Tuesday, July 19, 2016
Monday, July 11, 2016
|A rendering of the enormous LHCb detector, which registers approximately 10 million proton collisions per second. Scientists study the debris from these collisions to better understand the building blocks of matter and the forces controlling them.|
|Thomas Britton G'16|
Thursday, June 23, 2016
For 3 billion years, one of the major carriers of information needed for life, RNA, has had a glitch that creates errors when making copies of genetic information. Researchers at The University of Texas at Austin have developed a fix that allows RNA to accurately proofread for the first time. The new discovery, published June 23 in the journal Science, will increase precision in genetic research and could dramatically improve medicine based on a person's genetic makeup.
Certain viruses called retroviruses can cause RNA to make copies of DNA, a process called reverse transcription. This process is notoriously prone to errors because an evolutionary ancestor of all viruses never had the ability to accurately copy genetic material.
The new innovation engineered at UT Austin is an enzyme that performs reverse transcription but can also "proofread," or check its work while copying genetic code. The enzyme allows, for the first time, for large amounts of RNA information to be copied with near perfect accuracy.
"We created a new group of enzymes that can read the genetic information inside living cells with unprecedented accuracy," says Jared Ellefson, a postdoctoral fellow in UT Austin's Center for Systems and Synthetic Biology. "Overlooked by evolution, our enzyme can correct errors while copying RNA."
Reverse transcription is mainly associated with retroviruses such as HIV. In nature, these viruses' inability to copy DNA accurately may have helped create variety in species over time, contributing to the complexity of life as we know it.
Since discovering reverse transcription, scientists have used it to better understand genetic information related to inheritable diseases and other aspects of human health. Still, the error-prone nature of existing RNA sequencing is a problem for scientists.
"With proofreading, our new enzyme increases precision and fidelity of RNA sequencing," says Ellefson. "Without the ability to faithfully read RNA, we cannot accurately determine the inner workings of cells. These errors can lead to misleading data in the research lab and potential misdiagnosis in the clinical lab."
Ellefson and the team of researchers engineered the new enzyme using directed evolution to train a high-fidelity (proofreading) DNA polymerase to use RNA templates. The new enzyme, called RTX, retains the highly accurate and efficient proofreading function, while copying RNA. Accuracy is improved at least threefold, and it may be up to 10 times as accurate. This new enzyme could enhance the methods used to read RNA from cells.
"As we move towards an age of personalized medicine where everyone's transcripts will be read out almost as easily as taking a pulse, the accuracy of the sequence information will become increasingly important," said Andy Ellington, a professor of molecular biosciences. "The significance of this is that we can now also copy large amounts of RNA information found in modern genomes, in the form of the RNA transcripts that encode almost every aspect of our physiology. This means that diagnoses made based on genomic information are far more likely to be accurate. "
Synthetic evolutionary origin of a proofreading reverse transcriptase
Science 24 Jun 2016:
Vol. 352, Issue 6293, pp. 1590-1593
Nanotechnology World Association
Tuesday, June 21, 2016
Scientists can now detect magnetic behavior at the atomic level with a new electron microscopy technique developed by a team from the Department of Energy’s Oak Ridge National Laboratory and Uppsala University, Sweden. The researchers took a counterintuitive approach by taking advantage of optical distortions that they typically try to eliminate.
“It’s a new approach to measure magnetism at the atomic scale,” ORNL’s Juan Carlos Idrobo said.
“We will be able to study materials in a new way. Hard drives, for instance, are made by magnetic domains, and those magnetic domains are about 10 nanometers apart.” One nanometer is a billionth of a meter, and the researchers plan to refine their technique to collect magnetic signals from individual atoms that are ten times smaller than a nanometer.
“If we can understand the interaction of those domains with atomic resolution, perhaps in the future we will able to decrease the size of magnetic hard drives,” Idrobo said. “We won’t know without looking at it.”
Researchers have traditionally used scanning transmission electron microscopes to determine where atoms are located within materials. This new technique allows scientists to collect more information about how the atoms behave.
“Magnetism has its origins at the atomic scale, but the techniques that we use to measure it usually have spatial resolutions that are way larger than one atom,” Idrobo said. “With an electron microscope, you can make the electron probe as small as possible and if you know how to control the probe, you can pick up a magnetic signature.”
The ORNL-Uppsala team developed the technique by rethinking a cornerstone of electron microscopy known as aberration correction. Researchers have spent decades working to eliminate different kinds of aberrations, which are distortions that arise in the electron-optical lens and blur the resulting images.
Instead of fully eliminating the aberrations in the electron microscope, the researchers purposely added a type of aberration, called four-fold astigmatism, to collect atomic level magnetic signals from a lanthanum manganese arsenic oxide material. The experimental study validates the team’s theoretical predictions presented in a 2014 Physical Review Lettersstudy.
“This is the first time someone has used aberrations to detect magnetic order in materials in electron microscopy,” Idrobo said. “Aberration correction allows you to make the electron probe small enough to do the measurement, but at the same time we needed to put in a specific aberration, which is opposite of what people usually do.”
Idrobo adds that new electron microscopy techniques can complement existing methods, such as x-ray spectroscopy and neutron scattering, that are the gold standard in studying magnetism but are limited in their spatial resolution.
The study is published as “Detecting magnetic ordering with atomic size electron probes,” in the journal of Advanced Structural and Chemical Imaging. Coauthors are ORNL’s Juan Carlos Idrobo, Michael McGuire, Christopher Symons, Ranga Raju Vatsavai, Claudia Cantoni and Andrew Lupini; and Uppsala University’s Ján Rusz and Jakob Spiegelberg.
The electron microscopy experiments were conducted at the Center for Nanophase Materials Sciences, a DOE Office of Science User Facility at ORNL. The research was supported by DOE’s Office of Science.
ORNL is managed by UT-Battelle for the Department of Energy's Office of Science, the single largest supporter of basic research in the physical sciences in the United States. DOE’s Office of Science is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.
Nanotechnology World Association
Monday, June 20, 2016
|Three “accelerators on a chip” made of silicon are mounted on a clear base. Credit: SLAC National Accelerator Laboratory|
The Gordon and Betty Moore Foundation has awarded 13.5 million US dollars (12.6 million euros) to promote the development of a particle accelerator on a microchip. DESY and the University of Hamburg are among the partners involved in this international project, headed by Robert Byer of Stanford University (USA) and Peter Hommelhoff of the University of Erlangen-Nürnberg. Within five years, they hope to produce a working prototype of an “accelerator-on-a-chip”.
For decades, particle accelerators have been an indispensable tool in countless areas of research – from fundamental research in physics to examining the structure of biomolecules in order to develop new drugs. Accelerator-based research has repeatedly been awarded Nobel prizes. Until now, the necessary facilities have been very large and costly. Scientists and engineers are trying out a range of different approaches to build more compact and less expensive particle accelerators. For the time being, the big facilities will remain indispensable for many purposes, however there are some applications in which efficient miniature electron accelerators can provide completely new insights.
“The impact of shrinking accelerators can be compared to the evolution of computers that once occupied entire rooms and can now be worn around your wrist,” says Hommelhoff. This advance could mean that particle accelerators will become available in areas that have previously had no access to such technologies.
The aim of the project is to develop a new type of small, inexpensive particle accelerator for a wide range of different users. Apart from using the fast electrons themselves, they could also be used to produce high-intensity X-rays. “This prototype could set the stage for a new generation of ‘tabletop’ accelerators, with unanticipated discoveries in biology and materials science and potential applications in security scanning, medical therapy and X-ray imaging,” explains Byer.
|Some of the accelerator-on-a-chip designs being explored by the international collaboration. Credit: SLAC National Accelerator Laboratory|
The project is based on advances in nano-photonics, the art of creating and using nano structures to generate and manipulate different kinds of light. A laser using visible or infrared light is used to accelerate the electrically charged elementary particles, rather than the radio-frequency (RF) waves currently used. The wavelength of this radiation is some ten to one hundred thousand times shorter than that of the radio waves, meaning that steeper accelerator gradients can be achieved than those using RF technology. “The advantage is that everything is up to fifty times smaller,” explains Franz Kärtner who is a Leading Scientist at DESY, as well as a professor at the University of Hamburg and the Massachusetts Institute of Technology (MIT) in the US, and a member of Hamburg’s Centre for Ultrafast Imaging (CUI), and who heads a similar project in Hamburg, funded by the European Research Council.
“The typical transverse dimensions of an accelerator cell shrink from ten centimetres to one micrometre,” adds Ingmar Hartl, head of the laser group in DESY’s Photon Science Division. At the moment, the material of choice for the miniature accelerator modules is silicon. “The advantage is that we can draw on the highly advanced production technologies that are already available for silicon microchips,” explains Hartl.
DESY will bring its vast knowhow as an internationally leader in laser technology to the project, which has already paid off in other collaborations involving the University of Erlangen-Nürnberg. There, Hommelhoff’s group showed that for slow electrons a micro-structured accelerator module is able to achieve steeper acceleration gradients than RF technology.
Byer’s group had demonstrated independently the same effect for fast, so-called relativistic electrons.
However, it is still a long way from an experimental set-up in a laboratory to a working prototype. Individual components of the system will have to be developed from scratch.
Among other things, DESY is working on a high-precision electron source to feed the elementary particles into the accelerator modules, a powerful laser for accelerating them, and an electron undulator for creating X-rays. In addition, the interaction between the miniature components is not yet a routine matter, especially not when it comes to joining up several accelerator modules.
The SINBAD (“Short Innovative Bunches and Accelerators at DESY”) accelerator lab that is currently being set up at DESY will provide the ideal testing environment for the miniature accelerator modules. “SINBAD will allow us to feed high-quality electron beams into the modules, to test the quality of the radiation and work out an efficient way of coupling the laser.
DESY offers unique opportunities in this respect,” explains Ralph Aßmann, Leading Scientist at DESY.
Apart from DESY, the Universities of Stanford, Erlangen-Nürnberg and Hamburg, SLAC National Accelerator Laboratory in the US, the Swiss Paul Scherrer Institute (PSI) and the University of California in Los Angeles (UCLA), the Purdue University, the Swiss Federal Institute of Technology in Lausanne (EPFL) and the Technical University of Darmstadt are also involved in the project, as well as the US company Tech-X.
The Gordon and Betty Moore Foundation fosters path-breaking scientific discovery, environmental conservation, patient care improvements and the preservation of the special character of the San Francisco Bay Area. Gordon Moore is one of the founders of the chip manufacturer Intel and the author of “Moore's Law”, which predicts that the number of transistors in an integrated circuit doubles approximately every two years.
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