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  • richardmitnick 11:40 am on October 30, 2019 Permalink | Reply
    Tags: , , Microscopy, , , Stretched S-DNA   

    From Sandia Lab: “Advanced microscopy reveals unusual DNA structure” 

    From Sandia Lab

    October 30, 2019
    Melissae Fellet

    Sandia scientist pushes technology’s limits to see fundamental feature of stretched S-DNA.

    Adam Backer, an optical scientist at Sandia National Laboratories, helped develop an advanced microscopy technique that revealed highly tilted base pairs in a stretched form of DNA. (Photo by Randy Montoya).

    An advanced imaging technique reveals new structural details of S-DNA, ladder-like DNA that forms when the molecule experiences extreme tension. This work conducted at Sandia National Laboratories and Vrije University in the Netherlands provides the first experimental evidence that S-DNA contains highly tilted base pairs.

    The predictable pairing and stacking of the DNA base pairs help to define the molecule’s double-helical shape. Understanding how the base pairs realign when DNA is stretched might provide insight into a range of biological processes and improve the design and performance of nanodevices built with DNA. Tilted base pairs in stretched S-DNA have been previously predicted using computer simulations, but never conclusively demonstrated in experiments until now, according to a recent article in Science Advances.

    DNA is most commonly known as the molecular carrier of genetic information. However, in research labs around the world, it also has another use: construction material for nanoscale devices. To do this, scientists prepare computer-generated sequences of single-stranded DNA so that certain sections form base pairs with other sections. This forces the strand to bend and fold like origami. Researchers have used this principle to fold DNA into microscopic smiley faces, nanomachines with moving hinges and pistons and “smart” materials that spontaneously adjust to changes in the surrounding chemical environment.

    “To build an airplane or a bridge, it’s important to know the structure, strength and stretchiness of every material that went into it,” said Adam Backer, an optical scientist at Sandia and lead author of the study. “The same thing is true when designing nanostructures with DNA.”

    While much is known about the mechanical properties of DNA’s double helix, mysteries remain about the details of its shape when the molecule is stretched in a laboratory to form the ladder-like structure of S-DNA. Standard ways of visualizing DNA structure cannot track structural changes while the molecule untwists.

    Seeing stretched DNA

    To characterize the structure and stretchiness of S-DNA, Backer worked with colleagues in the Physics of Living Systems research group at LaserLaB Amsterdam at Vrije University. The researchers described their process in the journal article. Using instrumentation developed by his colleagues, Backer first attached a microscopic bead to each end of a short piece of viral DNA. These beads served as handles to manipulate a single molecule of DNA.

    Next, the researchers trapped the beaded DNA in a narrow fluid-filled chamber using two tightly focused laser beams. Because the beads stay trapped inside the laser beams, the researchers could move the beads in the chamber by redirecting the laser beams. This enabled them to stretch the attached DNA to form S-DNA. This technique for manipulating microscopic particles, called optical tweezers, also provided precise control over the amount of stretching force applied to a single DNA molecule.

    However, the structural changes occurring within the stretched DNA molecule were too small to be directly observed with a standard optical microscope. To address this challenge, Backer helped his colleagues combine an imaging method called fluorescence polarization microscopy with the optical tweezers instrument. First, they added small, rod-like fluorescent dye molecules to the solution containing optically trapped DNA. In unstretched DNA, the dye molecules sandwich themselves between neighboring sets of base pairs and align perpendicular to the central axis of the double helix. If a stretching force causes the DNA base pairs to tilt, the dyes would also tilt.

    Next, the researchers used the fluorescent signals from the dyes to determine if the base pairs in stretched DNA tilted. The fluorescent dyes emit green fluorescent light when they interact with light waves from a laser beam pointing along the same axis as the dye molecules. The researchers changed the orientation of the light waves by rotating the polarization of a laser beam through various angles. Then, they stretched the DNA and watched for green fluorescent signals to appear under the microscope. From these measurements, and computational analysis methods developed at Sandia, the researchers determined that the dyes, and thus the base pairs, aligned at a 54-degree angle relative to the DNA’s central axis.

    “This experiment provides the most direct evidence to date supporting the hypothesis that S-DNA contains tilted base pairs,” said Backer. “To gain this fundamentally new understanding of DNA, it was necessary to combine a number of cutting-edge technologies and bring scientists from a range of different technical disciplines together to work toward a common goal.”

    There is widespread speculation among scientists that structures resembling S-DNA may form during the daily activities of human cells, but, at present, the biological purpose of S-DNA is still unknown. S-DNA might facilitate the repair of damaged or broken DNA, helping to guard against cell death and cancer. Backer hopes this clearer understanding of the physical principles governing DNA deformation will guide further research into the role of S-DNA in cells.

    When Backer joined Sandia as a Truman Fellow in November 2016, he had the opportunity to start an independent research program of his own design. He had developed a method for polarization microscopy during graduate school at Stanford University and thought the technique had potential. Said Backer: “At Sandia I wanted to push this technique as far as it could go. The fact that this work has led to results with potential relevance to fields such as biology and nanotechnology has been extraordinary.”

    See the full article here .


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    Sandia Campus
    Sandia National Laboratory

    Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy’s National Nuclear Security Administration. With main facilities in Albuquerque, N.M., and Livermore, Calif., Sandia has major R&D responsibilities in national security, energy and environmental technologies, and economic competitiveness.

  • richardmitnick 3:03 pm on May 3, 2019 Permalink | Reply
    Tags: , , Microscopy,   

    From UC Santa Cruz: “Microscope expert develops powerful new tools for biologists” 

    UC Santa Cruz

    From UC Santa Cruz

    May 01, 2019
    Tim Stephens

    With Sara Abrahamsson’s arrival in the Baskin School of Engineering, UC Santa Cruz is becoming a hotbed of advanced microscopy and microscope development.

    Sara Abrahamsson at the nanofabrication facility where her team makes their custom-designed optics components. (Photo by Gustav Pettersson)

    For biologists, the golden age of microscopy is now. Powerful techniques developed in recent decades enable scientists to study living cells in unprecedented detail, and new techniques continue to push the limits of light microscopes.

    Sara Abrahamsson, an assistant professor of electrical and computer engineering at UC Santa Cruz, is at the forefront of innovations in optical microscopy. She invented a technique called aberration-corrected multi-focus microscopy (MFM), which enables 3-dimensional imaging of living cells. More recently (in 2017), she showed that MFM can be combined with another technique, called structured illumination microscopy (SIM), that provides “super-resolution” beyond the classical limits of light microscopes.

    The aberration-corrected multi-focus microscopy (MFM) technology developed by Abrahamsson requires custom-made diffractive gratings. (Photo by Carolyn Lagattuta)

    “The 2017 paper [BOE] was a proof-of-concept study. Now we want to build the microscope and show that it works for 3-D imaging of living cells with super-resolution,” said Abrahamsson, who won a $700,000 major research instrumentation grant from the National Science Foundation to fund the project.

    Her collaborators in the Department of Molecular, Cell, and Developmental (MCD) Biology are thrilled to be working with Abrahamsson. “Sara is a uniquely talented inventor of microscopes,” said Grant Hartzog, professor of MCD biology.

    Hartzog is one of several UCSC biologists who will be using Abrahamsson’s optical technology to study chromatin (the complex of DNA, RNA, and proteins that forms chromosomes) in the cells of various organisms. He explained that Abrahamsson’s MFM technique improves on the widely used technology of confocal microscopy. A confocal microscope blocks out-of-focus light to obtain sharp images of thin sections at different depths in a sample.

    “You can take multiple slices and build up a 3-D image. The problem is the time that elapses between each image when you’re taking multiple slices of a living cell. Because the components of the cell are in constant motion, the resulting image is blurry,” Hartzog said. “Sara figured out how to focus the light so you can collect all the slices in one shot for an instant 3-D image. That’s really important for imaging living cells.”

    UCSC Microscopy Center

    Abrahamsson’s lab has already built one multi-focus microscope and installed it in the UCSC Life Sciences Microscopy Center, where Hartzog and others have started using it and optimizing their techniques. A SIM system currently under construction will add super-resolution capabilities to the multi-focus microscope.

    The M25 multi-focus microscope uses separate cameras to capture images from 25 focal planes at different depths in a sample. (Photo by Eduardo Hirata)

    Super-resolution is important because the dimensions of the structures of interest to the biologists are so small. The resolution of a light microscope is limited by the wavelengths of visible light to about 200 nanometers. Chromatin structures are much smaller than that, on the order of 10 to 30 nanometers in diameter.

    But scientists have developed ways to get past the classical limits of optical microscopy. Structured illumination microscopy is one of several super-resolution techniques that have been developed, with the first practical implementations appearing in the 1990s. By combining multi-focus and structured illumination microscopy, Abrahamsson’s lab is pushing the technology to the limit in terms of both speed and spatial resolution.

    Meanwhile, Abrahamsson’s graduate student Eduardo Hirata-Miyasaki has developed an extended version of MFM, called the M25, which increases the number of focal planes (or “slices”) from nine to 25 and uses separate cameras to capture the images from each focal plane. This instrument does not have super-resolution capability, but is super-fast. It can record live 3-D volumes at more than 100 frames per second and is designed for functional imaging of living neural circuits of the brain and spinal cord.

    “Thanks to the advances in CMOS sensor technology, we can improve the optical design of the MFM system to create a fast and sensitive method for live 3-D imaging,” said Hirata, who presented the new system at a recent Focus on Microscopy conference in London.

    Custom-designed optics

    The MF-SIM microscope requires building and combining two highly specialized, custom-designed optical systems. Abrahamsson’s team designs and fabricates their own optics components, using a nanofabrication facility at UC Santa Barbara to make the diffractive gratings needed for multi-focus microscopy.

    Hirata explained that the diffractive gratings can be easily customized depending on the region of interest and the target depth of the sample. “The M25 images simultaneously at 25 different depths, and we can vary the separation between those focal planes. Having more focal planes allows us to image greater volumes with higher resolutions,” he said.

    The biologists working with Abrahamsson’s lab are using a range of different organisms in their research. Hartzog and Hinrich Boeger study the effects of chromatin packaging on RNA transcription in yeast cells; Needhi Bhalla studies chromosome dynamics during cell division in C. elegans worms; and William Sullivan studies what happens to damaged chromosomes in fruit flies.

    Abrahamsson did some of her early work at the Advanced Imaging Center at HHMI’s Janelia Research Campus in Ashburn, Virginia, and one of Sullivan’s students went there last year to use their specialized systems. The results only reinforced the need for Abrahamsson’s MF-SIM technology.

    “We’re looking at what happens when a chromosome is broken, which can lead to cancerous cells,” said Sullivan, a professor of MCD biology. “We want to follow this in real time in three dimensions, but we haven’t been able to do that. What Sara’s doing is really pretty ground-breaking.”

    Having the microscopy experts here on campus makes a big difference, he added.

    “There’s always a lot of back and forth, the biologists talking to the engineers to figure out how to get the end result we want,” Sullivan said. “Being able to just take our samples downstairs, instead of traveling to Janelia with live flies, we can make much faster progress.”

    Abrahamsson’s expertise in optics is in high demand, and she is developing and teaching new courses in optics and microscopy for students at UC Santa Cruz. She is also starting a project with researchers at NASA’s Jet Propulsion Laboratory working on a planned space probe. In all these projects, Abrahamsson is excited not only about the new technology, but also about what scientists will be able to learn with it.

    “I can’t wait to see my collaborators take the first data set of living cells on the MF-SIM that we are building. Who knows what they are going to be able to discover with it?” she said.

    See the full article here .


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    UCSC Lick Observatory, Mt Hamilton, in San Jose, California, Altitude 1,283 m (4,209 ft)


    UCO Lick Shane Telescope
    UCO Lick Shane Telescope interior
    Shane Telescope at UCO Lick Observatory, UCSC

    Lick Automated Planet Finder telescope, Mount Hamilton, CA, USA

    Lick Automated Planet Finder telescope, Mount Hamilton, CA, USA

    UC Santa Cruz campus
    The University of California, Santa Cruz, opened in 1965 and grew, one college at a time, to its current (2008-09) enrollment of more than 16,000 students. Undergraduates pursue more than 60 majors supervised by divisional deans of humanities, physical & biological sciences, social sciences, and arts. Graduate students work toward graduate certificates, master’s degrees, or doctoral degrees in more than 30 academic fields under the supervision of the divisional and graduate deans. The dean of the Jack Baskin School of Engineering oversees the campus’s undergraduate and graduate engineering programs.

    UCSC is the home base for the Lick Observatory.

    Lick Observatory's Great Lick 91-centimeter (36-inch) telescope housed in the South (large) Dome of main building
    Lick Observatory’s Great Lick 91-centimeter (36-inch) telescope housed in the South (large) Dome of main building

    Search for extraterrestrial intelligence expands at Lick Observatory
    New instrument scans the sky for pulses of infrared light
    March 23, 2015
    By Hilary Lebow
    The NIROSETI instrument saw first light on the Nickel 1-meter Telescope at Lick Observatory on March 15, 2015. (Photo by Laurie Hatch) UCSC Lick Nickel telescope

    Astronomers are expanding the search for extraterrestrial intelligence into a new realm with detectors tuned to infrared light at UC’s Lick Observatory. A new instrument, called NIROSETI, will soon scour the sky for messages from other worlds.

    “Infrared light would be an excellent means of interstellar communication,” said Shelley Wright, an assistant professor of physics at UC San Diego who led the development of the new instrument while at the University of Toronto’s Dunlap Institute for Astronomy & Astrophysics.

    Wright worked on an earlier SETI project at Lick Observatory as a UC Santa Cruz undergraduate, when she built an optical instrument designed by UC Berkeley researchers. The infrared project takes advantage of new technology not available for that first optical search.

    Infrared light would be a good way for extraterrestrials to get our attention here on Earth, since pulses from a powerful infrared laser could outshine a star, if only for a billionth of a second. Interstellar gas and dust is almost transparent to near infrared, so these signals can be seen from great distances. It also takes less energy to send information using infrared signals than with visible light.

    Frank Drake, professor emeritus of astronomy and astrophysics at UC Santa Cruz and director emeritus of the SETI Institute, said there are several additional advantages to a search in the infrared realm.

    “The signals are so strong that we only need a small telescope to receive them. Smaller telescopes can offer more observational time, and that is good because we need to search many stars for a chance of success,” said Drake.

    The only downside is that extraterrestrials would need to be transmitting their signals in our direction, Drake said, though he sees this as a positive side to that limitation. “If we get a signal from someone who’s aiming for us, it could mean there’s altruism in the universe. I like that idea. If they want to be friendly, that’s who we will find.”

    Scientists have searched the skies for radio signals for more than 50 years and expanded their search into the optical realm more than a decade ago. The idea of searching in the infrared is not a new one, but instruments capable of capturing pulses of infrared light only recently became available.

    “We had to wait,” Wright said. “I spent eight years waiting and watching as new technology emerged.”

    Now that technology has caught up, the search will extend to stars thousands of light years away, rather than just hundreds. NIROSETI, or Near-Infrared Optical Search for Extraterrestrial Intelligence, could also uncover new information about the physical universe.

    “This is the first time Earthlings have looked at the universe at infrared wavelengths with nanosecond time scales,” said Dan Werthimer, UC Berkeley SETI Project Director. “The instrument could discover new astrophysical phenomena, or perhaps answer the question of whether we are alone.”

    NIROSETI will also gather more information than previous optical detectors by recording levels of light over time so that patterns can be analyzed for potential signs of other civilizations.

    “Searching for intelligent life in the universe is both thrilling and somewhat unorthodox,” said Claire Max, director of UC Observatories and professor of astronomy and astrophysics at UC Santa Cruz. “Lick Observatory has already been the site of several previous SETI searches, so this is a very exciting addition to the current research taking place.”

    NIROSETI will be fully operational by early summer and will scan the skies several times a week on the Nickel 1-meter telescope at Lick Observatory, located on Mt. Hamilton east of San Jose.

    The NIROSETI team also includes Geoffrey Marcy and Andrew Siemion from UC Berkeley; Patrick Dorval, a Dunlap undergraduate, and Elliot Meyer, a Dunlap graduate student; and Richard Treffers of Starman Systems. Funding for the project comes from the generous support of Bill and Susan Bloomfield.

  • richardmitnick 9:16 am on August 21, 2018 Permalink | Reply
    Tags: , Building phylogenetic trees, Chronograms, , , , , Investigating Earth’s earliest life, Kelsey Moore, Microscopy, ,   

    From MIT News: Women in STEM- “Investigating Earth’s earliest life” Kelsey Moore 

    MIT News
    MIT Widget

    From MIT News

    August 18, 2018
    Fatima Husain

    Kelsey Moore. Image: Ian MacLellan

    Graduate student Kelsey Moore uses genetic and fossil evidence to study the first stages of evolution on our planet.

    In the second grade, Kelsey Moore became acquainted with geologic time. Her teachers instructed the class to unroll a giant strip of felt down a long hallway in the school. Most of the felt was solid black, but at the very end, the students caught a glimpse of red.

    That tiny red strip represented the time on Earth in which humans have lived, the teachers said. The lesson sparked Moore’s curiosity. What happened on Earth before there were humans? How could she find out?

    A little over a decade later, Moore enrolled in her first geoscience class at Smith College and discovered she now had the tools to begin to answer those very questions.

    Moore zeroed in on geobiology, the study of how the physical Earth and biosphere interact. During the first semester of her sophomore year of college, she took a class that she says “totally blew my mind.”

    “I knew I wanted to learn about Earth history. But then I took this invertebrate paleontology class and realized how much we can learn about life and how life has evolved,” Moore says. A few lectures into the semester, she mustered the courage to ask her professor, Sara Pruss in Smith’s Department of Geosciences, for a research position in the lab.

    Now a fourth-year graduate student at MIT, Moore works in the geobiology lab of Associate Professor Tanja Bosak in MIT’s Department of Earth, Atmospheric, and Planetary Sciences. In addition to carrying out her own research, Moore, who is also a Graduate Resident Tutor in the Simmons Hall undergraduate dorm, makes it a priority to help guide the lab’s undergraduate researchers and teach them the techniques they need to know.

    Time travel

    “We have a natural curiosity about how we got here, and how the Earth became what it is. There’s so much unknown about the early biosphere on Earth when you go back 2 billion, 3 billion, 4 billion years,” Moore says.

    Moore studies early life on Earth by focusing on ancient microbes from the Proterozoic, the period of Earth’s history that spans 2.5 billion to 542 million years ago — between the time when oxygen began to appear in the atmosphere up until the advent and proliferation of complex life. Early in her graduate studies, Moore and Bosak collaborated with Greg Fournier, the Cecil and Ida Green Assistant Professor of Geobiology, on research tracking cyanobacterial evolution. Their research is supported by the Simons Collaboration on the Origins of Life.

    An image of Cyanobacteria, Tolypothrix

    The question of when cyanobacteria gained the ability to perform oxygenic photosynthesis, which produces oxygen and is how many plants on Earth today get their energy, is still under debate. To track cyanobacterial evolution, MIT researchers draw from genetics and micropaleontology. Moore works on molecular clock models, which track genetic mutations over time to measure evolutionary divergence in organisms.

    Clad with a white lab coat, lab glasses, and bright purple gloves, Moore sifts through multiple cyanobacteria under a microscope to find modern analogs to ancient cyanobacterial fossils. The process can be time-consuming.

    “I do a lot of microscopy,” Moore says with a laugh. Once she’s identified an analog, Moore cultures that particular type of cyanobacteria, a process which can sometimes take months. After the strain is enriched and cultured, Moore extracts DNA from the cyanobacteria. “We sequence modern organisms to get their genomes, reconstruct them, and build phylogenetic trees,” Moore says.

    By tying information together from ancient fossils and modern analogs using molecular clocks, Moore hopes to build a chronogram — a type of phylogenetic tree with a time component that eventually traces back to when cyanobacteria evolved the ability to split water and produce oxygen.

    Moore also studies the process of fossilization, on Earth and potentially other planets. She is collaborating with researchers at NASA’s Jet Propulsion Laboratory to help them prepare for the upcoming Mars 2020 rover mission.

    “We’re trying to analyze fossils on Earth to get an idea for how we’re going to look at whatever samples get brought back from Mars, and then to also understand how we can learn from other planets and potentially other life,” Moore says.

    After MIT, Moore hopes to continue research, pursue postdoctoral fellowships, and eventually teach.

    “I really love research. So why stop? I’m going to keep going,” Moore says. She says she wants to teach in an institution that emphasizes giving research opportunities to undergraduate students.

    “Undergrads can be overlooked, but they’re really intelligent people and they’re budding scientists,” Moore says. “So being able to foster that and to see them grow and trust that they are capable in doing research, I think, is my calling.”

    Geology up close

    To study ancient organisms and find fossils, Moore has traveled across the world, to Shark Bay in Australia, Death Valley in the United States, and Bermuda.

    “In order to understand the rocks, you really have to get your nose on the rocks. Go and look at them, and be there. You have to go and stand in the tidal pools and see what’s happening — watch the air bubbles from the cyanobacteria and see them make oxygen,” Moore says. “Those kinds of things are really important in order to understand and fully wrap your brain around how important those interactions are.”

    And in the field, Moore says, researchers have to “roll with the punches.”

    “You don’t have a nice, beautiful, pristine lab set up with all the tools and equipment that you need. You just can’t account for everything,” Moore says. “You have to do what you can with the tools that you have.”


    As a Graduate Resident Tutor, Moore helps to create supporting living environments for the undergraduate residents of Simmons Hall.

    Each week, she hosts a study break in her apartment in Simmons for her cohort of students — complete with freshly baked treats. “[Baking] is really relaxing for me,” Moore says. “It’s therapeutic.”

    “I think part of the reason I love baking so much is that it’s my creative outlet,” she says. “I know that a lot of people describe baking as like chemistry. But I think you have the opportunity to be more creative and have more fun with it. The creative side of it is something that I love, that I crave outside of research.”

    Part of Moore’s determination to research, trek out in the field, and mentor undergraduates draws from her “biggest science inspiration” — her mother, Michele Moore, a physics professor at Spokane Falls Community College in Spokane, Washington.

    “She was a stay-at-home mom my entire childhood. And then when I was in middle school, she decided to go and get a college degree,” Moore says. When Moore started high school, her mother earned her bachelor’s degree in physics. Then, when Moore started college, her mother earned her PhD. “She was sort of one step ahead of me all the time, and she was a big inspiration for me and gave me the confidence to be a woman in science.”

    See the full article here .

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    MIT Seal

    The mission of MIT is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of the MIT community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

    MIT Campus

  • richardmitnick 1:13 pm on July 28, 2018 Permalink | Reply
    Tags: , Guinness World Record for micro view into hidden worlds, Microscopy, Record-breaking microscope developed using methods pioneered by Sheffield scientists,   

    From U Sheffield and Cornell University: “Record-breaking microscope developed using methods pioneered by Sheffield scientists” 

    From U Sheffield

    23 July 2018
    Sean Barton
    Media Relations Officer
    University of Sheffield
    0114 222 9852

    A revolutionary microscope that has produced images in the highest resolution ever obtained has been developed by researchers using microscopic techniques pioneered by scientists at the University of Sheffield.

    Revolutionary microscope produces images in the highest resolution ever obtained
    Electron microscope developed using computational algorithms pioneered by University of Sheffield scientists
    Record-breaking microscope could be used to study 3D atomic structure at unprecedented resolution

    The record-breaking electron microscope, built by researchers at Cornell University in the USA, can produce images at a higher resolution than conventional approaches. It could be used to determine the atomic structure of materials that are normally damaged using existing methods.

    The microscope may eventually allow researchers to study 2D materials, such graphene, using unprecedented precision to provide new insights into this burgeoning class of useful materials that have extraordinary physical and electrical properties, and which could revolutionise many modern technologies.

    It may also lead to the development of a method that can image individual atoms in 3D objects without damaging the structure by using ‘slow’ low-energy electrons.

    Electron imaging is usually conducted using expensive lenses and high-energy electrons that damage many types of material. Alternatively, the Cornell research team recorded electrons that had been scattered through high angles to get around these problems.

    Once scattered, the electrons don’t look anything like an image, so the Cornell research team used computational algorithms developed by scientists at the University of Sheffield to work out backwards what the specimen looked like. This is what enabled the microscope to generate the record-breaking high resolution image.

    For many years, this backwards calculation, known as the phase problem, was regarded as impossible to solve for a large image.

    Professor John Rodenburg from the University of Sheffield’s Department of Electronic and Electrical Engineering, who developed the computational algorithms together with his colleague Andrew Maiden, commented:

    “The electron microscope developed by the Cornell research team is the most powerful microscope we’ve ever seen. It is capable of capturing images that have an unprecedented level of detail, which is important because it now paves the way for us to develop new insights into material structure at the atomic scale.

    “Such an advanced electron microscope wasn’t possible previously because although the technique we developed here at the University of Sheffield works well for X-ray and light microscopes, in the case of electron microscopy it needs a near-perfect detector to get good enough quality data. Now, due to the advances in detector technology made by the Cornell team, this record-breaking microscope can successfully run the Sheffield algorithm.”

    Cornell Bloc

    From Cornell Chronicle

    Guinness World Record for micro view into hidden worlds


    July 25, 2018
    Tom Fleischman

    In a recent research paper published in Nature, a group led by physics professors David Muller and Sol Gruner claimed a world record for electron microscope resolution using a high-powered detector and a technique called ptychography. Their technique was shown to measure down to 0.39 ångströms or 0.039 nanometers (one-billionth of a meter).

    Guinness World Records has officially recognized the Cornell collaboration’s achievement, listing it alongside such notables as Robert Pershing Wadlow (at 8 feet, 11.1 inches, the world’s tallest human) and Lee Redmond (longest fingernails, with a combined length of 28 feet, 4 inches).

    Gruner, former director of the Cornell High Energy Synchrotron Source, said he’d always dreamed of making the Guinness grade, but didn’t figure microscopy would be his ticket to fame.

    “I always thought that I’d need to eat 40 hamburgers in five minutes or stand on one foot for days to get into the Guinness book,” he said. “Who would have thought that seeing a few atoms would do the trick?”

    That brings to four the number of current Cornell University-affiliated record-holders. Muller also shares the record for thinnest glass (three atoms thick, 2013); the other records are held in part by applied and engineering physics professor Harold Craighead, who shares records for smallest replica guitar (1997) and lightest object weighed (2004). In addition, the current record for furthest distance covered by a quadruped robot (83.28 miles, in 2015) eclipsed the mark of 40.5 miles set by Cornell’s Ranger robot in 2011.

    See the full Sheffield article here .
    See the full Cornell Chronicle article here .


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    Once called “the first American university” by educational historian Frederick Rudolph, Cornell University represents a distinctive mix of eminent scholarship and democratic ideals. Adding practical subjects to the classics and admitting qualified students regardless of nationality, race, social circumstance, gender, or religion was quite a departure when Cornell was founded in 1865.

    Today’s Cornell reflects this heritage of egalitarian excellence. It is home to the nation’s first colleges devoted to hotel administration, industrial and labor relations, and veterinary medicine. Both a private university and the land-grant institution of New York State, Cornell University is the most educationally diverse member of the Ivy League.

    On the Ithaca campus alone nearly 20,000 students representing every state and 120 countries choose from among 4,000 courses in 11 undergraduate, graduate, and professional schools. Many undergraduates participate in a wide range of interdisciplinary programs, play meaningful roles in original research, and study in Cornell programs in Washington, New York City, and the world over.

    U Sheffield campus

    The University of Sheffield (informally Sheffield University) is a public research university in Sheffield, South Yorkshire, England. It received its royal charter in 1905 as successor to the University College of Sheffield, which was established in 1897 by the merger of Sheffield Medical School (founded in 1828), Firth College (1879) and Sheffield Technical School (1884).

    Sheffield is a multi-campus university predominantly over two campus areas: the Western Bank and the St George’s. The university is organised into five academic faculties composed of multiple departments. It had 20,005 undergraduate and 8,710 postgraduate students in 2016/17. The annual income of the institution for 2016–17 was £623.6 million of which £155.9 million was from research grants and contracts, with an expenditure of £633.0 million. Sheffield ranks among the top 10 of UK universities for research grant funding.

    Sheffield was placed 75th worldwide according to QS World University Rankings and 104th worldwide according to Times Higher Education World University Rankings. It was ranked 12th in the UK amongst multi-faculty institutions for the quality (GPA) of its research and for its Research Power in the 2014 Research Excellence Framework. In 2011, Sheffield was named ‘University of the Year’ in the Times Higher Education awards. The Times Higher Education Student Experience Survey 2014 ranked the University of Sheffield 1st for student experience, social life, university facilities and accommodation, among other categories.

    It is one of the original red brick universities, a member of the Russell Group of research-intensive universities, the Worldwide Universities Network, the N8 Group of the eight most research intensive universities in Northern England and the White Rose University Consortium. There are eight Nobel laureates affiliated with Sheffield and six of them are the alumni or former long-term staffs of the university.

  • richardmitnick 5:10 am on November 15, 2017 Permalink | Reply
    Tags: , , Microscopy   

    From COSMOS: “Need a better microscope? Add mirrors” 

    Cosmos Magazine bloc

    COSMOS Magazine

    15 November 2017
    Andrew Masterson

    Anthony Van Leeuwenhoek’s first microscope, from the seventeenth century, looks nothing like a modern SPIM microscope, but both are products of a quest to improve optics. Stegerphoto.

    From pre-classical times onwards, it could be argued, lens-makers have been the unsung heroes of science.

    As early as 750 BCE the Assyrians were shaping lenses from quartz. From there, the history of optics both underpins and enables discovery in both the macro and micro worlds.

    Where would science be today had it not been for the patient work of myriad lens grinders and optics theorists, including Francis Bacon, Galileo, van Leeuwenhoek, right up to Roberts and Young – inventors in 1951 of photon scanning microscopy – and beyond?

    Even today, the quest for better, clearer, more detailed images from lenses continues apace, with the latest advance, declared in the journal Nature Communications, coming from the US National Institutes of Health and the University of Chicago.

    The images obtained by the combination of the new coverslip and computer algorithms show clearer views of small structures. Credit: Yicong Wu, National Institute of Biomedical Imaging and Bioengineering

    In this diagram, you can see how the mirrored coverslip allows for four simultaneous views. Credit: Yicong Wu, National Institute of Biomedical Imaging and Bioengineering

    A team of researchers, led by Hari Shroff, head of the National Institute of Biomedical Imaging and Bioengineering’s lab section on High Resolution Optical Imaging (HROI), report the solution to a mechanical problem in microscope optics that was, in a way, of their own making.

    Several years ago, Shroff and colleagues developed a new type of microscope that performed “selective plane illumination microscopy” or SPIM. These microscopes use light sheets to illuminate only sections of specimens being examined, thereby doing less damage and better preserving the sample.

    In 2013, Shroff’s team created a SPIM microscope that used two lenses instead of one, which improved image quality and depth perception, In 2016, a third lens was added, allowing improved resolution and 3D-imagery.

    A fourth lens would have boosted matters even more, but at this point van Leeuwenhoek’s twenty-first century heirs hit a snag.

    “Once we incorporated three lenses, we found it became increasingly difficult to add more,” says Shroff. “Not because we reached the limit of our computational abilities, but because we ran out of physical space.”

    Proximity was a real issue. Not only were the three lenses crowded together, but all had to be positioned extremely close to the sample being examined to allow the imaging goal – detailed views of structures within a single cell, say – to be achieved.

    In their new paper, Shroff and his colleagues reveal a solution to the problem that is nothing if not elegant. Rather than try to cram an extra lens in, they have put mirrors on the coverslip – the thin piece of glass that sits on top of the sample.

    The result – especially when coupled with new algorithms in the computerised back-end of a SPIM microscope – is better speed, efficiency and resolution.

    “It’s a lot like looking into a mirror,” Shroff explains. “If you look at a scene in a mirror, you can view perspectives that are otherwise hidden. We used this same principle with the microscope.

    “We can see the sample conventionally using the usual views enabled by the lenses themselves, while at the same time recording the reflected images of the sample provided by the mirror.”

    The addition of the tiny mirrors was not without its own problems. Every microscope raw image contains unwanted data from the source of illumination used to light up the sample. With three lenses, there are three sources of this interference; with mirrors added, these too are multiplied.

    Shroff, however, took this problem to computational imaging researcher Patrick La Riviere at the University of Chicago, who, with his team, was able to modify the processing software to eliminate the extra noise and further improve the signal.

    Francis Bacon, one thinks, would have approved.

    See the full article here .

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  • richardmitnick 3:34 pm on July 31, 2017 Permalink | Reply
    Tags: 3-D microscope gives Johns Hopkins scientists a clearer view, , , , , Microscopy,   

    From Hopkins: “3-D microscope gives Johns Hopkins scientists a clearer view” 

    Johns Hopkins
    Johns Hopkins University

    Jill Rosen

    Light-sheet technology allows researchers like Kavli Neuroscience Discovery Institute fellow Audrey Branch to observe how cells, ducts, or veins connect without damaging the cells in the sample Image credit: Will Kirk / Homewood Photography.

    Audrey Branch is trying to learn more about aging by studying old and young brains. Specifically, she’s interested in how cells connect to form memories and what might be going wrong with those connections when older people start to forget things.

    Until recently, getting at that question meant months of tedious specimen preparation. And even then, the very prep that made getting a glimpse of the brain’s core possible—slicing what’s already tiny into thousands of pieces—very likely destroyed the delicate connections the Johns Hopkins neuroscientist needed to see.

    That changed this spring when a new, three-dimensional microscope arrived at the university’s Homewood campus, a cutting-edge tool that not only condenses what had been months of work into just hours, but allows researchers unprecedented views of organs, tissue, and even live specimens.

    Just practicing with it, Branch knew it was a game-changer. She cried when she saw the first pictures of a mouse brain, its individual neurons glowing red, and its spindly dendrites, too—showing quite clearly the links between those cells.

    “It feels so amazing to see the brain in a way that no one has ever seen it before,” she said. “It’s pretty much the greatest thing I’ve ever experienced in science.”

    The selective plane florescence light sheet microscope arrived on campus in April, one of the first in operation on the East Coast and the only one in Maryland. Purchased with a grant from the National Institutes of Health, it cost $360,000.

    Unlike other microscopes, this one illuminates specimens from the side, shooting two perfectly aligned planes of light across an object, illuminating a wafer-thin slice of the whole while the camera captures the image—thousands of times over as the specimen moves through the light. When the images are displayed together, the result is a three-dimensional image or video clip of the full object, sort of like the more familiar CAT scan.

    The technology is very new, but Michael McCaffery, director of the university’s Integrated Imaging Center, expects researchers everywhere will be using it within a few years. Just among the Johns Hopkins community, word of the light sheet is already out and scientists have been lining up to use it—even if that requires the minor inconvenience of bringing specimens over from the medical campus.

    “People really want to use this,” McCaffery said. “It fills a niche that until now was unavailable at Hopkins. Simply, there was no instrument that allowed a researcher to take a whole organ, brain, or cardiac muscle, and image them in three-dimensions, in their entirety.”

    The light sheet is the latest advance in modern microscopy—a world that’s been evolving since fluorescence microscopy became the standard in the 1960s. Now, most researchers use confocal microscopes, which use lasers to illuminate a sample point by point—only extremely tiny samples will work—then create computerized images, pixel by pixel.

    Confocals produce vivid, high-resolution images, but the sample size limitations—nothing thicker than about 70 microns, which is about as wide as a strand of human hair—severely handicapped scientists.

    The new light sheet allows samples up to 12 to 15 millimeters, or about a half an inch. Researchers can study much larger samples, even entire organs. And because the samples don’t have to be cut up, researchers like Branch who are interested in how cells, ducts, or veins connect have a chance to observe them, unspoiled.

    “It’s a very big deal for researchers, particularly those interested in the science of connectomics,” McCaffery said. “Mapping the neuronal connections of the brain is the holy grail of neurology.”

    It’s certainly Branch’s holy grail.

    Branch is a Kavli Neuroscience Discovery Institute fellow working in the Krieger School of Arts and Sciences. She wants to know how newborn neurons, which are key to making memories, connect to other cells in the brain—and how those connections might change as people age.

    Scientists know the number of newborn neurons declines with age, and that likely has something to do with why short-term memory declines with age. What Branch wants to do is audit these newborn cells in a young brain, determining how many there are, where they are, and what other cells they communicate with. She can compare that with an older brain and possibly see which connections have broken when memory loss occurs. If she can target the broken connections, there could be a way to treat the area with a drug and stop or slow cognitive decline.

    Branch has been practicing on the light sheet with mouse brains, and she plans to formally investigate her hypothesis with rat brains, which are bigger and more human-like.

    If she didn’t have the light sheet, Branch would have to slice the brain, which is about the size of an olive pit, into tissue-thin sections—about 250 pieces. Each slice would need to be stained, mounted onto a slide, and then imaged. Each of those images would need to be manually assembled into a composite to approximate the whole.

    All of this work would take about a month. Since Branch’s experiment involves 30 brains, it would take her about two and a half years, “if,” she says, “that’s all I did day in and day out.”

    Worse yet, by slicing the brain, she would lose most of the newborn neurons she needed to find, and probably all of the connections. She figures if she had marked 50 newborn neurons, she’d be lucky to find five.

    “It would be impossible to find the connections,” she says. “And it would be impossible to get an idea of who each of those cells is talking to. Maybe it’s not important, but I’m guessing that’s not the case. Neurons in isolation aren’t interesting; it’s who they’re talking to, it’s how they’re wired.

    “I was just going to have to estimate. I’d have missed a lot of the picture, and that’s all anyone’s been able to do.”

    Guy Bar-Klein, a neuroscientist working in the Hal Dietz Lab at the School of Medicine, has been crossing town to spend time at Homewood’s Dunning Hall with the light sheet to study blood vessels in the heart and brain, hoping to better understand what causes aneurysms.

    Without the light-sheet technology, his view would be limited to a minuscule section of tissue, much too small to get a true sense of its vasculature. Now, he has been looking at samples with intact blood vessels, making it possible to spot and track aneurysms—and possibly pinpoint the underlying issues that caused it to form.

    “It’s very exciting,” Bar-Klein said. “I think it gives us a very substantial advantage in understanding the signaling involved in aneurysm formation.”

    Michael Noë, a pathology resident who studies pancreatic cancer, hopes the light sheet’s three-dimensional perspective will allow him to see relationships between tumors and the surrounding nerves and blood vessels. Tumors often grow around nerves, and Noë expects the new perspective of cancerous ducts and nerves could shed light on why.

    “For almost 200 years, pathologists looked at tissue the same way,” he says. “Three-dimensional is almost a whole new world for us. There is a lot of excitement in the department of pathology to apply this technology for the first time to human samples.”

    Before researchers can view tissue of any sort with the light-sheet, their samples must be treated to make them translucent, so the microscope’s light can pass through and create an image. Noë has developed a protocol for clearing human tissue and tumors, work he’s hoping to publish.

    Branch expects to have 3-D images of all 30 of her rat brains in three to six months.

    She’ll see every newborn neuron. She’ll see each dendrite. And hopefully, she’ll find answers – she already knows she’ll find more questions.

    “The technology makes it easier to have confidence about our findings,” she says, “It also opens up an opportunity to ask even more questions — things that before, we didn’t even know we could ask.”

    See the full article here .

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    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

  • richardmitnick 6:50 am on July 12, 2016 Permalink | Reply
    Tags: , Microscopy, , UW researchers improve microscopy method to ‘swell’ cellular structures bringing fine details into view   

    From U Washington: “UW researchers improve microscopy method to ‘swell’ cellular structures, bringing fine details into view” 

    U Washington

    University of Washington

    July 11, 2016
    James Urton

    Cellular biologists work at a frustratingly small scale. Like their colleagues in particle physics, these scientists investigate fundamental questions about our lives and our world — but at a scale beyond the skill of our primate eyes. Microscopes have helped bring this erstwhile invisible world into focus — and over the past several centuries since their invention, advances in microscopy have helped scientists visualize many details of life on the cellular level. But these approaches have costs — expensive equipment and complex specimen treatments — that ultimately restrict their widespread use.

    Microscopy also has its limit. Light’s inherent wavelike behavior limits any microscope’s resolving power. The most minute details of our existence — from twisted strands of DNA to bulbous cellular organelles — are difficult or impossible for even the best and most expensive microscopes to visualize directly.

    In this rat kangaroo kidney call, bundles of tubulin protein strands (green) snag on to chromosomes (blue) as the cell prepares to divide. Joshua Vaughan

    But scientists from the University of Washington recently reported a relatively simple method that would allow ordinary laboratory microscopes to illuminate many of these cellular structures quickly and efficiently. They did not modify microscopes to boost resolution. Instead, they used an approach to swell the tiny, complex structures within cells, bringing them within range of a microscope’s existing resolving range.

    “This is a radically new way of doing microscopy,” said UW chemistry professor Joshua Vaughan, who is senior author on a paper detailing their approach in Nature Methods. “The focus had largely been on hardware — improving the resolution of microscopes. Here, we expand the cell’s interior to bring it into view.”

    Appropriately, this technique is known as expansion microscopy.

    “This is a simple and robust approach that is surprisingly effective,” added Vaughan.

    His team was inspired by the expansion approach developed at the Massachusetts Institute of Technology. The MIT researchers stained cells with a complex, DNA-based fluorescent probe that would make cellular contents visible. They then treated cells with an expandable polymer that linked to the custom probes and would “inflate” the specimens to as much as four times their original size. But, this approach was laborious, and required specialized, expensive reagents.

    “When I saw their approach, I thought it was amazing,” said Vaughan. “But we were wondering if there was a way to do this using simpler staining strategies and conventional probes. That would make expansion microscopy accessible to thousands of labs.”

    Instead of complex fluorescent probes, Vaughan’s team turned to conventional fluorescent dyes bound to antibodies, which are easier to use, and developed a simple chemical treatment that would allow the antibodies to become linked to the polymer. They then treated their stained samples — slices of mammalian brain tissue and cultured cells — with the expandable polymer as well as enzymes that could create small “snips” in proteins to help them expand.

    Zooming in to a mammalian kidney cell, long strands of tubulin proteins before (top) and after (bottom) expansion treatment, showing the improved resolution of expansion microscopy.Joshua Vaughan

    They used this basic approach to come up with two staining protocols for expansion microscopy — one that worked better for individual cells and another for slices of tissue. Under the microscope, their images showed substantially brighter stains while maintaining excellent resolution. As an added bonus, their approach also enables expansion microscopy with fluorescent proteins, another popular fluorescent probe used by biologists. Critically, the UW team was able to obtain these high-resolution images on conventional, widely used laboratory microscopes.

    “We think this will make expansion microscopy a widely used technique for researchers who want to visualize what they’re studying with a relatively simple, low-cost approach that also has excellent performance,” said Vaughan.

    Vaughan said he hopes that other research groups will modify his team’s basic approach for other organisms or cell types, especially structures like cell walls that would resist expansion. Given the details illuminated by expansion microscopy, a hidden world awaits.

    Two scientists from the UW Department of Chemistry, doctoral student Tyler Chozinski and postdoctoral researcher Aaron Halpern, were co-first authors on the paper. Other authors were postdoctoral researcher Haruhisa Okawa and professor Rachel Wong — both in UW Medicine’s biological structure department — and UW undergraduates Hyeon-Jin Kim and Grant Tremel. The work was funded by the National Institutes of Health, the National Science Foundation, the Burroughs-Wellcome Fund and the University of Washington.

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    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

  • richardmitnick 3:00 pm on September 18, 2015 Permalink | Reply
    Tags: , Microscopy, ,   

    From MIT: “Extending super-resolution techniques” 

    MIT News

    Department of Physics graduate student Takuma Inoue built the super-resolution microscopy set up in the Cissé lab at MIT to study single molecule behavior of enzyme clusters that enable gene copying and protein production within living cells. On the table, five different lasers excite different fluorescent proteins at different wavelengths and image their location.

    Photo: Denis Paiste/Materials Processing Center

    Overcoming limitations of super-resolution microscopy to optimize imaging of RNA in living cells is a key motivation for physics graduate student Takuma Inoue, who works in the lab of MIT assistant professor of physics Ibrahim Cissé.

    Inoue, 26, was the first student to join Cissé’s lab at MIT in January 2014, and he built the lab’s super-resolution microscopy setup to study enzyme clusters that enable gene copying and protein production within living cells. Inoue, who this September enters his fourth year toward his PhD, originally started his experimental work in an atomic physics lab, where he worked on an imaging setup to trap extremely cold atoms in a vacuum. He is studying biophysics, atomic physics, and condensed matter physics.

    After learning that Cissé needed someone to set up his super-resolution microscopy, Inoue switched to Cissé’s lab. Because he did not have a biology background, Inoue says, “I wasn’t very much familiar with that, but the tools that you use and the methods for imaging are very common with what I had previously done. By building the setup, I got used to what things we can do in the lab. Then I made the transition to actually targeting some biomolecules within the cell to image and for me that was RNA.”

    “Initially, I had to start with building the microscope, which took me several months, and then I tried doing the continuation of his previous work which is imaging some kind of protein inside of a living cell,” Inoue says. “But then he gave (me) this project of RNA imaging as my main project for my PhD, because that will be more challenging, and we thought no one has ever achieved this big goal.”

    “My project makes sure that we overcome as many limitations as possible because there are different aspects of this for all the projects that we do,” Inoue adds. “There is the setup and there is this data analysis software and also we need to label the target molecules of interest properly. Each of them is, of course, not perfect. There are many challenges and limitations. But if you have a final goal in your project, I think you need to care about all of those different aspects and try optimizing. I’ve been doing experiments for a long time, so overcoming such limitations in the lab was one of my interests.”

    Inoue is developing techniques for easily tagging and visualizing RNA directly in living cells. “For me as an experimentalist, it’s a very exciting challenge to achieve the imaging of RNA within a live cell and to bring it to the level of a single molecule. My goal is achieve a technique to image single molecules of RNA inside of a living cell. That can have very broad applications. I think it’s very transformative,” Inoue says.

    The common approach to such imaging is genetic modification that adds a derivative of green fluorescent protein to the target of study — for example, RNA polymerase II. Inoue says his approach is to avoid genetic modification by developing oligonucleotide probes, which are short strands of genetic material that can bind to the target. “I try to deliver these probes into these natural cells and try to see if the target molecules get this fluorescence. And then I bring those cells to the imaging room and then do imaging,” he says. The technique is called fluorescent in situ hybridization. The oligonucleotide and the RNA target both start out as single strand molecules, but when they bind they can form a double helix like DNA, Inoue explains.

    “There already are approaches for looking at RNA inside dead cells. That’s I think the easy part,” Takuma’s mentor, Cissé, explains. “A handful of labs have also reported on promising ways of labeling RNA in living cells, but those require extensive genetic modifications. Takuma’s whole point is actually bringing new techniques for easily tagging and visualizing any arbitrary RNA, without genetic modification, and directly inside the living cell. And his preliminary demonstrations also, I think, look very promising.”

    Inoue has high hopes for the project. “This project is about labeling arbitrary RNA that exist inside a living cell, and I am at the developing stage of these techniques,” he says. “I’m hoping that through this project I can contribute and help many researchers in studying their RNAs of interest and also I, myself, am interested in studying different kinds of RNA.”

    The Cissé lab’s single molecule studies of the role that enzymes, proteins, and RNA play in gene expression is funded under National Institutes of Health Project No. 1DP2CA195769-01 with additional funds from the National Cancer Institute.

    The super-resolution imaging setup captures images through the microscope onto an electron-multiplying charge-coupled device (EM-CCD). “It can detect very sensitive signals, even single photons, and also it’s a very fast camera,” Inoue explains. The EM-CCD has millisecond exposure times but overall it takes several minutes to get one super-resolution image made from about 10,000 images.

    A native of Yokohama, Japan, Inoue moved to the U.S. at age 18, three years after his father, Hiroshi Inoue, accepted a position in Maryland starting up a life sciences subsidiary for Canon. Now a resident of Rockville, Maryland, Takuma Inoue received his bachelor’s in physics with a minor in mathematics at the University of Maryland at College Park, where his father currently holds the title of Professor of the Practice in Bioengineering.

    “I’ve got a lot of influence from my dad because he was initially an engineer, but then it was a very big surprise to me that he switched to biology and started doing some kind of engineering that could help biologists or could help people. So, that was maybe one of the key events in my life,” he says.

    “I like to think about scientific challenges and also there are many engineering challenges, and I really like that I am doing that, and also that I am trying to solve the world’s most interesting problems in the field of biology using my physics background. I want to see first how this project goes, and if possible, I’d like to continue doing research, and I hope that my career becomes exciting,” Inoue says.

    See the full article here .

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    The mission of MIT is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of the MIT community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

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  • richardmitnick 1:53 pm on August 31, 2015 Permalink | Reply
    Tags: , , Microscopy   

    From Caltech: “New, Ultrathin Optical Devices Shape Light in Exotic Ways” 

    Caltech Logo

    Ker Than

    Schematic drawing of generation and focusing of radially polarized light by a metasurface. Credit: Dr. Amir Arbabi/Faraon Lab/Caltech

    Caltech engineers have created flat devices capable of manipulating light in ways that are very difficult or impossible to achieve with conventional optical components.

    The new devices are not made of glass, but rather of silicon nanopillars that are precisely arranged into a honeycomb pattern to create a “metasurface” that can control the paths and properties of passing light waves.

    These metasurface devices, described in a paper published online on August 31, 2015, in the journal Nature Nanotechnology, could lead to ultracompact optical systems such as advanced microscopes, displays, sensors, and cameras that can be mass-produced using the same photolithography techniques used to manufacture computer microchips.

    “Currently, optical systems are made one component at a time, and the components are often manually assembled,” says Andrei Faraon (BS ’04), an assistant professor of applied physics and materials science, and the study’s principal investigator. “But this new technology is very similar to the one used to print semiconductor chips onto silicon wafers, so you could conceivably manufacture millions of systems such as microscopes or cameras at a time.”

    Seen under a scanning electron microscope [SEM], the new metasurfaces that the team created resemble a cut forest where only the stumps remain. Each silicon stump, or pillar, has an elliptical cross section, and by carefully varying the diameters of each pillar and rotating them around their axes, the scientists were able to simultaneously manipulate the phase and polarization of passing light. Light is an electromagnetic field, and the field of single-color, or monochromatic, light oscillates at all points in space with the same frequency but varying relative delays, or phases.

    Scanning electron microscope

    Manipulating this relative delay, or phase, influences the degree to which a light ray bends, which in turn influences whether an image is in or out of focus.

    Polarization refers to the trajectory of the oscillations of the electromagnetic field at each point in space. Manipulating the polarization of light is essential for the operation of advanced microscopes, cameras, and displays; the control of polarization also enables simple gadgets such as 3-D glasses and polarized sunglasses.

    “Using our metasurfaces, we have complete control of the polarization and phase of light,” says study first author Amir Arbabi, a senior researcher at Caltech. “We can take any incoming light and shape its phase and polarization profiles arbitrarily and with very high efficiency.”

    While the same goal can be achieved using an arrangement of multiple conventional optical components such as glass lenses, prisms, spatial light modulators, polarizers, and wave plates, these many components lead to much bulkier systems. “If you think of a modern microscope, it has multiple components that have to be carefully assembled inside,” Faraon says. “But with our platform, we can actually make each of these optical components and stack them atop one another very easily using an automated process. Each component is just a millionth of a meter thick, or less than a hundredth of the thickness of a human hair. ”

    In addition to being compact, a metasurface device could manipulate light in novel ways that are very hard and sometimes impossible to do using current setups. For example, the Caltech team showed that one of their metasurfaces can project one image when illuminated by a horizontally polarized beam of light, and a different image when illuminated by a vertically polarized beam. “The two images will appear overlapped under illumination with light polarized at 45 degrees,” Faraon says.

    In another experiment, the team was able to use a metasurface to create a beam with radial polarization, that is, a beam whose polarization is pointing toward the beam axis. Such beams have doughnut-shaped intensity profiles and have applications in superresolution microscopy, laser cutting, and particle acceleration. “You generally would need a large optical setup, consisting of multiple components, to create this effect using conventional instruments,” Arbabi says. “With our setup, we can compress all of the optical components into one device and generate these beams with higher efficiency and more purity.”

    The team is currently working with industrial partners to create metasurfaces for use in commercial devices such as miniature cameras and spectrometers, but a limited number have already been produced for use in optical experiments by collaborating scientists in other disciplines.

    In addition, the Faraon lab current is investigating ways to combine different metasurfaces to create functioning optical systems and to correct for color distortions and other optical aberrations. “Like any optical system, you get distortions,” Faraon said. “That’s why expensive cameras have multiple lenses inside. Right now, we are experimenting with stacking different metasurfaces to correct for these aberrations and achieve novel functionalities.”

    The paper is entitled Dielectric metasurfaces for complete control of phase and polarization with sub wavelength spatial resolution and high transmission. In addition to Faraon and Arbabi, other Caltech coauthors include graduate student Yu Horie and Mahmood Bagheri, a microdevices engineer at JPL. The work was supported by the Caltech/JPL President’s and Director’s Fund and the Defense Advanced Research Projects Agency. Yu Horie was supported by the Department of Energy’s Energy Frontier Research Center program and a Japan Student Services Organization fellowship. The device nanofabrication was performed in the Kavli Nanoscience Institute at Caltech.

    See the full article here.

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 7:56 am on May 14, 2015 Permalink | Reply
    Tags: , , , Microscopy, , ,   

    From MIT: “Researchers build new fermion microscope” 

    MIT News

    May 13, 2015
    Jennifer Chu

    Graduate student Lawrence Cheuk adjusts the optics setup for laser cooling of sodium atoms. Photo: Jose-Luis Olivares/MIT

    Laser beams are precisely aligned before being sent into the vacuum chamber. Photo: Jose-Luis Olivares/MIT

    Sodium atoms diffuse out of an oven to form an atomic beam, which is then slowed and trapped using laser light. Photo: Jose-Luis Olivares/MIT

    A Quantum gas microscope for fermionic atoms. The atoms, potassium-40, are cooled during imaging by laser light, allowing thousands of photons to be collected by the microscope. Credit: Lawrence Cheuk/MIT

    The Fermi gas microscope group: (from left) graduate students Katherine Lawrence and Melih Okan, postdoc Thomas Lompe, graduate student Matt Nichols, Professor Martin Zwierlein, and graduate student Lawrence Cheuk. Photo: Jose-Luis Olivares/MIT

    Instrument freezes and images 1,000 individual fermionic atoms at once.

    Fermions are the building blocks of matter, interacting in a multitude of permutations to give rise to the elements of the periodic table. Without fermions, the physical world would not exist.

    Examples of fermions are electrons, protons, neutrons, quarks, and atoms consisting of an odd number of these elementary particles. Because of their fermionic nature, electrons and nuclear matter are difficult to understand theoretically, so researchers are trying to use ultracold gases of fermionic atoms as stand-ins for other fermions.

    But atoms are extremely sensitive to light: When a single photon hits an atom, it can knock the particle out of place — an effect that has made imaging individual fermionic atoms devilishly hard.

    Now a team of MIT physicists has built a microscope that is able to see up to 1,000 individual fermionic atoms. The researchers devised a laser-based technique to trap and freeze fermions in place, and image the particles simultaneously.

    The new imaging technique uses two laser beams trained on a cloud of fermionic atoms in an optical lattice. The two beams, each of a different wavelength, cool the cloud, causing individual fermions to drop down an energy level, eventually bringing them to their lowest energy states — cool and stable enough to stay in place. At the same time, each fermion releases light, which is captured by the microscope and used to image the fermion’s exact position in the lattice — to an accuracy better than the wavelength of light.

    With the new technique, the researchers are able to cool and image over 95 percent of the fermionic atoms making up a cloud of potassium gas. Martin Zwierlein, a professor of physics at MIT, says an intriguing result from the technique appears to be that it can keep fermions cold even after imaging.

    “That means I know where they are, and I can maybe move them around with a little tweezer to any location, and arrange them in any pattern I’d like,” Zwierlein says.

    Zwierlein and his colleagues, including first author and graduate student Lawrence Cheuk, have published their results today in the journal Physical Review Letters.

    Seeing fermions from bosons

    For the past two decades, experimental physicists have studied ultracold atomic gases of the two classes of particles: fermions and bosons — particles such as photons that, unlike fermions, can occupy the same quantum state in limitless numbers. In 2009, physicist Marcus Greiner at Harvard University devised a microscope that successfully imaged individual bosons in a tightly spaced optical lattice. This milestone was followed, in 2010, by a second boson microscope, developed by Immanuel Bloch’s group at the Max Planck Institute of Quantum Optics.

    These microscopes revealed, in unprecedented detail, the behavior of bosons under strong interactions. However, no one had yet developed a comparable microscope for fermionic atoms.

    “We wanted to do what these groups had done for bosons, but for fermions,” Zwierlein says. “And it turned out it was much harder for fermions, because the atoms we use are not so easily cooled. So we had to find a new way to cool them while looking at them.”

    Techniques to cool atoms ever closer to absolute zero have been devised in recent decades. Carl Wieman, Eric Cornell, and MIT’s Wolfgang Ketterle were able to achieve Bose-Einstein condensation in 1995, a milestone for which they were awarded the 2001 Nobel Prize in physics. Other techniques include a process using lasers to cool atoms from 300 degrees Celsius to a few ten-thousandths of a degree above absolute zero.

    A clever cooling technique

    And yet, to see individual fermionic atoms, the particles need to be cooled further still. To do this, Zwierlein’s group created an optical lattice using laser beams, forming a structure resembling an egg carton, each well of which could potentially trap a single fermion. Through various stages of laser cooling, magnetic trapping, and further evaporative cooling of the gas, the atoms were prepared at temperatures just above absolute zero — cold enough for individual fermions to settle onto the underlying optical lattice. The team placed the lattice a mere 7 microns from an imaging lens, through which they hoped to see individual fermions.

    However, seeing fermions requires shining light on them, causing a photon to essentially knock a fermionic atom out of its well, and potentially out of the system entirely.

    “We needed a clever technique to keep the atoms cool while looking at them,” Zwierlein says.

    His team decided to use a two-laser approach to further cool the atoms; the technique manipulates an atom’s particular energy level, or vibrational energy. Each atom occupies a certain energy state — the higher that state, the more active the particle is. The team shone two laser beams of differing frequencies at the lattice. The difference in frequencies corresponded to the energy between a fermion’s energy levels. As a result, when both beams were directed at a fermion, the particle would absorb the smaller frequency, and emit a photon from the larger-frequency beam, in turn dropping one energy level to a cooler, more inert state. The lens above the lattice collects the emitted photon, recording its precise position, and that of the fermion.

    Zwierlein says such high-resolution imaging of more than 1,000 fermionic atoms simultaneously would enhance our understanding of the behavior of other fermions in nature — particularly the behavior of electrons. This knowledge may one day advance our understanding of high-temperature superconductors, which enable lossless energy transport, as well as quantum systems such as solid-state systems or nuclear matter.

    “The Fermi gas microscope, together with the ability to position atoms at will, might be an important step toward the realization of a quantum computer based on fermions,” Zwierlein says. “One would thus harness the power of the very same intricate quantum rules that so far hamper our understanding of electronic systems.”

    Zwierlein says it is a good time for Fermi gas microscopists: Around the same time his group first reported its results, teams from Harvard and the University of Strathclyde in Glasgow also reported imaging individual fermionic atoms in optical lattices, indicating a promising future for such microscopes.

    Zoran Hadzibabic, a professor of physics at Trinity College, says the group’s microscope is able to detect individual atoms “with almost perfect fidelity.”

    “They detect them reliably, and do so without affecting their positions — that’s all you want,” says Hadzibabic, who did not contribute to the research. “So far they demonstrated the technique, but we know from the experience with bosons that that’s the hardest step, and I expect the scientific results to start pouring out.”

    This research was funded in part by the National Science Foundation, the Air Force Office of Scientific Research, the Office of Naval Research, the Army Research Office, and the David and Lucile Packard Foundation.

    See the full article here.

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