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  • richardmitnick 2:23 pm on May 14, 2015 Permalink | Reply
    Tags: , Electron Microscopy,   

    From LBL: “CLAIRE Brings Electron Microscopy to Soft Materials” 

    Berkeley Logo

    Berkeley Lab

    May 14, 2015
    Lynn Yarris (510) 486-5375

    Berkeley Researchers Develop Breakthrough Technique for Non-invasive Nano-scale Imaging

    CLAIRE image of Al nanostructures with an inset that shows a cluster of six Al nanostructures.

    Soft matter encompasses a broad swath of materials, including liquids, polymers, gels, foam and – most importantly – biomolecules. At the heart of soft materials, governing their overall properties and capabilities, are the interactions of nano-sized components. Observing the dynamics behind these interactions is critical to understanding key biological processes, such as protein crystallization and metabolism, and could help accelerate the development of important new technologies, such as artificial photosynthesis or high-efficiency photovoltaic cells. Observing these dynamics at sufficient resolution has been a major challenge, but this challenge is now being met with a new non-invasive nanoscale imaging technique that goes by the acronym of CLAIRE.

    CLAIRE stands for “cathodoluminescence activated imaging by resonant energy transfer.” Invented by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley, CLAIRE extends the incredible resolution of electron microscopy to the dynamic imaging of soft matter.

    “Traditional electron microscopy damages soft materials and has therefore mainly been used to provide topographical or compositional information about robust inorganic solids or fixed sections of biological specimens,” says chemist Naomi Ginsberg, who leads CLAIRE’s development. “CLAIRE allows us to convert electron microscopy into a new non-invasive imaging modality for studying soft materials and providing spectrally specific information about them on the nanoscale.”

    Naomi Ginsberg

    Ginsberg holds appointments with Berkeley Lab’s Physical Biosciences Division and its Materials Sciences Division, as well as UC Berkeley’s departments of chemistry and physics. She is also a member of the Kavli Energy NanoScience Institute (Kavli-ENSI) at Berkeley. She and her research group recently demonstrated CLAIRE’s imaging capabilities by applying the technique to aluminum nanostructures and polymer films that could not have been directly imaged with electron microscopy.

    “What microscopic defects in molecular solids give rise to their functional optical and electronic properties? By what potentially controllable process do such solids form from their individual microscopic components, initially in the solution phase? The answers require observing the dynamics of electronic excitations or of molecules themselves as they explore spatially heterogeneous landscapes in condensed phase systems,” Ginsberg says. “In our demonstration, we obtained optical images of aluminum nanostructures with 46 nanometer resolution, then validated the non-invasiveness of CLAIRE by imaging a conjugated polymer film. The high resolution, speed and non-invasiveness we demonstrated with CLAIRE positions us to transform our current understanding of key biomolecular interactions.”

    CLAIRE imaging chip consists of a YAlO3:Ce scintillator film supported by LaAlO3 and SrTiO3 buffer layers and a Si frame. Al nanostructures embedded in SiO2 are positioned below and directly against the scintillator film. ProTEK B3 serves as a protective layer for etching.

    CLAIRE works by essentially combining the best attributes of optical and scanning electron microscopy into a single imaging platform. Scanning electron microscopes use beams of electrons rather than light for illumination and magnification. With much shorter wavelengths than photons of visible light, electron beams can be used to observe objects hundreds of times smaller than those that can be resolved with an optical microscope. However, these electron beams destroy most forms of soft matter and are incapable of spectrally specific molecular excitation.

    Ginsberg and her colleagues get around these problems by employing a process called “cathodoluminescence,” in which an ultrathin scintillating film, about 20 nanometers thick, composed of cerium-doped yttrium aluminum perovskite, is inserted between the electron beam and the sample. When the scintillating film is excited by a low-energy electron beam (about 1 KeV), it emits energy that is transferred to the sample, causing the sample to radiate. This luminescence is recorded and correlated to the electron beam position to form an image that is not restricted by the optical diffraction limit.

    Developing the scintillating film and integrating it into a microchip imaging device was an enormous undertaking, Ginsberg says, and she credits the “talent and dedication” of her research group for the success. She also gives much credit to the staff and capabilities of the Molecular Foundry, a DOE Office of Science User Facility, where the CLAIRE imaging demonstration was carried out.

    “The Molecular Foundry truly enabled CLAIRE imaging to come to life,” she says. “We collaborated with staff scientists there to design and install a high efficiency light collection apparatus in one of the Foundry’s scanning electron microscopes and their advice and input were fantastic. That we can work with Foundry scientists to modify the instrumentation and enhance its capabilities not only for our own experiments but also for other users is unique.”

    While there is still more work to do to make CLAIRE widely accessible, Ginsberg and her group are moving forward with further refinements for several specific applications.

    “We’re interested in non-invasively imaging soft functional materials like the active layers in solar cells and light-emitting devices,” she says. “It is especially true in organics and organic/inorganic hybrids that the morphology of these materials is complex and requires nanoscale resolution to correlate morphological features to functions.”

    Ginsberg and her group are also working on the creation of liquid cells for observing biomolecular interactions under physiological conditions. Since electron microscopes can only operate in a high vacuum, as molecules in the air disrupt the electron beam, and since liquids evaporate in high vacuum, aqueous samples must either be freeze-dried or hermetically sealed in special cells.

    “We need liquid cells for CLAIRE to study the dynamic organization of light-harvesting proteins in photosynthetic membranes,” Ginsberg says. “We should also be able to perform other studies in membrane biophysics to see how molecules diffuse in complex environments, and we’d like to be able to study molecular recognition at the single molecule level.”

    In addition, Ginsberg and her group will be using CLAIRE to study the dynamics of nanoscale systems for soft materials in general.

    “We would love to be able to observe crystallization processes or to watch a material made of nanoscale components anneal or undergo a phase transition,” she says. “We would also love to be able to watch the electric double layer at a charged surface as it evolves, as this phenomenon is crucial to battery science.”

    A paper describing the most recent work on CLAIRE has been published in the journal Nano Letters. The paper is titled Cathodoluminescence-Activated Nanoimaging: Noninvasive Near-Field Optical Microscopy in an Electron Microscope. Ginsberg is the corresponding author. Other authors are Connor Bischak, Craig Hetherington, Zhe Wang, Jake Precht, David Kaz and Darrell Schlom.

    This research was primarily supported by the DOE Office of Science and by the National Science Foundation.

    See the full article here.

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    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 12:18 pm on March 28, 2015 Permalink | Reply
    Tags: , Electron Microscopy,   

    From Scripps: “Team Breaks Imaging Barrier” 


    Scripps Research Institute

    March 30, 2015
    Madeline McCurry-Schmidt

    Advances in Electron Microscopy Could Aid Drug Design

    A team from the Carragher lab has imaged a protein complex at the highest resolution ever achieved with single particle cryo-electron microscopy. The image reveals individual molecules at 2.8 Å and is, to the researchers’ knowledge, the first published research using this technique that shows individual water molecules.

    Scientists at The Scripps Research Institute (TSRI) have broken a major barrier in structural imaging. Their study, published recently in the journal eLife, shows a protein complex at the highest resolution ever achieved with a standard technique called single particle cryo-electron microscopy.

    “The instruments and software are now so good that we do not know what the barriers are any more,” said Bridget Carragher, a professor at TSRI with a joint appointment at the New York Structural Biology Center.

    With single particle cryo-electron microscopy, scientists freeze a sample and then expose it to a beam of high-energy electrons. This excites electrons in the sample, allowing scientists to capture an image.

    While the technique has many practical advantages over other structural biology methods, scientists have so far not been able to reach resolutions more detailed than 3 Angstroms (one ten-billionth of a meter, marked with the symbol Å). At this resolution, some of the details of the structure that are important for guiding drug design are not discernable.

    The new study shows that reaching resolutions greater than 3 Å is possible using single particle cryo-electron microscopy. The imaged protein complex reveals individual molecules at 2.8 Å and is, to the researchers’ knowledge, the first time a paper has been published showing individual water molecules using this technique.

    Better Imaging, Better Drugs

    The scientists used a new type of electron microscope, called the FEI Titan Krios, and a new-generation camera, called a Gatan K2 Summit, to break the 3 Å barrier.

    Titan Krios

    Gatan K2 Summit

    The FEI Titan Krios is housed on TSRI’s La Jolla, California, campus. It has a higher energy electron source and a more stable platform than other types of electron microscopes. It also operates with software developed at TSRI through the National Resource for Automated Molecular Microscopy to find the best parts of a sample for imaging.

    The Gatan K2 Summit camera improves imaging by directly detecting electrons, instead of losing resolution by converting electrons to light. The camera can also capture a series of images, essentially a movie, giving scientists the ability to correct for movements in the specimen and make the images as sharp as possible.

    Revealing high-resolution details in a structure helps researchers develop new drugs to treat disease. Structures seen at greater than 3 Å might show vulnerabilities in a virus where drugs could bind, for example.

    “By seeing everything in more detail, you can design more effective drugs,” said Melody Campbell, a TSRI graduate student and co-first author of the new paper with David Veesler, previously a post-doctoral fellow at TSRI and now an assistant professor at the University of Washington.

    The advances in single particle cryo-electron microscopy also allow scientists to image more kinds of structures, more quickly. For many years, scientists have relied on a high-resolution imaging technique called X-ray crystallography. Although X-ray crystallography has led to many advances in drug design, figuring out how to grow a crystal can take years and not all structures can be crystallized.

    Electron microscopy does not require a crystal, however, and many projects take only weeks or months.

    In the new study, the researchers imaged a protein complex from a microbe called Thermoplasma acidophilum. This protein complex, called a proteasome, is also found in humans and is an important target for treating many types of cancer.

    The team spent several months setting up the instruments—since the FEI Titan Krios was new to the institute—and then they captured all the raw data over a single weekend. They then used computational programs to select the clearest images and refine them over several months to build a 3D model of the proteasome.

    “It was a relief to know we had finally done it,” said Campbell. “Now we hope other people can just hop on the microscope, use similar strategies and also get high-resolution structures.”

    In addition to Carragher, Campbell and Veesler, authors of the study, “2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20 S proteasome using cryo-electron microscopy,” were Anchi Cheng and Clinton S. Potter of the New York Structural Biology Center. For more information on the paper, see http://elifesciences.org/content/4/e06380.

    This research was supported by the National Institutes of Health’s National Institute of General Medical Sciences (grant GM103310), a FP7 Marie Curie IOF fellowship (273427) and an American Heart Association fellowship (14PRE18870036).

    See the full article here.

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    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

  • richardmitnick 3:31 pm on January 28, 2013 Permalink | Reply
    Tags: , , Electron Microscopy,   

    From PNNL Lab: “Seeing a Common Catalyst with New Eyes” 

    Chemical imaging microscope shows corrugated gamma-alumina surface
    January 2013
    Suraiya Farukhi
    Christine Sharp

    Results: Neither smooth nor disordered, gamma-alumina nanoparticles are corrugated with tiny pores inside, according to scientists at Pacific Northwest National Laboratory. Using a powerful transmission electron microscope, the team obtained ultrahigh-resolution images and chemical data about the particle’s surface. They found that the particles were covered with ridges made from a more open, yet symmetrical, arrangement of atoms. The open arrangement on the surfaces, notated as (110), covers 70% of the nanoparticle.

    The surface of the plate-like particles is far from smooth, according to a new transmission electron microscopy study conducted by Pacific Northwest National Laboratory and the FEI Company.

    By understanding the structure and function of tiny gamma-alumina particles, scientists are taking crucial steps to optimizing and realizing new useful properties for these materials. ‘If we can learn about the surfaces, then we can tailor them and make them more efficient in catalytic applications,’ said Dr. Libor Kovarik, who led the imaging study as part of PNNL’s Chemical Imaging Initiative.

    Why It Matters: Reducing refineries’ energy demands or car and truck emissions requires efficient catalysts on durable support materials. The supporting material must withstand severe temperature and pressure changes. Gamma-alumina has been studied extensively, but its atomic arrangement has not been established because of the challenge of getting a detailed view of this complex material. Accurately describing the atomic structure is crucial for understanding and taking advantage of the best properties of gamma-alumina.

    ‘Catalytic research demands this type of state-of-the-art chemical imaging research,’ said Dr. Charles Peden, a heterogeneous catalysis scientist who worked on the study, and an Associate Director of PNNL’s Institute for Integrated Catalysis. ‘Dr. Kovarik’s outstanding new images from this powerhouse microscope have yielded unprecedented new information about a catalyst material of enormous practical utility.'”

    See the full article here.

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.


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  • richardmitnick 1:14 pm on January 17, 2013 Permalink | Reply
    Tags: , , Electron Microscopy   

    From Berkeley Lab: “New Key to Organism Complexity Identified” 

    Berkeley Lab

    Berkeley Scientists Find that a Critical Transcription Factor Co-exists in Two Distinct States

    January 17, 2013
    Lynn Yarris

    The enormously diverse complexity seen amongst individual species within the animal kingdom evolved from a surprisingly small gene pool. For example, mice effectively serve as medical research models because humans and mice share 80-percent of the same protein-coding genes.

    The ‘rearranged’ state of the lobe A (yellow) of the horseshoe-like TFIID transcription factor enables TFIID to bind with DNA (green) and start the process by which DNA is copied into RNA.

    The key to morphological and behavioral complexity, a growing body of scientific evidence suggests, is the regulation of gene expression by a family of DNA-binding proteins called ‘transcription factors.’ Now, a team of researchers with the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley has discovered the secret behind how one these critical transcription factors is able to perform – a split personality.

    Using a technique called single-particle cryo-electron microscopy, the team, which was led by biophysicist Eva Nogales, showed that the transcription factor known as ‘TFIID’ can co-exist in two distinct structural states.”

    two people
    Michael Cianfrocco and Eva Nogales used single-particle cryo-electron microscopy to learn how the TFIID transcription factor helps regulate of gene expression, a process critical to the growth, development, health and survival of all organisms. (Photo by Roy Kaltschmidt)

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California


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