of DNA-binding drugs, for example, in cancer therapy because they can be ascertained with the method developed at the HZDR.

More information: doi: 10.1021/ja108863v

Provided by Helmholtz Association of German Research Centres (news : web)

Chemists fabricate 'impossible' material

When atoms combine to form compounds, they must follow certain bonding and valence rules. For this reason, many compounds simply cannot exist. But there are some compounds that, although they follow the bonding and valence rules, still are thought to not exist because they have unstable structures. Scientists call these compounds "impossible compounds." Nevertheless, some of these impossible compounds have actually been fabricated (for example, single sheets of graphene were once considered impossible compounds). In a new study, scientists have synthesized another one of these impossible compounds -- periodic mesoporous hydridosilica -- which can transform into a photoluminescent material at high temperatures.

The researchers, led by Professor Geoffrey Ozin of the Chemistry Department at the University of Toronto, along with coauthors from institutions in Canada, China, Turkey, and Germany, have published their study in a recent issue of the Journal of the American Chemical Society.

Like graphene, periodic mesoporous hydridosilica (meso-HSiO1.5) consists of a honeycomb-like lattice structure. Theoretically, the structure should be so thermodynamically unstable that the mesopores (the holes in the honeycomb) should immediately collapse into a denser form, HSiO1.5, upon the removal of the template on which the material was synthesized.

In their study, the researchers synthesized the mesoporous material on an aqueous acid-catalyzed template. When they removed the template, they discovered that the impossible material remains stable up to 300 °C. The researchers attribute the stability to hydrogen bonding effects and steric effects, the latter of which are related to the distance between atoms. Together, these effects contribute to the material’s mechanical stability by making the mesopores resistant to collapse upon removal of the template.

“The prevailing view for more than 50 years in the massive field of micro-, meso-, or macroporous materials is that a four-coordinate, three-connected open framework material (called disrupted frameworks) should be thermodynamically unstable with respect to collapse of the porosity and therefore should not exist,” Ozin told PhysOrg.com. “The discovery that this class of material can indeed exist with impressive stability is not a special effect related to the choice of the template, but rather that intrinsic hydrogen bonding between the silicon hydride O3SiH units and silanol O3SiOH that pervade the pore walls is strong enough to provide the meso-HSiO1.5 open-framework material with sufficient mechanical strength for it to be able to sustain the porosity intact in the as-synthesized template-containing and template-free material. This discovery is the big scientific surprise – so never say never when it comes to chemical synthesis.”

When raising the temperature above 300 °C, the researchers discovered that the mesoporous material undergoes a “metamorphic” transformation. This transformation eventually yields a silicon-silica nanocomposite material embedded with brightly photoluminescent silicon nanocrystals. Because the novel nanocomposite material retains its periodic mesoporous structure, the nanocrystals are evenly distributed throughout the structure. According to the researchers, the origin of the photoluminescence likely arises from quantum confinement effects inside the silicon nanocrystals.

In addition, the researchers found that they could control the photoluminescent properties of the nanocrystals by changing the thermal treatment. They predict that this ability could allow the bright nanocrystals to be used in the development of light-emitting devices, solar energy devices, and biological sensors.

“Now we have a periodic mesoporous hydridosilica in which we can exploit the chemistry of the silicon-hydride bonds that permeate the entire void space of the material,” Ozin said. “Every silicon in the structure has a Si-H bond to play creative synthetic games. This is a big deal in terms of it serving as a novel solid-state reactive host material within which one can perform novel chemistry limited only by one’s imagination, and a myriad new materials will emerge with a cornucopia of opportunities for creative discovery and invention.”

More information: Zhuoying Xie, et al. “Periodic Mesoporous Hydridosilica – Synthesis of an ‘Impossible’ Material and Its Thermal Transformation into Brightly Photoluminescent Periodic Mesoporous Nanocrystal Silicon-Silica Composite.” Journal of the American Chemical Society. DOI:10.1021/ja111495x

Copyright 2010 PhysOrg.com.
All rights reserved. This material may not be published, broadcast, rewritten or redistributed in whole or part without the express written permission of PhysOrg.com.

NJIT professor develops biologically-inspired catalysis active, yet inert materials

NJIT Associate Professor Sergiu M. Gorun is leading a research team to develop biologically-inspired catalysis active, yet inert, materials. The work is based on organic catalytic framework made sturdy by the replacement of carbon-hydrogen bonds with a combination of aromatic and aliphatic carbon-fluorine bonds. Graduate students involved with this research recently received first place recognition at the annual NJIT Dana Knox student research showcase.

The newest focus of Gorun's research has been the cobalt complex as a catalyst for which the known degradation pathways appear to have been suppressed. "Broadening the Reactivity Spectrum of a Phthalocyanine Catalyst While Suppressing Its Nucleophilic, Electrophilic and Radical Degradation Pathways" by Gorun and others appeared in the web issue of Dalton Transactions (2011), ASAP Communication. Similar to a previous publication, this recent one addresses an important industrial process, the "sweetening" of petroleum products by the transformation of smelly and corrosive thiols into disufides. The extreme electronic deficiency of the new catalyst metal center allows it to process molecules that are not reactive in the presence of regular catalysts that perform this chemistry industrially.

Two years ago Gorun and his team reported that the related zinc perfluoroalkylated phthalocyanine, a molecule resembling the porphyrin core of several heme enzymes, exhibit highly-efficient photochemical oxygenation of an organic substrate. This was of great interest to the fragrance industry ("Rational design of a reactive yet stable organic-based photocatalyst" Dalton Transactions, 2009, 1098).

Concurrently, the unusual properties of Gorun's new materials are explored in parallel in constructing surface coatings, an area in which Gorun was awarded US patent 7,670,684. Several publications describe the properties of the new coatings.

More information: DOI: 10.1039/C1DT10458F

Provided by New Jersey Institute of Technology

Discovery of relationship between proteins may impact development of cancer therapies

By identifying a surprising association of two intracellular proteins, University of Iowa researchers have laid the groundwork for the development of new therapies to treat B cell lymphomas and autoimmune disease.

The researchers studied mouse B cells expressing the viral protein Latent Membrane Protein 1 (LMP1), which has been implicated in several types of cancer because of its role in the proliferation and survival of Epstein-Barr virus infected B cells. They discovered that LMP1 needs the cellular protein Tumor Necrosis Factor Receptor-Associated Factor 6 (TRAF6) to promote its B cell activation signaling pathways.

The study, published recently in the Journal of Biological Chemistry, also shows that LMP1 and CD40 – a normal activating receptor of B cells – both use TRAF6 as a key signaling protein, but in different ways. LMP1 mimics CD40 in delivering activation signals to B cells, but LMP1's signals are amplified and sustained, resulting in B cell hyper-activation.

B cells are a type of white blood cell. They normally mature into plasma cells that produce proteins called antibodies necessary to fight off infections. But in the process of modifying antibody genes, mistakes can cause mutations. With an accumulation of such mutations, B cells can become cancerous, which is why B cell malignancies are relatively common.

"We found that TRAF6 is essential for LMP1 functions, and that it interacts with LMP1 in a way that is distinct from the way in which TRAF6 interacts with CD40," said lead author Kelly Arcipowski, a Ph.D. candidate in the UI Molecular and Cellular Biology Interdisciplinary Graduate Program. "Thus, it might be possible to target LMP1 signaling without disrupting normal immune function. This information is valuable to the development of new therapies to target LMP1-mediated pathogenesis, including B cell lymphomas and autoimmune disease."

B-cell lymphomas include Hodgkin's lymphomas and most non-Hodgkin's lymphomas. Examples of autoimmune diseases in which LMP1 is implicated are rheumatoid arthritis and systemic lupus erythematosus (SLE).

LMP1 is produced by a normally latent gene that is expressed when Epstein-Barr virus, a herpes virus that infects greater than 90 percent of humans, becomes reactivated from its inactive state. This can occur in flares of autoimmune disease, and in people who are immune-deficient. Epstein-Barr virus can thus become activated in cases of late-stage AIDS or organ and bone marrow transplant recipients who are immunosuppressed to prevent rejection of the transplant.

While LMP1 contributes to the formation of a tumor, it isn't an ideal target for therapeutics. LMP1 is a protein that is being constantly internalized from the cell surface, prompting researchers to instead target the signaling pathway.

"(Researchers) first thought you would be targeting the normal protein (CD40), too," said senior study author Gail Bishop, Ph.D., professor of microbiology at the UI Carver College of Medicine and director of the Immunology Interdisciplinary Graduate Program. "What our lab has discovered over the years is that LMP1 produces CD40-like effects using the same proteins in different ways, and therefore that opens a window to targeting just LMP1."

Arcipowski currently is researching how TRAF6 is activating the LMP1 signaling pathway.
"If you figured out exactly which part of TRAF6 was binding to LMP1, you could target that specific interaction while leaving TRAF6's association with CD40 intact," Arcipowski said.

Provided by University of Iowa Health Care

Biophysicist targeting IL-6 to halt breast, prostate cancer

An Ohio State biophysicist used a supercomputer to search thousands of molecular combinations for the best configuration to block a protein that can cause breast or prostate cancer.

Chenglong Li, Ph.D., an assistant professor of medicinal chemistry and pharmacognosy at The Ohio State University (OSU), is leveraging a powerful computer cluster at the Ohio Supercomputer Center (OSC) to develop a drug that will block the small protein molecule Interleukin-6 (IL-6). The body normally produces this immune-response messenger to combat infections, burns, traumatic injuries, etc. Scientists have found, however, that in people who have cancer, the body fails to turn off the response and overproduces IL-6.

"There is an inherent connection between inflammation and cancer," explained Li. "In the case of breast cancers, a medical review systematically tabulated IL-6 levels in various categories of cancer patients, all showing that IL-6 levels elevated up to 40-fold, especially in later stages, metastatic cases and recurrent cases."

In 2002, Japanese researchers found that a natural, non-toxic molecule created by marine bacteria – madindoline A (MDL-A) – could be used to mildly suppress the IL-6 signal. Unfortunately, the researchers also found the molecule wouldn't bind strongly enough to be effective as a cancer drug and would be too difficult and expensive to synthesize commercially. And, most surprisingly, they found the bacteria soon mutated to produce a different, totally ineffectual compound. Around the same time, Stanford scientists were able to construct a static image of the crystal structure of IL-6 and two additional proteins.

Li recognized the potential of these initial insights and partnered last year with an organic chemist and a cancer biologist at OSU's James Cancer Hospital to further investigate, using an OSC supercomputer to construct malleable, three-dimensional color simulations of the protein complex.

"The proximity of two outstanding research organizations – the James Cancer Hospital and OSC – provide a potent enticement for top medical investigators, such as Dr. Li, to conduct their vital computational research programs at Ohio State University," said Ashok Krishnamurthy, interim co-executive director of OSC.

"We proposed using computational intelligence to re-engineer a new set of compounds that not only preserve the original properties, but also would be more potent and efficient," Li said. "Our initial feasibility study pointed to compounds with a high potential to be developed into a non-toxic, orally available drug."

Li accessed 64 nodes of OSC's Glenn IBM 1350 Opteron cluster to simulate IL-6 and the two additional helper proteins needed to convey the signal: the receptor IL-6R and the common signal-transducing receptor GP130. Two full sets of the three proteins combine to form a six-sided molecular machine, or "hexamer," that transmits the signals that will, in time, cause cellular inflammation and, potentially, cancer.

 

An electrostatic representation (red: negative; blue: positive; white: hydrophobic) created at the Ohio Supercomputer Center by Ohio State?s Chenglong Li, Ph.D., shows IL-6 in ribbon representation. The two larger yellow ellipses indicate the two binding "hot spots" between IL-6 and GP130, key to blocking a protein that plays a role in breast and prostate cancer. Credit: Chenglong Li/OSU

Li employed the AMBER (Assisted Model Building with Energy Refinement) and AutoDock molecular modeling simulation software packages to help define the interactions between those proteins and the strength of their binding at five "hot spots" found in each half of the IL-6/IL-6R/GP130 hexamer.

By plugging small molecules, like MDL-A, into any of those hot spots, Li could block the hexamer from forming. So, he examined the binding strength of MDL-A at each of the hexamer hotspots, identifying most promising location, which turned out to be between IL-6 and the first segment, or modular domain (D1), of the GP130.

To design a derivative of MDL-A that would dock with D1 at that specific hot spot, Li used the CombiGlide screening program to search through more than 6,000 drug fragments. So far, he has identified two potential solutions by combining the "top" half of the MDL-A molecule with the "bottom" half of a benzyl molecule or a pyrazole molecule. These candidates preserve the important binding features of the MDL-A, while yielding molecules with strong molecular bindings that also are easier to synthesize than the original MDL-A.

"While we didn't promise to have a drug fully developed within the two years of the project, we're making excellent progress," said Li. "The current research offers us an exciting new therapeutic paradigm: targeting tumor microenvironment and inhibiting tumor stem cell renewal, leading to a really effective way to overcome breast tumor drug resistance, inhibiting tumor metastasis and stopping tumor recurrence."

While not yet effective enough to be considered a viable drug, laboratory tests on tissue samples have verified the higher potency of the derivatives over the original MDL-A. Team members are preparing for more sophisticated testing in a lengthy and carefully monitored evaluation process.

Li's project is funded by a grant from the Department of Defense (CDMRP grant number BC095473) and supported by the award of an OSC Discovery Account. The largest funding areas of Congressionally Directed Medical Research Programs (CDMRP) are breast cancer, prostate cancer and ovarian cancer. Another Defense CDMRP grant involving Li supports a concurrent OSU investigation of the similar role that IL-6 plays in causing prostate cancer. Those projects are being conducted in collaboration with Li's Medicinal Chemistry colleague, Dr. James Fuchs, as well as Drs. Tushar Patel, Greg Lesinski and Don Benson at OSU's College of Medicine and James Cancer Hospital, and Dr. Jiayuh Lin at Nationwide Children's Hospital in Columbus.

"In addition to leading the center's user group this year, the number and depth of Dr. Li's computational chemistry projects have ranked him one of our most prolific research clients," Krishnamurthy noted.

Provided by Ohio Supercomputer Center

Toward new medications for chronic brain diseases

A needle-in-the-haystack search through nearly 390,000 chemical compounds had led scientists to a substance that can sneak through the protective barrier surrounding the brain with effects promising for new drugs for Parkinson's and Huntington's disease. They report on the substance, which blocks formation of cholesterol in the brain, in the journal, ACS Chemical Biology.

Aleksey G. Kazantsev and colleagues previously discovered that blocking cholesterol formation in the brain could protect against some of the damage caused by chronic brain disorders like Parkinson's disease. Several other studies have suggested that too much cholesterol may kill brain cells in similar neurodegenerative diseases. So they launched a search for a so-called "small molecules" — substances ideal for developing into medicines — capable of blocking formation of cholesterol.

They describe discovery of a small molecule that blocks the activity of a key protein involved in cholesterol production. It successfully lowered cholesterol levels in isolated nerve cells and brain slices from mice. If the molecule proves to be a good target for developing new drugs, the scientists note, "it could have a broader application in other neurological conditions, such as Alzheimer's disease, for which modulation of cholesterol and other associated metabolic pathways might be of therapeutic benefit."

Provided by American Chemical Society (news : web)

Researchers combine active proteins with material derived from fruit fly

 

Researchers at Rice University and Texas A&M have discovered a way to pattern active proteins into bio-friendly fibers. The "eureka" moment came about because somebody forgot to clean up the lab one night.

The new work from the Rice lab of biochemist Kathleen Matthews, in collaboration with former Rice faculty fellow and current Texas A&M assistant professor Sarah Bondos, simplifies the process of making materials with fully functional proteins. Such materials could find extensive use as chemical catalysts and biosensors and in tissue engineering, for starters.

Their paper in today's online edition of Advanced Functional Materials details a method to combine proteins with a transcription factor derived from fruit flies and then draw it into fine, strong strands that can be woven into any configuration.

Bondos and Matthews led the team that included primary author Zhao Huang and research technician Taha Salim, both of Rice, and research assistants Autumn Brawley and Jan Patterson, both of Texas A&M.

The research had its genesis while Bondos was in Matthews' Rice lab studying Ultrabithorax (Ubx), a recombinant transcription factor protein found in Drosophila melanogaster (the common fruit fly). This protein regulates the development of wings and legs.

"It's biodegradable, nontoxic and made of naturally occurring proteins -- though we have no reason to believe that fruit flies ever produce enough of these proteins to actually make fibers," Bondos said.

It was a surprise, then, to find that Ubx self-assembles into a film under relatively mild conditions.

"I was cleaning up in the lab one morning and I noticed what appeared to be a drop of water suspended in midair beneath a piece of equipment I was using the previous night," Bondos recalled.

It turned out the droplet was water encased in a sac of Ubx film. The sac was hanging by a Ubx fiber so thin that it was more difficult to see than a strand of a spider's web, Bondos said.

"It clued us in that this was making materials," said Matthews, Rice's Stewart Memorial Professor of Biochemistry and Cell Biology and former dean of the Wiess School of Natural Sciences.

The chance discovery prompted a 2009 paper in the journal Biomacromolecules about the material they dubbed "ultrax," a superstrong and highly elastic natural fiber.

"We found that if you put a little drop of this protein solution on a slide, the Ubx forms a film. And if you touch a needle to that film, you can draw a fiber," Matthews said. "Then we asked, What if we could incorporate other functions into these materials? Can we make chimeras?" The answer was yes, though it took ingenuity to prove.

Chimeras in the biological world contain genetically distinct cells from two or more sources. In Greek mythology, chimeras are beings with parts from multiple animals; a pig with wings, for instance, would qualify. But real chimeras are usually more subtle. On the molecular level, chimeras are proteins that are fused into a single polypeptide and can be purified as a single molecular entity.

As a proof of principle, the team used gene-fusion techniques to create chimeras by combining Ubx with fluorescent and luminescent proteins to see if they remained functional. They did. The combined materials still formed a film on water. Drawn into fibers and put under a microscope, Ubx combined with enhanced green fluorescent protein (EGFP) kept its bright green color. Ubx-mCherry was bright red, the brown protein myoglobin (from sperm whales) was brown, and luciferase glowed.

Huang was able to make patterns with strands generated by the chimeras by twisting red and green fluorescent proteins into candy cane-like tubes, or lacing them on a frame. "This patterning technique is pretty unique and very simple," said Huang, who recently defended his thesis on the subject. He said making solid materials with functional proteins often requires harsh chemical or physical processing that damages the proteins' effectiveness. But creating complex three-dimensional structures with Ubx is efficient and requires no specialized equipment.

Bondos is studying how many proteins are amenable to fusion with Ubx. "It looks like it's a fairly wide range, and even though Ubx is positively charged, both positively and negatively charged proteins can be incorporated." She said even proteins that don't directly fuse with Ubx may be able to connect through intermediary binding partners.

Bondos said the 2009 paper "showed we could make three-dimensional scaffolds. We can basically make rods and sheets and meld them together; anything you can build with Legos, we can build with Ubx."

Ubx-based materials can match the natural properties of elastin, the protein that makes skin and other tissues pliable, Bondos said. "You don't want to make a heart out of something hard, and you don't want to make a bone out of something soft," she said. "We can tune the mechanical properties by changing the diameter of the fibers."

She said functionalized Ubx offers a path to growing three-dimensional organs layer by layer. "We should be able to build something shaped like a heart, and because we can pattern the chimeras within fibers and films, we can build instructions into the material that cause cells to differentiate as muscle, nerves, vasculature and other things."

Bondos suggested the material might also be useful for replacing damaged nerves. "We should be able to stimulate cell attachment and nerve growth along the middle and factors on the ends to enhance attachment to existing nerve cells, to tie it into the patient. It really is pretty exciting."

Matthews said the ability to characterize and pattern fibers for different functions should find many uses, because enzymes, antibodies, growth factors and peptide recognition sequences can now be incorporated into biomaterials. She said sequential arrays of functional fibers for step-by-step catalysis of materials is also possible.

"You're only limited by your mechanical imagination," she said.

More information: http://onlinelibra … 067/abstract

Provided by Rice University (news : web)

A scratched coating heals itself quickly and easily, with light not heat (w/ video)

 Imagine you're driving your own new car--or a rental car--and you need to park in a commercial garage. Maybe you're going to work, visiting a mall or attending an event at a sports stadium, and you're in a rush. Limited and small available spots and concrete pillars make parking a challenge. And it happens that day: you slightly misjudge a corner and you can hear the squeal as you scratch the side of your car--small scratches, but large anticipated repair costs.

Now imagine that that you can repair these unsightly scratches yourself--quickly, easily and inexpensively. . . . or that you can go through a car wash that can detect these and other more minor scratches and fix them as the car goes through the washing garage. Fantasy? Not exactly. Not anymore. Not according to a new discovery detailed in the April 21 issue of the journal Nature, and depicted in a short video interview and simulation:

This video is not supported by your browser at this time.

A team of researchers in the United States and Switzerland have developed a polymer-based material that can heal itself with the help of a widely used type of lighting. Called "metallo-supramolecular polymers," the material is capable of becoming a supple liquid that fills crevasses and gaps left by scrapes and scuffs when placed under ultraviolet light for less than a minute and then resolidifying.

"This is ingenious and transformative materials research," said Andrew Lovinger, polymers program director in NSF's Division of Materials Research. "It demonstrates the versatility and power of novel polymeric materials to address technological issues and serve society while creating broadly applicable scientific concepts."

The team involves researchers at Case Western Reserve University in Cleveland, Ohio, led by Stuart J. Rowan; the Adolphe Merkle Institute of the University of Fribourg in Switzerland, led by Christoph Weder; and the Army Research Laboratory at Aberdeen Proving Ground in Maryland, led by Rick Beyer.

The scientists envision widespread uses in the not-so-distant future for re-healable materials like theirs, primarily as coatings for consumer goods such as automobiles, floors and furniture. While their polymers are not yet ready for commercial use, they acknowledge, they now have proved that the concept works. And with that, what happens next is up to the market place. Necessity, the mother of invention, will expand the possibilities for commercial applications.

"These polymers have a Napoleon Complex," explains lead author Stuart Rowan, a professor of macromolecular engineering and science and director of the Institute for Advanced Materials at Case Western Reserve University. "In reality they're pretty small but are designed to behave like they're big by taking advantage of specific weak molecular interactions."

"Our study is really a fundamental research study," said Christoph Weder, a professor of polymer chemistry and materials and the director of the Adolphe Merkle Institute. "We tried to create materials that have a unique property matrix, that have unique functionality and that in principle could be very useful."

Specifically, the new materials were created by a mechanism known as supramolecular assembly. Unlike conventional polymers, which consist of long, chain-like molecules with thousands of atoms, these materials are composed of smaller molecules, which were assembled into longer, polymer-like chains using metal ions as "molecular glue" to create the metallo-supramolecular polymers.

While these metallo-supramolecular polymers behave in many ways like normal polymers, when irradiated with intense ultraviolet light the assembled structures become temporarily unglued. This transforms the originally solid material into a liquid that flows easily. When the light is switched off, the material re-assembles and solidifies again; its original properties are restored.

Using lamps such as those dentists use to cure fillings, the researchers repaired scratches in their polymers. Wherever they waved the light beam, the scratches filled up and disappeared, much like a cut that heals and leaves no trace on skin. While skin's healing process can be represented by time-lapse photography that spans several days or weeks, self-healing polymers heal in just seconds.

In addition, unlike the human body, durability of the material does not seem to be compromised by repeated injuries. Tests showed the researchers could repeatedly scratch and heal their materials in the same location.

Further, while heat has provided a means to heal materials for a long time, the use of light provides distinct advantages, says Mark Burnworth, a graduate student at Case Western Reserve University. "By using light, we have more control as it allows us to target only the defect and leave the rest of the material untouched."

The researchers systematically investigated several new polymers to find an optimal combination of mechanical properties and healing ability. They found that metal ions that drive the assembly process via weaker chemical interactions serve best as the light-switchable molecular glue.

They also found the materials that assembled in the most orderly microstructures had the best mechanical properties. But, healing efficiency improved as structural order decreased.

"Understanding these relationships is critical for allowing us improve the lifetime of coatings tailored to specific applications, like windows in abrasive environments" Beyer said.

And what's next? According to Rowan, "One of our next steps is to use the concepts we have shown here to design a coating that would be more applicable in an industrial setting."

Film director and art curator Aaron Rose was at least partially right when he said, "In the right light, at the right time, everything is extraordinary." Self-healing polymers certainly are extraordinary.

Provided by National Science Foundation (news : web)

On the way to hydrogen storage?

The car of the future could be propelled by a fuel cell powered with hydrogen. But what will the fuel tank look like? Hydrogen gas is not only explosive but also very space-consuming. Storage in the form of very dense solid metal hydrides is a particularly safe alternative that accommodates the gas in a manageable volume. As the storage tank should also not be too heavy and expensive, solid-state chemists worldwide focus on hydrides containing light and abundant metals like magnesium.

Sjoerd Harder and his co-workers at the Universities of Groningen (Netherlands) and Duisburg-Essen (Germany) now take the molecular approach. As the researchers report in the journal Angewandte Chemie, extremely small clusters of molecular magnesium hydride could be a useful model substance for more precise studies about the processes involved in hydrogen storage.

Magnesium hydride (MgH2) can release hydrogen when needed and the resulting magnesium metal reacts back again to form the hydride by pressurizing with hydrogen at a "gas station". Unfortunately, this is an idealized picture. Not only is the speed of hydrogen release/uptake excessively slow (kinetics) but it also only operates at higher temperatures (thermodynamics). The hydrides, the negatively charged hydrogen atoms (H-), are bound so strongly in the crystal lattice of magnesium cations (Mg2+) that temperatures of more than 300 °C are needed to release the hydrogen gas.

Particularly intensive milling has made it possible to obtain nanocrystalline materials, which, on account of its larger surface, rapidly release or take up hydrogen. However, the high stability of the magnesium hydride still translates to rather high release temperatures. According to recent computer calculations, magnesium hydride clusters of only a few atoms possibly could generate hydrogen at temperatures far below 300 °C. Clusters with less than 20 Mg2+ ions are smaller than one nanometer and behave differently from the bulk material. Their hydride ions have fewer Mg2+ neighbors and are more weakly bound. However, it is extremely difficult to obtain such tiny clusters by milling. In Harder's "bottom-up" approach, magnesium hydride clusters are made by starting from molecules. The challenge is to prevent such clusters from forming very stable bulk material. Using a special ligand system, they could trap a cluster that resembles a paddle wheel made of eight Mg2+ and ten H- ions. For the first time it was shown that molecular clusters indeed release hydrogen already at the temperature of 200 °C.

This largest magnesium hydride cluster reported to date is not practical for efficient hydrogen storage but shines new light on a current problem. It is easily studied by molecular methods and as a model system could provide detailed insights in hydrogen storage.

More information: Sjoerd Harder, Hydrogen Storage in Magnesium Hydride: The Molecular Approach, Angewandte Chemie International Edition 2011, 50, No. 18, 4156–4160, http://dx.doi.org/ … ie.201101153

Provided by Wiley (news : web)