Diamond X-rays used to discover tooth decay enzymes

Scientists using Diamond Light Source have made a breakthrough in the battle against tooth decay, with research published in the leading Journal of Molecular Biology (JMB) on 29 April 2011.

Researchers from the UK and Japan used the Diamond synchrotron in Oxfordshire and the Photon Factory in Tsukuba city, Japan, to solve the 3D structure of an enzyme that plays a key role in tooth decay caused by sugar.
Tooth decay can occur when a biofilm, or dental plaque as it is more commonly known, is formed by a large and sticky glucose polymer called glucan. The glucan biofilm contains bacteria and food debris and forms on the surface of the tooth. As they grow, the bacteria secrete acids which break down the tooth’s hard enamel on the surface. The structural information published in JMB provides a critical insight into how the enzyme ‘GTF-SI’, a glucansucrase, forms glucan, the sticky biofilm substance.

“With the use of the Diamond synchrotron and the Photon Factory we have been able to solve not only the structure of the enzyme alone but also its structure when bound to an existing inhibitor. Several inhibitors that prevent this type of enzyme forming glucan have been identified but to date there has been little structural information available. With the data we collected at Diamond and the Photon Factory, we now have a better understanding of how the enzyme functions and how it can be stopped. This structural information should be useful in the design of novel inhibitors that will prevent the biofilm formation by glucansucrases and reduce the risk of possible side effects such as hypoglycaemia. These novel inhibitors could be incorporated into toothpaste and mouthwash, making them more effective at preventing tooth decay," said Sohei Ito, Laboratory of Food Protein Engineering, University of Shizuoka in Japan, and lead researcher on the project.

The structural data collection at the Diamond synchrotron was carried out on the I02 Macromolecular Crystallography (MX) experimental station. Principal Beamline Scientist, Professor Thomas Sorensen, says, “Knowing the 3D structure of the enzyme is like knowing the shape of a lock you need to find a key for – it makes it much easier to find the right key that will fit. In this case, the inhibitor acts like the key, fitting into the lock in just the right way so that it can do its job.”

Sweet is an important favourable taste quality linked to food intake in humans and sucrose, the most common form of sugar, is the most highly consumed sweetener. But sucrose causes tooth decay, or dental caries as it is known. According to the World Oral Health Report 2003, dental caries is a major health problem in most industrialized countries, affecting 60-90% of school children and the vast majority of adults. If left untreated for a long period of time it can result in pain and tooth loss, and can lead to additional infections, periodontitis (gum disease), halitosis (bad breath) and in some cases even death by sepsis. Novel inhibitors open up the potential of reducing the risk of tooth decay by preventing the formation of dental plaque.
Diamond Light Source produces the extremely intense X-ray beams required for looking at the molecular interactions involved in a variety of biological processes. Advances in structural biology have accelerated greatly as a result of access to the synchrotron facilities that have been developed around the world in the past 25 years. Biologists have been swift to recognise the huge potential that lies behind understanding the multitude of processes that take place within living organisms at a molecular level. Researchers in the UK are at the forefront of this work and Diamond Light Source plays its part in providing cutting edge facilities for protein structure determination.
Diamond currently has five experimental stations dedicated to structural biology as well as an on-site Membrane Protein Laboratory. The work carried out at the synchrotron has the potential to affect our everyday lives. Previous breakthroughs using structural data from Diamond include gaining a better understanding of hypertension in the pre-natal condition pre-eclampsia, learning how a key tuberculosis drug is activated, understanding how bird flu can affect humans, and revealing the mechanism used by HIV to attack the body.

More information: ‘Crystal Structure of Glucansucrase from the Dental Caries Pathogen Streptococcus mutans’ Keisuke Ito, et al. Journal of Molecular Biology, Volume 408, Issue 2, Pages 177-378 (29 April 2011) http://dx.doi.org/ … 02.028 

Provided by Diamond Light Source

Tail hair tells tale of cattle`s diet -- Scientists trace grassland production

 Tail hair can show if cattle have been grass-fed or not, according to scientists. By chemically analysing the tail hair, it is also possible for scientists to tell if, and when, a grass diet has been substituted for other types of feed over the past 12 months.

The findings published in the Journal of Agricultural and Food Chemistry show a clear scientific traceability and verification of grassland production.

“We can no longer depend on paperwork alone to trace production methods or feeds given to farm animals,” says Professor Frank Monahan from the UCD School of Agriculture, Food Science, and Veterinary Medicine at University College Dublin, and the UCD Institute of Food and Health, the first author of the scientific study.

“A tail hair of approximately 30 centimetres in length contains over a year’s information on the animal’s diet, with the hair closest to the skin holding clues to the most recent diet,” he explains.

“By plucking a hair from the tail, cutting it into millimetre segments, and analysing these in sequence we can get information about the diet over the previous days, weeks and months and, importantly, when the diet was changed,” explains Professor Monahan.

The method involves combusting the tail hair and measuring the isotopes of hydrogen, carbon, nitrogen and sulphur emitted.

Following the analysis, the scientists can almost identify the precise day when the grass diet of the animal may have been substituted with cereal or concentrate.

According to the scientists, omega 3 fatty acids are significantly higher in grass-fed beef than they are in cereal-fed beef.  As a result, beef from grass-fed cattle is often labelled and marketed on the basis of having high levels of omega 3 fatty acids and CLA (which together have been linked to several health benefits in humans).

“Consumers are increasingly interested in the origin and authenticity of the food they consume. So there is a clear need for reliable methods to verify the dietary history of farm animals,” says Dr. Aidan Moloney from the Animal and Grassland Research and Innovation Centre at Teagasc, the Irish Agriculture and Food Development Authority, who co-authored the study.

In the US food labels identifying if a farm animal has been ‘grass-fed’ allows for a premium to be charged for the product.

The scientists believe that a similar labelling could help the Irish beef industry to introduce a premium for its products.

The research was funded by the Irish Government’s Department of Agriculture, Fisheries and Food.

In 2006, US scientists used a similar method of chemically analysing tail hair to track the movement of elephants in Kenya. The aim was to help conservationists decide where to locate Elephant sanctuaries. The analysis showed that some elephants in the sanctuaries had raided nearby crop fields for food, a cause for concern among the local populations.

More information: 'Beef authentication and retrospective dietary verification using stable isotope ratio analysis of bovine muscle and tail hair.' Osorio, M.T, et al. (2011) Journal of Agricultural and Food Chemistry, 59 (7), pp 3295–3305

Provided by University College Dublin

New forensic laser technique for hair analysis can reveal historical data

Using a new laser technique, Jim Moran and his colleagues at Pacific Northwest National Laboratory, have devised a method of separating out the parts of hair samples that can reveal details about the recent history of the person to whom it belongs.

In their paper, published in Rapid Communications in Mass Spectrometry, they describe a process they’ve devised whereby hair samples are pulled apart, rather than burned as a whole before being measured by a mass spectrometer. Such a process could be used to reveal personal details about someone, such as what they eaten recently; clues that might provide forensic scientists insight into the behavior of victims of foul play for example, or reveal information as the whereabouts of the accused during the time frame surrounding a crime.

Because traditional laser analysis techniques tended to obliterate entire samples as they burned all of its parts together as a whole (leaving their gases to be released and measured in a spectrometer) Moran and his team chose to use a less destructive type of laser that uses only ultraviolet light (similar to the kind used for LASIK eye corrective surgery). They discovered that by doing so they could essentially break apart the individual pieces and parts of the hair as a hole was bored, which could then be burned separately and tested with the spectrometer; sort of like burning the filings left over when drilling into a piece of wood with an iron bit. Because hair grows slowly over time, it creates a timeline of sorts, with different stages representing differing days, weeks or even months The new technique allows for dozens of such holes up to be burned up and down the length of a single strand of hair, retrieving different samples that represent different points in time. Then, by studying the different stages of that timeline, analysts are able to piece together a historical picture of what someone has been eating during different times in the past.

Currently the technique only looks at carbon isotopes released when hair is burned, which is how a historical diet is put together; subsequent experiments however will look at oxygen and nitrogen isotopes as well, to get a better picture of water, sulfur and other mineral intakes which could help identify other environmental circumstances prior to the sample being taken.

More information: Laser ablation isotope ratio mass spectrometry for enhanced sensitivity and spatial resolution in stable isotope analysis, James J. Moran, Matt K. Newburn, M. Lizabeth Alexander, Robert L. Sams, James F. Kelly, Helen W. Kreuzer, Rapid Communications in Mass Spectrometry, Article first published online: 12 APR 2011 DOI:10.1002/rcm.4985

DOI: 10.1002/rcm.4985

Abstract
Stable isotope analysis permits the tracking of physical, chemical, and biological reactions and source materials at a wide variety of spatial scales. We present a laser ablation isotope ratio mass spectrometry (LA-IRMS) method that enables ?13C measurement of solid samples at 50?µm spatial resolution. The method does not require sample pre-treatment to physically separate spatial zones. We use laser ablation of solid samples followed by quantitative combustion of the ablated particulates to convert sample carbon into CO2. Cryofocusing of the resulting CO2 coupled with modulation in the carrier flow rate permits coherent peak introduction into an isotope ratio mass spectrometer, with only 65?ng carbon required per measurement. We conclusively demonstrate that the measured CO2 is produced by combustion of laser-ablated aerosols from the sample surface. We measured ?13C for a series of solid compounds using laser ablation and traditional solid sample analysis techniques. Both techniques produced consistent isotopic results but the laser ablation method required over two orders of magnitude less sample. We demonstrated that LA-IRMS sensitivity coupled with its 50?µm spatial resolution could be used to measure ?13C values along a length of hair, making multiple sample measurements over distances corresponding to a single day's growth. This method will be highly valuable in cases where the ?13C analysis of small samples over prescribed spatial distances is required. Suitable applications include forensic analysis of hair samples, investigations of tightly woven microbial systems, and cases of surface analysis where there is a sharp delineation between different components of a sample.

 

Copper ions as morphogens for the formation of polymer films by click chemistry

Scientists are envious of nature because of its ability to build up highly complex structures like organs and tissues in an ordered fashion without any problem; it takes a great deal of effort for scientists to produce defined microscale structures. Pierre Schaaf and a team of scientists from Strasbourg have now imitated a few of nature’s tricks in order to get a polymer film to "grow" onto a surface. As the researchers report in the journal Angewandte Chemie, they used morphogens as nature does. These signal molecules show a reaction which way it should go.

The growth of our bones, seashells, or the complicated forms of diatoms, requires the processes involved in biomineralization to occur along precisely controlled tracks. Molecules cannot simply be allowed to react in an uncontrolled fashion as soon as they encounter each other. In order for a complex organism to develop, every individual cell must know where it is located within a growing organ. Special signal molecules called morphogens inform the cell. They are formed in a specific location and then spread out into the surrounding tissue. This results in concentration gradients, which the cells can use to "orient" themselves.

Schaaf and his co-workers chose a similar strategy to form thin films on a substrate. They also used a sort of morphogen to steer the process. The reactants involved were polymers, one containing azide groups (–N3) and the other with alkyne groups (–C?CH) as side chains. In the presence of positively charged copper ions (CuI), these groups react with each other to form a carbon- and nitrogen-containing five-membered ring, crosslinking the polymers. This type of reaction is called “click chemistry”, because the reaction partners simply snap together.

In a solution containing both click partner and CuI ions, the reaction would immediately proceed at random. This would not result in a thin polymer film. The scientists’ idea was thus to place the CuI ions as a morphogen only on the surface to be coated. Their approach was to place CuII ions in the solution. They then applied an electric voltage to the surface. When CuII ions come into contact with this surface, they take an electron to become CuI. These are thus primarily to be found on the surface. Where there are CuI ions, the click reaction can proceed; the polymers only crosslink into a continuous film on the surface. The magnitude of the applied voltage can be used to control the number of CuI ions and thus the thickness of the film.

More information: Pierre Schaaf, Electrochemically Triggered Film Formation by Click Chemistry, Angewandte Chemie International Edition 2011, 50, No. 19, 4374–4377, http://dx.doi.org/ … ie.201007436

Provided by Wiley (news : web)

Large or small, platinum clusters provide new insights

Using Environmental Molecular Sciences Laboratory's high-performance supercomputing capabilities, scientists helped resolve longstanding controversies about the effect of platinum cluster size on some emissions-reducing reactions in automobile catalysts.

The research team included scientists from the University of California, Nanostellar, Inc., the University of Virginia and Lawrence Berkeley National Laboratory.

Carbon monoxide (CO) removal from combustion exhaust, typically carried out by oxidation on three-way catalysts containing platinum, is critically important for cleaner-burning engines.

The researchers used EMSL’s Chinook supercomputer to carry out detailed ab initio quantum mechanical calculations on very large (201-atom) platinum clusters to model the environment of platinum nanoparticles fully covered with CO.

The team integrated rigorous kinetic, isotopic, and in-situ spectroscopy studies of platinum clusters with theoretical simulations of CO oxidation catalysis at conditions prevalent in many industrial applications to gain a better understanding of catalytic activity on platinum clusters.

When a platinum catalyst covered with CO is at low temperatures, the size of the platinum cluster makes little difference in the rate of oxidation.

For other reactions catalyzed by platinum clusters in automobile exhaust, larger clusters will oxidize nitric oxide or dimethyl ether much faster.

CO oxidation is also a critical step in the production of pure hydrogen streams for use in fuels cells and in many chemical processes.

More information: Allian AD, et al. 2011. "Chemisorption of CO and Mechanism of CO Oxidation on Supported Platinum Nanoclusters." J. Am. Chem. Soc., 2011, 133 (12), pp 4498–4517 DOI: 10.1021/ja110073u

Provided by Environmental Molecular Sciences Laboratory