Researchers create more powerful 'lab-on-a-chip' for genetic analysis

UBC researchers have invented a silicone chip that could make genetic analysis far more sensitive, rapid, and cost-effective by allowing individual cells to fall into place like balls in a pinball machine.

The UBC device – about the size of a nine-volt battery – allows scientists to simultaneously analyze 300 cells individually by routing fluid carrying cells through microscopic tubes and valves. Once isolated into their separate chambers, the cells' RNA can be extracted and replicated for further analysis.

By enabling such "single-cell analysis," the device could accelerate genetic research and hasten the use of far more detailed tests for diagnosing cancer.

Single-cell analysis is emerging as the gold standard of genetic research because tissue samples, even those taken from a single tumour, contain a mixture of normal cells and various types of cancer cells – the most important of which may be present in only very small numbers and impossible to distinguish.

So standard genetic tests, which require large numbers of cells, capture only an average "composite picture" of thousands or millions of different cells – obscuring their true nature and the interactions between them.

"It's like trying to trying to understand what makes a strawberry different from a raspberry by studying a blended fruit smoothie," says Carl Hansen, an assistant professor in the Dept. of Physics and Astronomy and the Centre for High-Throughput Biology, who led the team that developed the device.

The device, described and validated in this week's issue of the Proceedings of the National Academy of Sciences, was developed by Hansen's team, in collaboration with researchers from BC Cancer Agency and the Centre for Translational and Applied Genomics.

The device's ease of use and cost-effectiveness arise from its integration of almost the entire process of cell analysis – not just separating the cells, but mixing them with chemical reagents to highlight their genetic code and analyzing the results by measuring fluorescent light emitted from the reaction. Now all of that can be done on the chip.

"Single-cell genetic analysis is vital in a host of areas, including stem cell research and advanced cancer biology and diagnostics," Hansen says. "But until now, it has been too costly to become widespread in research, and especially for use in health care. This technology, and other approaches like it, could radically change the way we do both basic and applied biomedical research, and would make single-cell analysis a more plausible option for treating patients – allowing clinicians to distinguish various cancers from one another and tailor their treatments accordingly."

Provided by University of British Columbia (news : web)

Shuttle service in cells: Scientists find new components for protein transport

Research scientists at the Ruhr University Bochum discovered a new enzyme, which gives decisive insights into protein import into specific cellular organelles (peroxisomes). In the Journal of Biological Chemistry, the team of Prof. Erdmann (Medical Faculty, Department of Systemic Biochemistry) reports that the enzyme Ubp15p collaborates with two other proteins to convert the protein transport machinery back into its initial condition after work has been completed.

The enzyme detaches a specific signal sequence from a protein which is important for transportation and recycling of this protein. A new sequence of protein can then commence. "With Ubp15p we could unravel a further mystery concerning the transport of proteins into peroxisomes", explains Prof. Erdmann. "The comprehension of these organelles at a molecular level is a decisive prerequisite for the development of new diagnostic and therapeutic approaches for patients with peroxisomal disorders who only seldom survive the first year of their life."

Peroxisomes are multifunctional "tools." They are involved, for example, in the catabolism of fatty acids, and detoxify poisonous hydrogen peroxide. A malfunction of these organelles, as is the case in Zellweger Syndrome disorders, can have disastrous influences on the functioning of the liver, kidneys and brain. To be able to function correctly, peroxisomes need specific proteins, but they cannot produce these themselves. Thus, a shuttle system consisting of several receptors has to import them from the cytosol. The receptors recognize the proteins specified for the peroxisomes within the cytosol and escort them to their destination. Here they bond with the membrane of the peroxisome and form part of the "gate" through which the proteins are transported into the interior. An export signal (ubiquitin) is attached to the receptors, which ensures that they are released from the peroxisome membrane and available for transport yet again. What subsequently happens to the ubiquitin signal remains to be clarified.

In an earlier publication in Nature Cell Biology, Prof. Erdmann's team had already described two motor proteins that withdraw the ubiquitin-marked receptor Pex5p from the membrane and transport it back into the cytosol. In a further paper (Nature Reviews Molecular Cell Biology), they postulated that this export of the receptor is mechanistically linked to the import of the peroxisomal protein. To date, it has however not been possible to detect the ubiquitin together with Pex5p in the cytosol. "We thus assumed that the ubiquitin is removed from the receptor during or shortly after export", states Prof. Erdmann. His team, funded by the collaborative research center 642 of the German National Science Foundation (Sonderforschungsbereich 642 der Deutschen Forschungsgemeinschaft), has now established that the enzyme Ubp15p disconnects the export signal and collaborates with the two motor proteins to remove the receptor from the membrane of the peroxisome.

The scientists managed to locate Ubp15p in living yeast cells and to prove that the enzyme comes into direct contact with one of the motor proteins to reach the peroxisomes. When Prof. Erdmann's team deactivated the Ubp15p in the cells, the amount of ubiquitinated Pex5p increased. This result confirms the role of Ubp15p in cleaving the ubiquitin signal. The enzyme seems to have an important function in the import of proteins into the peroxisomes, particularly under stress conditions. "Ubp15p appears to play a vital role in the recycling of the receptor", points out Prof. Erdmann.

Provided by Ruhr-University Bochum

Chemists transform acids into bases

Chemists at the University of California, Riverside have accomplished in the lab what until now was considered impossible: transform a family of compounds which are acids into bases.

As our chemistry lab sessions have taught us, acids are substances that taste sour and react with metals and bases (bases are the chemical opposite of acids). For example, compounds of the element boron are acidic while nitrogen and phosphorus compounds are basic.

The research, reported in the July 29 issue of Science, makes possible a vast array of chemical reactions – such as those used in the pharmaceutical and biotechnology industries, manufacturing new materials, and research academic institutions.

"The result is totally counterintuitive," said Guy Bertrand, a distinguished professor of chemistry, who led the research. "When I presented preliminary results from this research at a conference recently, the audience was incredulous, saying this was simply unachievable. But we have achieved it. We have transformed boron compounds into nitrogen-like compounds. In other words, we have made acids behave like bases."

Bertrand's lab at UC Riverside specializes on catalysts. A catalyst is a substance – usually a metal to which ions or compounds are bound – that facilitates or allows a chemical reaction, but is neither consumed nor altered by the reaction itself. Crucial to the reaction's success, a catalyst is like the car engine enabling an uphill drive. While only about 30 metals are used to form catalysts, the binding ions or molecules, called ligands, can number in the millions, allowing for numerous catalysts. Currently, the majority of these ligands are nitrogen- or phosphorus-based.

"The trouble with using phosphorus-based catalysts is that phosphorus is toxic and it can contaminate the end products," Bertrand said. "Our work shows that it is now possible to replace phosphorus ligands in catalysts with boron ligands. And boron is not toxic. Catalysis research has advanced in small, incremental steps since the first catalytic reaction took place in 1902 in France. Our work is a quantum leap in catalysis research because a vast family of new catalysts can now be added to the mix. What kind of reactions these new boron-based catalysts are capable of facilitating is as yet unknown. What is known, though, is that they are potentially numerous."

Bertrand explained that acids cannot be used as ligands to form a catalyst. Instead, bases must be used. While all boron compounds are acids, his lab has succeeded in making these compounds behave like bases. His lab achieved the result by modifying the number of electrons in boron, with no change to the atom's nucleus.

"It's almost like changing one atom into another atom," Bertrand said.

His research group stumbled upon the idea during one of its regular brainstorming meetings.

"I encourage my students and postdoctoral researchers to think outside the box and not be inhibited or intimidated about sharing ideas with the group," he said. "The smaller these brainstorming groups are, the freer the participants feel about bringing new and unconventional ideas to the table, I have found. About 90 percent of the time, the ideas are ultimately not useful. But then, about 10 percent of the time we have something to work with."

The research was supported by grants to Bertrand from the National Science Foundation and the U.S. Department of Energy.

An internationally renowned scientist, Bertrand came to UCR in 2001 from France's national research agency, the Centre National de la Recherche Scientifique (CNRS). He is the director of the UCR-CNRS Joint Research Chemistry Laboratory.

A recipient of numerous awards and honors, most recently he won the 2009-2010 Sir Ronald Nyholm Prize for his seminal research on the chemistry of phosphorus-phosphorus bonds and the chemistry of stable carbenes and their complexes.

He is a recipient of the Japanese Society for Promotion of Science Award, the Humboldt Award, the International Council on Main Group Chemistry Award, and the Grand Prix Le Bel of the French Chemical Society. He is a fellow of the American Association for the Advancement of Sciences, and a member of the French Academy of Sciences, the European Academy of Sciences, Academia Europea, and Academies des Technologies.

He has authored more than 300 scholarly papers and holds 35 patents.

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

How to tell real whiskey from fake -- faster

Methods for distinguishing between authentic and counterfeit Scotch whisky brands have been devised by scientists at the University of Strathclyde in Glasgow.

Researchers from the Department of Pure and Applied Chemistry have found new ways to compare the content of whisky samples to determine if they are the whisky on the label or an imitation brand.

A series of blind tests successfully put the real whisky brand and the fakes in the right categories. The system could enhance the technology industry uses to tackle the trade in illicit whisky, which costs huge sums in lost revenue and threatens brand reputation.

Professor David Littlejohn, who led the research, said: "The whisky industry has tools at its disposal for telling authentic and counterfeit whisky brands apart but many of them involve lab-based analysis, which isn't always the most convenient system if a sample needs to be identified quickly.

"There's a growing need for methods that can provide simpler and faster identification and we have developed a system which could be adapted for devices to use on site, without the need to return samples to a lab. It could be of great benefit to an industry which is hugely important to the economy."

The researchers analysed 17 samples of blended whisky, looking at the concentration of ethanol in the samples without diluting them and the residue of dried whisky. They did so with mid-infrared spectrometry, used with immersion probes that incorporate novel optical fibres developed by Scottish based company Fibre Photonics Ltd, who co-sponsored the research. The procedures developed can provide prompt, accurate analysis without the complexity and cost of some other systems.

The levels of ethanol and colourant led them to identify correctly the eight authentic and nine counterfeit samples.

The project research paper has been published in Analytica Chimica Acta.

Provided by University of Strathclyde