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  • richardmitnick 9:13 am on December 14, 2015 Permalink | Reply
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    From LBL: @Nanocarriers May Carry New Hope for Brain Cancer Therapy:” 

    Berkeley Logo

    Berkeley Lab

    November 19, 2015
    Lynn Yarris (510) 486-5375

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    Berkeley Lab researchers have developed a new family of nanocarriers, called “3HM,” that meets all the size and stability requirements for effectively delivering therapeutic drugs to the brain for the treatment of a deadly form of cancer known as glioblastoma multiforme.

    Glioblastoma multiforme, a cancer of the brain also known as “octopus tumors” because of the manner in which the cancer cells extend their tendrils into surrounding tissue, is virtually inoperable, resistant to therapies, and always fatal, usually within 15 months of onset. Each year, glioblastoma multiforme (GBM) kills approximately 15,000 people in the United States. One of the major obstacles to treatment is the blood brain barrier, the network of blood vessels that allows essential nutrients to enter the brain but blocks the passage of other substances. What is desperately needed is a means of effectively transporting therapeutic drugs through this barrier. A nanoscience expert at Lawrence Berkeley National Laboratory (Berkeley Lab) may have the solution.

    Ting Xu, a polymer scientist with Berkeley Lab’s Materials Sciences Division who specializes in self-assembling bio/nano hybrid materials, has developed a new family of nanocarriers formed from the self-assembly of amphiphilic peptides and polymers. Called “3HM” for coiled-coil 3-helix micelles, these new nanocarriers meet all the size and stability requirements for effectively delivering a therapeutic drug to GBM tumors. Amphiphiles are chemical compounds that feature both hydrophilic (water-loving) and lipophilic (fat-loving) properties. Micelles are spherical aggregates of amphiphiles.

    In a recent collaboration between Xu, Katherine Ferrara at the University of California (UC) Davis, and John Forsayeth and Krystof Bankiewicz of UC San Francisco, 3HM nanocarriers were tested on GBM tumors in rats. Using the radioactive form of copper (copper-64) in combination with positron emission tomography (PET) and magnetic resonance imaging (MRI), the collaboration demonstrated that 3HM can cross the blood brain barrier and accumulate inside GBM tumors at nearly double the concentration rate of current FDA-approved nanocarriers.

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    Ting Xu holds joint appointments with Berkeley Lab’s Materials Sciences Division and UC Berkeley’s Departments of Materials Sciences and Engineering, and Chemistry. (Photo by Roy Kaltschmidt)

    “Our 3HM nanocarriers show very good attributes for the treatment of brain cancers in terms of long circulation, deep tumor penetration and low accumulation in off-target organs such as the liver and spleen,” says Xu, who also holds a joint appointment with the UC Berkeley’s Departments of Materials Sciences and Engineering, and Chemistry. “The fact that 3HM is able to cross the blood brain barrier of GBM-bearing rats and selectively accumulate within tumor tissue, opens the possibility of treating GBM via intravenous drug administration rather than invasive measures. While there is still a lot to learn about why 3HM is able to do what it does, so far all the results have been very positive.”

    Glial cells provide physical and chemical support for neurons. Approximately 90-percent of all the cells in the brain are glial cells which, unlike neurons, undergo a cycle of birth, differentiation, and mitosis. Undergoing this cycle makes glial cells vulnerable to becoming cancerous. When they do, as the name “multiforme” suggests, they can take on different shapes, which often makes detection difficult until the tumors are dangerously large. The multiple shapes of a cancerous glial cell also make it difficult to identify and locate all of the cell’s tendrils. Removal or destruction of the main tumor mass while leaving these tendrils intact is ineffective therapy: like the mythical Hydra, the tendrils will sprout new tumors.

    Although there are FDA approved therapeutic drugs for the treatment of GBM, these treatments have had little impact on patient survival rate because the blood brain barrier has limited the accumulation of therapeutics within the brain. Typically, GBM therapeutics are ferried across the blood brain barrier in special liposomes that are approximately 110 nanometers in size. The 3HM nanocarriers developed by Xu and her group are only about 20 nanometers in size. Their smaller size and unique hierarchical structure afforded the 3HM nanocarriers much greater access to rat GBM tumors than 110-nanometer liposomes in the tests carried out by Xu and her colleagues.

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    At only 20 nanometers and featuring a unique hierarchical structure, 3HM nanocarriers meet all the size and stability requirements for effectively delivering therapeutic drugs to brain cancer tumor. No image credit.

    “3HM is a product of basic research at the interface of materials science and biology,” Xu says. “When I first started at Berkeley, I explored hybrid nanomaterials based on proteins, peptides and polymers as a new family of biomaterials. During the process of understanding the hierarchical assembly of amphiphilic peptide-polymer conjugates, my group and I noticed some unusual behavior of these micelles, especially their unusual kinetic stability in the 20 nanometer size range. We looked into critical needs for nanocarriers with these attributes and identified the treatment of GBM cancer as a potential application.”

    Copper-64 was used to label both 3HM and liposome nanocarriers for systematic PET and MRI studies to find out how a nanocarrier’s size might affect the pharmacokinetics and biodistribution in rats with GBM tumors. The results not only confirmed the effectiveness of 3HM as GBM delivery vessels, they also suggest that PET and MRI imaging of nanoparticle distribution and tumor kinetics can be used to improve the future design of nanoparticles for GBM treatment.

    “I thought our 3HM hybrid materials could bring new therapeutic opportunities for GBM but I did not expect it to happen so quickly,” says Xu, who has been awarded a patent for the 3HM technology.

    A paper describing this research has been published in The Journal of Controlled Release. The paper is titled Self-assembled 20-nm 64Cu-micelles enhance accumulation in rat glioblastoma. Xu, Ferrara and Bankiewicz are the senior authors. Other authors, in addition to Forsayeth, are Jai Woong Seo, Joo Chuan Ang, Lisa Mahakian, Sarah Tam, Brett Fite, Elizabeth Ingham and Janine Beyer.

    This research was funded by the National Institutes of Health and the UC Davis Research Investments in Science and Engineering.

    See the full article here .

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  • richardmitnick 4:50 pm on December 1, 2015 Permalink | Reply
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    From LBL: “Berkeley Lab Opens State-of-the-Art Facility for Computational Science” 

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    Berkeley Lab

    November 12, 2015 [This just became available]
    Jon Weiner

    A new center for advancing computational science and networking at research institutions and universities across the country opened today at the Department of Energy’s (DOE) Lawrence Berkeley National Laboratory (Berkeley Lab).

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    Berkeley Lab’s Shyh Wang Hall

    Named Shyh Wang Hall, the facility will house the National Energy Research Scientific Computing Center, or NERSC, one of the world’s leading supercomputing centers for open science which serves nearly 6,000 researchers in the U.S. and abroad. Wang Hall will also be the center of operations for DOE’s Energy Sciences Network, or ESnet, the fastest network dedicated to science, which connects tens of thousands of scientists as they collaborate on solving some of the world’s biggest scientific challenges.

    Complementing NERSC and ESnet in the facility will be research programs in applied mathematics and computer science, which develop new methods for advancing scientific discovery. Researchers from UC Berkeley will also share space in Wang Hall as they collaborate with Berkeley Lab staff on computer science programs.

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    The ceremonial “connection” marking the opening of Shyh Wang Hall.

    The 149,000 square foot facility built on a hillside overlooking the UC Berkeley campus and San Francisco Bay will house one of the most energy-efficient computing centers anywhere, tapping into the region’s mild climate to cool the supercomputers at the National Energy Research Scientific Computing Center (NERSC) and eliminating the need for mechanical cooling.

    “With over 5,000 computational users each year, Berkeley Lab leads in providing scientific computing to the national energy and science user community, and the dedication of Wang Hall for the Computing program at Berkeley Lab will allow this community to continue to flourish,” said DOE Under Secretary for Science and Energy Lynn Orr.

    Modern science increasingly relies on high performance computing to create models and simulate problems that are otherwise too big, too small, too fast, too slow or too expensive to study. Supercomputers are also used to analyze growing mountains of data generated by experiments at specialized facilities. High speed networks are needed to move the scientific data, as well as allow distributed teams to share and analyze the same datasets.

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    Shyh Wang

    Wang Hall is named in honor of Shyh Wang, a professor at UC Berkeley for 34 years who died in 1992. Well-known for his research in semiconductors, magnetic resonances and semiconductor lasers, which laid the foundation for optoelectronics, he supervised a number of students who are now well-known in their own right, and authored two graduate-level textbooks, “Solid State Electronics” and “Fundamentals of Semi-conductor Theory and Device Physics.” Dila Wang, Shyh Wang’s widow, was the founding benefactor of the Berkeley Lab Foundation.

    Solid state electronics, semiconductors and optical networks are at the core of the supercomputers at NERSC—which will be located on the second level of Wang Hall—and the networking routers and switches supporting the Energy Sciences Network (ESnet), both of which are managed by Berkeley Lab from Wang Hall. The Computational Research Division (CRD), which develops advanced mathematics and computing methods for research, will also have a presence in the building.

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    NERSC’s Cray Cori supercomputer’s graphic panels being installed at Wang Hall.

    “Berkeley Lab is the most open, sharing, networked, and connected National Lab, with over 10,000 visiting scientists using our facilities and leveraging our expertise each year, plus about 1,000 UC graduate students and postdocs actively involved in the Lab’s world-leading research,” said Berkeley Lab Director Paul Alivisatos. “Wang Hall will allow us to serve more scientists in the future, expanding this unique role we play in the national innovation ecosystem. The computational power housed in Wang Hall will be used to advance research that helps us better understand ourselves, our planet, and our universe. When you couple the combined experience and expertise of our staff with leading-edge systems, you unlock amazing potential for solving the biggest scientific challenges.”

    The $143 million structure financed by the University of California provides an open, collaborative environment bringing together nearly 300 staff members from three lab divisions and colleagues from UC Berkeley to encourage new ideas and new approaches to solving some of the nation’s biggest scientific challenges.

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    UC President Janet Napolitano at the Shyh Wang Hall opening.

    “All of our University of California campuses rely on high performance computing for their scientific research,” said UC President Janet Napolitano. “The collaboration between UC Berkeley and Berkeley Lab to make this building happen will go a long ways towards advancing our knowledge of the world around us.”

    The building features unique, large, open windows on the lowest level, facing west toward the Pacific Ocean, which will draw in natural air conditioning for the computing systems. Heat captured from those systems will in turn be used to heat the building. The building will house two leading-edge Cray supercomputers – Edison and Cori [pictured above]– which operate around the clock 52 weeks a year to keep up with the computing demands of users.

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    Edison supercomputer

    Temp 1
    The disassembly of our Edison ‪‎supercomputer‬ has begun at NERSC. Edison is relocating to Berkeley from Oakland and into our all-new Shyh Wang Hall.

    Wang Hall will be occupied by Berkeley Lab’s Computing Sciences organization, which comprises three divisions:

    NERSC, the DOE Office of Science’s leading supercomputing center for open science. NERSC supports nearly 6,000 researchers at national laboratories and universities across the country. NERSC’s flagship computer is Edison, a Cray XC30 system capable of performing more than two quadrillion calculations per second. The first phase of Cori, a new Cray XC40 supercomputer designed for data-intensive science has already been installed in Wang Hall.

    ESnet, which links 40 DOE sites across the country and scientists at universities and other research institutions via a 100 gigabits-per second backbone network. ESnet also connects researchers in the U.S. and Europe over connections with a combined capacity of 340 Gbps. To support the transition of NERSC from its 15-year home in downtown Oakland to Berkeley Lab, NERSC and ESnet have developed and deployed a 400 Gbps link for moving massive datasets. This is the first-ever 400 Gbps production network deployed by a research and education network.

    The Computational Research Division, the center for one of DOE’s strongest research programs in applied mathematics and computer science, where more efficient computer architectures are developed alongside more effective algorithms and applications that help scientists make the most effective use of supercomputers and networks to tackle problems in energy, the environment and basic science.

    About Berkeley Lab Computing Sciences
    The Berkeley Lab Computing Sciences organization provides the computing and networking resources and expertise critical to advancing the Department of Energy’s research missions. ESnet, the Energy Sciences Network, provides the high-bandwidth, reliable connections that link scientists at 40 DOE research sites to each other and to experimental facilities and supercomputing centers around the country. The National Energy Research Scientific Computing Center (NERSC) powers the discoveries of 6,000 scientists at national laboratories and universities. The Computational Research Division conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation.

    See the full article here .

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  • richardmitnick 9:37 am on November 6, 2015 Permalink | Reply
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    From LBL- “Supernova Twins: Making Standard Candles More Standard Than Ever” 

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    Berkeley Lab

    November 5, 2015
    Paul Preuss 415-272-3253

    Less than 20 years ago the world learned that the universe is expanding ever faster, propelled by dark energy. The discovery was made possible by Type Ia supernovae; extraordinarily bright and remarkably similar in brightness, they serve as standard candles essential for probing the universe’s history.

    In fact, Type Ia supernovae are far from standard. Intervening dust can redden and dim them, and the physics of their thermonuclear explosions differs — a single white dwarf (an Earth-sized star as massive as our sun) may explode after borrowing mass from a companion star, or two orbiting white dwarfs may collide and explode. These “normal” Type Ia’s can vary in brightness by as much as 40 percent. Brightness dispersion can be reduced by well-proven methods, but cosmology continues to be done with catalogues of supernovae that may differ in brightness by as much as 15 percent.

    Now members of the international Nearby Supernova Factory (SNfactory), based at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), have dramatically reduced the scatter in supernova brightnesses. Using a sample of almost 50 nearby supernovae, they identified supernova twins — pairs whose spectra are closely matched — which reduced their brightness dispersion to a mere eight percent. The distance to these supernovae can be measured about twice as accurately as before.

    The SNfactory results are reported in Improving cosmological distance measurements using twin Type Ia supernovae, accepted for publication by the Astrophysical Journal (ApJ) and available online at arxiv.org/abs/1511.01102.

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    From left, Greg Aldering, Kyle Boone, Hannah Fakhouri and Saul Perlmutter of the Nearby Supernova Factory. Behind them is a poster of a supernova spectrum. Matching spectra among different supernovae can double the accuracy of distance measurements. (Photo by Roy Kaltschmidt/Berkeley Lab)

    Comparing apples to apples

    “Instead of concentrating on what’s causing the differences among supernovae, the supernova-twins approach is to look at the spectra and seek the best matches, so as to compare like with like,” says Greg Aldering, the Berkeley Lab cosmologist who leads the SNfactory. “The assumption we tested is that if two supernovae look the same, they probably are the same.”

    Hannah Fakhouri, the lead author of the ApJ paper, initiated the twin study for her doctoral thesis. She says that the theoretical advantages of a twins match-up had long been discussed at Berkeley Lab; for the researchers who founded the SNfactory, including her thesis advisor, Nobel laureate Saul Perlmutter, one of the main goals was gathering a dataset of sufficient quality to test hypotheses like supernova twinning.

    Fakhouri’s timing was good; she was able to take advantage of precise spectrophotometry — simultaneous measures of spectra and brightness — of numerous nearby Type Ia’s, collected using the SNfactory’s SuperNova Integral Field Spectrograph (SNIFS) on the University of Hawaii’s 2.2-meter telescope on Mauna Kea.

    U Hawaii 2.2 meter telescope
    U Hawaii 2.2 meter telescope interior
    U Hawaii’s 2.2-meter telescope

    “Nearby” is relative; some SNfactory supernovae are more than a billion light years away. But all yield more comprehensive and detailed measurements than the really distant supernovae also needed for cosmology. The twin study used data from the first years of the SNfactory’s observations; further work will use hundreds of high-quality Type Ia spectra from the SNfactory, so far the only large database in the world that can be used for this work.

    Despite the surprising results, Fakhouri describes the initial research as “a long slog,” requiring hard work and attention to detail. One challenge was making fair comparisons of time series, in which spectra are taken at frequent intervals as a supernova reaches maximum luminosity, then slowly fades; different colors (wavelengths) brighten and fade at different rates.

    Because of demands on telescope time and other issues like weather, the time series of different supernovae can’t be sampled uniformly. SNfactory member Rollin Thomas, of Berkeley Lab’s Computational Cosmology Center, recommended a mathematical procedure called Gaussian Process regression to fill the gaps. Fakhouri says the outcome “was a big breakthrough.”

    Cleaning up the spectra and ranking the supernovae for twinness was done completely “blind” — the researchers had no information about the supernovae except their spectra. “The unblinding process was suspenseful,” Fakhouri says. “We might have found that twinning was completely useless.” The result was a relief: the closer the twins’ spectra, the closer their brightnesses.

    The result strongly suggests that the long-accepted 15-percent uncertainty in Type Ia brightness is not merely statistical; it masks real but unknown differences in the nature of the supernovae themselves. The twin method’s dramatic reduction of brightness dispersion suggests that hidden unknowns about the physical explosion processes of twins have been severely reduced as well, a strong step toward using such supernovae as true standard candles.

    The best of the bunch

    When Fakhouri received her doctorate, graduate student Kyle Boone, second author of the ApJ paper, took over the final steps of the analysis. “I started by comparing the twin method to other methods for reducing dispersion in brightness.”

    The conventional approach has been to fit a curve through a series of data points of brightness versus time: a lightcurve. Dimmer Type Ia’s have narrower lightcurves and are redder; this fact is used to “standardize” supernovae, that is, to adjust their brightnesses to a common system.

    The twin method, says Boone, “beats the lightcurve method without even trying. Plus, we found this can be done with just one spectrum — an entire lightcurve is not needed.”

    Other recent methods are more subtle and detailed, but all have drawbacks compared to twinning. “The main competing technique gives excellent results but depends on wavelengths in the near infrared, where dispersion of the starting brightness is much less,” Boone says. “That will be difficult to use with distant supernovae, whose high redshift makes near-infrared wavelengths inaccessible.”

    Fakhouri says, “Supernovae offer unique advantages for cosmology, but we need multiple techniques,” including statistical methods charting how dark energy has shaped the structure of the universe. “The great thing about nature is that it provides different kinds of probes that can be decoupled from one another.”

    Supernovae are a singular asset, notes Aldering: “Supernovae found dark energy, and they still provide the strongest constraints on dark energy properties.”

    Says Boone, “We are working to see how well the twins technology can be applied to a very large sample of well-characterized, high-redshift supernovae that a space telescope like WFIRST could provide.” NASA plans to launch WFIRST, the Wide-Field Infrared Survey Telescope, in the mid-2020s. Among other investigations, it will capture the spectra of many thousands of distant Type Ia supernovae.

    When based on a reference sample of well-measured supernovae large enough for every new supernova to find its perfect twin, twin-supernova technology could lead to precise measures of dark energy’s effect on the universe over the past 10 billion years. Each point in space and time so labeled will be an accurate milestone on the journey that led to the universe we live in today.

    This work was supported by DOE’s Office of Science and by the National Center for Scientific Research/National Institute of Nuclear and Particle Physics (CNRS/IN2P3), the CNRS National Institute for Earth Sciences and Astronomy (CNRS/INSU), and the Laboratory of Nuclear and High-Energy Physics (LPNHE) in France; support in Germany was provided by the German Research Foundation (DFG) and in China by Tsinghua University. The researchers acknowledge the assistance of the Palomar Observatory, the High Performance Wireless Research and Education Network (HPWREN), the University of Hawaii 2.2-meter telescope, and DOE’s National Energy Research Scientific Computing Center (NERSC) for storage and computing time.

    See the full article here .

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  • richardmitnick 3:01 pm on October 28, 2015 Permalink | Reply
    Tags: , , , Unified Microbiome Initiative   

    From LBL: “Scientists Call for National Effort to Understand and Harness Earth’s Microbes for Health, Energy, Agriculture, and Environment” 

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    Berkeley Lab

    October 28, 2015
    Dan Krotz 510-486-4019


    Berkeley Lab’s Microbes to Biomes initiative is designed to reveal, decode and harness microbes. Its goals are closely aligned with that of the Unified Microbiome Initiative, a national effort proposed by scientists.
    download mp4 video here.

    Microbes are essential to life on Earth. They’re found in soil and water and inside the human gut. In fact, nearly every habitat and organism hosts a community of microbes, called a microbiome. What’s more, microbes hold tremendous promise for innovations in medicine, energy, agriculture, and understanding climate change.

    Scientists have made great strides learning the functions of many microbes and microbiomes, but this research also highlights how much more there is to know about the connections between Earth’s microorganisms and a vast number of processes. Deciphering how microbes interact with each other, their hosts, and their environment could transform our understanding of the planet. It could also lead to new antibiotics, ways to fight obesity, drought-resistant crops, or next-gen biofuels, to name a few possibilities.

    To understand and harness the capabilities of Earth’s microbial ecosystems, nearly fifty scientists from Department of Energy national laboratories, universities, and research institutions have proposed a national effort called the Unified Microbiome Initiative. The scientists call for the initiative in a policy forum entitled “A unified initiative to harness Earth’s microbiomes” published Oct. 30, 2015, in the journal Science.

    The Unified Microbiome Initiative would involve many disciplines, including engineering, physical, life, and biomedical sciences; and collaborations between government institutions, private foundations, and industry. It would also entail the development of new tools that enable a mechanistic and predictive understanding of Earth’s microbial processes.

    Among the authors of the Science article are several scientists from the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). These are Berkeley Lab Director Paul Alivisatos; Eoin Brodie, Deputy Director of the Climate and Ecosystem Sciences Division; Mary Maxon, the Biosciences Area Principal Deputy; Eddy Rubin, Director of the Joint Genome Institute; and Peidong Yang, a Faculty Scientist in the Materials Sciences Division. Alivisatos is also the Director of the Kavli Energy Nanoscience Institute, and Yang is the Co-Director.

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    This colorized microscopy image hints at the complexity of microbial life. It shows two bacterial cells in soil. The bacteria glue clay particles together and protect themselves from predators. This also stabilizes soil and stores carbon that could otherwise enter the atmosphere. (Credit: Manfred Auer, Berkeley Lab)

    Berkeley Lab has a long history of microbial research, from its pioneering work in metagenomics at the Joint Genome Institute, to the more recent Microbes to Biomes initiative, which is designed to harness microbes in ways that protect fuel and food supplies, environmental security, and health.

    The call for the Unified Microbiome Initiative comes at a critical time in microbial research. DNA sequencing has enabled scientists to detect microbes in every biological system, thriving deep underground and inside insects for example, and in mind-boggling numbers: Earth’s microbes outnumber the stars in the universe. But to benefit from this knowledge, this descriptive phase must transition to a new phase that explores how microbial communities function, how to predict their actions, and how to make use of them.

    “Technology has gotten us to the point where we realize that microbes are like dark matter in the universe. We know microbes are everywhere, and are far more complex than we previously thought, but we really need to understand how they communicate and relate to the environment,” says Brodie.

    “And just like physicists are trying to understand dark matter, we need to understand the functions of microbes and their genes. We need to study what life is like at the scale of microbes, and how they relate to the planet,” Brodie adds.

    This next phase of microbiome research will require strong ties between disciplines and institutions, and new technologies that accelerate discovery. The scientists map out several opportunities in the Science article. These include:

    Tools to understand the biochemical functions of gene products, a large portion of which are unknown.
    Technologies that quickly generate complete genomes from individual cells found in complex microbiomes.
    Imaging capabilities that visualize individual microbes, along with their interactions and chemical products, in complex microbial networks.
    Adaptive models that capture the complexity of interactions from molecules to microbes, and from microbial communities to ecosystems.

    Many of these new technologies would be flexible platforms, designed initially for microbial research, but likely to find uses in other fields.

    Ten years after the launch of the Unified Microbiome Initiative, the authors of the Science article envision an era in which a predictive understanding of microbial processes enables scientists to manage and design microbiomes in a responsible way—a key step toward harnessing their capabilities for beneficial applications.

    “This is an incredibly exciting time to be involved in microbial research,” says Brodie. “It has the potential to contribute to so many advances, such as in medicine, energy, agriculture, biomanufacturing, and the environment.”

    See the full article here .

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  • richardmitnick 1:51 pm on October 7, 2015 Permalink | Reply
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    From LBL: “Newly Discovered ‘Design Rule’ Brings Nature-Inspired Nanostructures One Step Closer” 

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    Berkeley Lab

    October 7, 2015
    Dan Krotz 510-486-4019

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    Snakes on a plane: This atomic-resolution simulation of a two-dimensional peptoid nanosheet reveals a snake-like structure never seen before. The nanosheet’s layers include a water-repelling core (yellow), peptoid backbones (white), and charged sidechains (magenta and cyan). The right corner of the top layer of the nanosheet has been “removed” to show how the backbone’s alternating rotational states give the backbones a snake-like appearance (red and blue ribbons). Surrounding water molecules are red and white. (Credit: Ranjan Mannige, Berkeley Lab)

    Scientists aspire to build nanostructures that mimic the complexity and function of nature’s proteins, but are made of durable and synthetic materials. These microscopic widgets could be customized into incredibly sensitive chemical detectors or long-lasting catalysts, to name a few possible applications.

    But as with any craft that requires extreme precision, researchers must first learn how to finesse the materials they’ll use to build these structures. A discovery by scientists from the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), and reported Oct. 7 in the advance online publication of the journal Nature, is a big step in this direction.

    The scientists discovered a design rule that enables a recently created material to exist. The material is a peptoid nanosheet. It’s a flat structure only two molecules thick, and it’s composed of peptoids, which are synthetic polymers closely related to protein-forming peptides.

    The design rule controls the way in which polymers adjoin to form the backbones that run the length of nanosheets. Surprisingly, these molecules link together in a counter-rotating pattern not seen in nature. This pattern allows the backbones to remain linear and untwisted, a trait that makes peptoid nanosheets larger and flatter than any biological structure.

    The Berkeley Lab scientists say this never-before-seen design rule could be used to piece together complex nanosheet structures and other peptoid assemblies such as nanotubes and crystalline solids.

    What’s more, they discovered it by combining computer simulations with x-ray scattering and imaging methods to determine, for the first time, the atomic-resolution structure of peptoid nanosheets.

    “This research suggests new ways to design biomimetic structures,” says Steve Whitelam, a co-corresponding author of the Nature paper. “We can begin thinking about using design principles other than those nature offers.”

    Whitelam is a staff scientist in the Theory Facility at the Molecular Foundry, a DOE Office of Science user facility located at Berkeley Lab. He led the research with co-corresponding author Ranjan Mannige, a postdoctoral researcher at the Molecular Foundry; and Ron Zuckermann, who directs the Molecular Foundry’s Biological Nanostructures Facility. They used the high-performance computing resources of the National Energy Research Scientific Computing Center (NERSC), another DOE Office of Science user facility located at Berkeley Lab.

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    Hopper at NERSC

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    The Molecular Foundry scientists who helped discover a new nano design rule. From left, Ellen Robertson, Alessia Battigelli, Ron Zuckermann, Caroline Proulx, Stephen Whitelam, and Ranjan Mannige. (Credit: Roy Kaltschmidt, Berkeley Lab)

    Peptoid nanosheets were discovered by Zuckermann’s group five years ago. They found that under the right conditions, peptoids self assemble into two-dimensional assemblies that can grow hundreds of microns across. This “molecular paper” has become a hot prospect as a protein-mimicking platform for molecular design.

    To learn more about this potential building material, the scientists set out to learn its atom-resolution structure. This involved feedback between experiment and theory. Microscopy and scattering data gathered at the Molecular Foundry and the Advanced Light Source, also a DOE Office of Science user facility located at Berkeley Lab, were compared with molecular dynamics simulations conducted at NERSC.

    The research revealed several new things about peptoid nanosheets. Their molecular makeup varies throughout their structure, they can be formed only from peptoids of a certain minimum length, they contain water pockets, and they are potentially porous when it comes to water and ions.

    These insights are intriguing on their own, but when the scientists examined the structure of the nanosheets’ backbone, they were surprised to see a design rule not found in the field of protein structural biology.

    Here’s the difference: In nature, proteins are composed of beta sheets and alpha helices. These fundamental building blocks are themselves composed of backbones, and the polymers that make up these backbones are all joined together using the same rule. Each adjacent polymer rotates incrementally in the same direction, so that a twist runs along the backbone.

    This rule doesn’t apply to peptoid nanosheets. Along their backbones, adjacent monomer units rotate in opposite directions. These counter-rotations cancel each other out, resulting in a linear and untwisted backbone. This enables backbones to be tiled in two dimensions and extended into large sheets that are flatter than anything nature can produce.

    “It was a big surprise to find the design rule that makes peptoid nanosheets possible has eluded the field of biology until now,” says Mannige. “This rule could perhaps be used to build many more unrealized structures.”

    Adds Zuckermann, “We also expect there are other design principles waiting to be discovered, which could lead to even more biomimetic nanostructures.”


    download the mp4 video here.
    A simulation of a peptoid nanosheet, shown first from a top-down view with the peptoid backbones colored to highlight their snake-like structure. The view then rotates to the side, and finally transitions to an all-atom representation. (Credit: Ron Zuckermann and Ranjan Mannige, Berkeley Lab)

    Other Molecular Foundry scientists who contributed to this research are Thomas Haxton, Caroline Proulx, Ellen Robertson, and Alessia Battigelli.

    This research was conducted at the Molecular Foundry, a DOE Office of Science user facility located at Berkeley Lab. The work was supported by the Defense Threat Reduction Agency, with additional funding provided by the Natural Sciences and Engineering Research Council of Canada. Part of this research was carried out through a User Project at the Molecular Foundry led by New York University’s Glenn Butterfoss.

    See the full article here .

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  • richardmitnick 1:00 pm on October 1, 2015 Permalink | Reply
    Tags: , Cyclotron Road,   

    From LBL: “Cyclotron Road Leads Energy Entrepreneurs Across the Innovation Gap” 

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    Berkeley Lab

    October 1, 2015
    Julie Chao (510) 486-6491

    Steven Kaye got his Ph.D. working on metal-organic frameworks (MOFs), one of the most exciting materials in chemistry today and especially effective for separating gases. But nearly a decade after earning his degree, he saw that the science-to-product gap was still gaping: despite the discovery of thousands of MOFs, there was not a single MOF material in commercial use.

    Then he discovered Cyclotron Road, a new technology-to-market program launched by Lawrence Berkeley National Laboratory (Berkeley Lab) last year. With a guaranteed salary, modest seed funding, and the opportunity to collaborate with some of the best scientists in his field, Kaye would finally be able to work on moving MOFs from the lab to marketplace, where it has the potential to radically reduce the energy use of chemical separations, which accounts for 10 percent of global energy consumption.

    He applied to the program and was accepted. In less than a year, Kaye has been able to demonstrate a scalable manufacturing approach, win $1 million in funding from the California Energy Commission, and spin out his own startup company, Mosaic Materials. “The challenge of solving the scale-up and engineering of these materials was not well suited for academia, and would have been difficult with venture capital,” Kaye said. “But Cyclotron Road was the perfect fit.”

    With support from the U.S. Department of Energy (DOE), Cyclotron Road is now entering its second year and seeking applications for a second cohort of scientist-entrepreneurs. “In an era of declining private-sector investment in early-stage energy technologies, many of our best and brightest engineers, scientists, and energy technology entrepreneurs are at risk of turning away from their pursuit of potentially groundbreaking new energy technologies,” wrote David Danielson, DOE’s Assistant Secretary for Energy Efficiency and Renewable Energy, in a recent blog post. “Cyclotron Road … was created just to address this problem.”

    More broadly, a key focus of Danielson’s Clean Energy Manufacturing Initiative has been to support national lab-industry partnerships that help the private sector leverage the labs’ world-class technology capabilities in order to better innovate and break down market barriers.

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    Sebastien Lounis (left) and Ilan Gur head up Cyclotron Road. (Photo credit: Berkeley Lab)

    So far, six Cyclotron Road teams have brought in more than $2 million in new funding from government grants and private investors. They’re driving key materials and manufacturing innovation in projects ranging from renewable plastics to ocean wave energy to electrochemical conversion of carbon dioxide to fuel.

    “We’re looking for the best and brightest technical founders, entrepreneurial researchers, and scientists who want to drive breakthrough energy technologies to market,” said Cyclotron Road Director Ilan Gur. “They can be individuals, teams, even small companies, as long as they’re at the pre-commercial stage, meaning they haven’t raised a significant amount of private funding.”

    Successful applicants get a two-year appointment and seed funding from DOE to support collaborations with Berkeley Lab researchers. “I think that’s the biggest benefit of this whole program—working with Berkeley Lab scientists and experts,” said Sebastien Lounis, member of the Cyclotron Road founding team.

    Another benefit is access to the cutting edge scientific facilities at Berkeley Lab, such as nanoscale labs, particle accelerators, and high-powered equipment for microscopy and spectroscopy. “This is hardware that most large companies—never mind startups—cannot afford to invest in,” Lounis said.

    The goal is to find another six teams for the second cohort of Cyclotron Road innovators. Lounis expects the application process to be highly competitive, given that more than 150 people applied for the first round and also given the dearth of similar programs.

    Once they’re accepted, Cyclotron Road does everything it can to help them succeed, from pairing them with collaborators to introducing them to its vast network of commercial, academic, and financial partners. Success, Lounis said, can come in any of a number of flavors. “One of the core philosophies of this program is there isn’t a one-size-fits-all business model for these projects,” he said. “The goal is for technologies to reach a scale where they can have an impact on the economy, on energy, on the climate change problem.”

    See the full article here .

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  • richardmitnick 7:19 am on August 25, 2015 Permalink | Reply
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    From LBL: “News Center Major Advance in Artificial Photosynthesis Poses Win/Win for the Environment” 

    Berkeley Logo

    Berkeley Lab

    April 16, 2015
    Lynn Yarris (510) 486-5375

    Berkeley Lab Researchers Perform Solar-powered Green Chemistry with Captured CO2

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    A major advance in artificial photosynthesis poses win/win for the environment – using sequestered CO2 for green chemistry, including renewable fuel production. (Photo by Caitlin Givens)

    A potentially game-changing breakthrough in artificial photosynthesis has been achieved with the development of a system that can capture carbon dioxide emissions before they are vented into the atmosphere and then, powered by solar energy, convert that carbon dioxide into valuable chemical products, including biodegradable plastics, pharmaceutical drugs and even liquid fuels.

    Scientists with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley have created a hybrid system of semiconducting nanowires and bacteria that mimics the natural photosynthetic process by which plants use the energy in sunlight to synthesize carbohydrates from carbon dioxide and water. However, this new artificial photosynthetic system synthesizes the combination of carbon dioxide and water into acetate, the most common building block today for biosynthesis.

    “We believe our system is a revolutionary leap forward in the field of artificial photosynthesis,” says Peidong Yang, a chemist with Berkeley Lab’s Materials Sciences Division and one of the leaders of this study. “Our system has the potential to fundamentally change the chemical and oil industry in that we can produce chemicals and fuels in a totally renewable way, rather than extracting them from deep below the ground.”

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    This break-through artificial photosynthesis system has four general components: (1) harvesting solar energy, (2) generating reducing equivalents, (3) reducing CO2 to biosynthetic intermediates, and (4) producing value-added chemicals. No image credit.

    Yang, who also holds appointments with UC Berkeley and the Kavli Energy NanoSciences Institute (Kavli-ENSI) at Berkeley, is one of three corresponding authors of a paper describing this research in the journal Nano Letters. The paper is titled Nanowire-bacteria hybrids for unassisted solar carbon dioxide fixation to value-added chemicals. The other corresponding authors and leaders of this research are chemists Christopher Chang and Michelle Chang. Both also hold joint appointments with Berkeley Lab and UC Berkeley. In addition, Chris Chang is a Howard Hughes Medical Institute (HHMI) investigator. (See below for a full list of the paper’s authors.)

    The more carbon dioxide that is released into the atmosphere the warmer the atmosphere becomes. Atmospheric carbon dioxide is now at its highest level in at least three million years, primarily as a result of the burning of fossil fuels. Yet fossil fuels, especially coal, will remain a significant source of energy to meet human needs for the foreseeable future. Technologies for sequestering carbon before it escapes into the atmosphere are being pursued but all require the captured carbon to be stored, a requirement that comes with its own environmental challenges.

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    (From left) Peidong Yang, Christopher Chang and Michelle Chang led the development of an artificial photosynthesis system that can convert CO2 into valuable chemical products using only water and sunlight. (Photo by Roy Kaltschmidt)

    The artificial photosynthetic technique developed by the Berkeley researchers solves the storage problem by putting the captured carbon dioxide to good use.

    “In natural photosynthesis, leaves harvest solar energy and carbon dioxide is reduced and combined with water for the synthesis of molecular products that form biomass,” says Chris Chang, an expert in catalysts for carbon-neutral energy conversions. “In our system, nanowires harvest solar energy and deliver electrons to bacteria, where carbon dioxide is reduced and combined with water for the synthesis of a variety of targeted, value-added chemical products.”

    By combining biocompatible light-capturing nanowire arrays with select bacterial populations, the new artificial photosynthesis system offers a win/win situation for the environment: solar-powered green chemistry using sequestered carbon dioxide.

    “Our system represents an emerging alliance between the fields of materials sciences and biology, where opportunities to make new functional devices can mix and match components of each discipline,” says Michelle Chang, an expert in biosynthesis. “For example, the morphology of the nanowire array protects the bacteria like Easter eggs buried in tall grass so that these usually-oxygen sensitive organisms can survive in environmental carbon-dioxide sources such as flue gases.”

    The system starts with an “artificial forest” of nanowire heterostructures, consisting of silicon and titanium oxide nanowires, developed earlier by Yang and his research group.

    “Our artificial forest is similar to the chloroplasts in green plants,” Yang says. “When sunlight is absorbed, photo-excited electron−hole pairs are generated in the silicon and titanium oxide nanowires, which absorb different regions of the solar spectrum. The photo-generated electrons in the silicon will be passed onto bacteria for the CO2 reduction while the photo-generated holes in the titanium oxide split water molecules to make oxygen.”

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    Cross-sectional SEM image of the nanowire/bacteria hybrid array used in a revolutionary new artificial photosynthesis system. No image credit

    Once the forest of nanowire arrays is established, it is populated with microbial populations that produce enzymes known to selectively catalyze the reduction of carbon dioxide. For this study, the Berkeley team used Sporomusa ovata, an anaerobic bacterium that readily accepts electrons directly from the surrounding environment and uses them to reduce carbon dioxide.

    “S. ovata is a great carbon dioxide catalyst as it makes acetate, a versatile chemical intermediate that can be used to manufacture a diverse array of useful chemicals,” says Michelle Chang. “We were able to uniformly populate our nanowire array with S. ovata using buffered brackish water with trace vitamins as the only organic component.”

    Once the carbon dioxide has been reduced by S. ovata to acetate (or some other biosynthetic intermediate), genetically engineered E.coli are used to synthesize targeted chemical products. To improve the yields of targeted chemical products, the S. ovata and E.coli were kept separate for this study. In the future, these two activities – catalyzing and synthesizing – could be combined into a single step process.

    A key to the success of their artificial photosynthesis system is the separation of the demanding requirements for light-capture efficiency and catalytic activity that is made possible by the nanowire/bacteria hybrid technology. With this approach, the Berkeley team achieved a solar energy conversion efficiency of up to 0.38-percent for about 200 hours under simulated sunlight, which is about the same as that of a leaf.

    The yields of target chemical molecules produced from the acetate were also encouraging – as high as 26-percent for butanol, a fuel comparable to gasoline, 25-percent for amorphadiene, a precursor to the antimaleria drug artemisinin, and 52-percent for the renewable and biodegradable plastic PHB. Improved performances are anticipated with further refinements of the technology.

    “We are currently working on our second generation system which has a solar-to-chemical conversion efficiency of three-percent,” Yang says. “Once we can reach a conversion efficiency of 10-percent in a cost effective manner, the technology should be commercially viable.”

    In addition to the corresponding authors, other co-authors of the Nano Letters paper describing this research were Chong Liu, Joseph Gallagher, Kelsey Sakimoto and Eva Nichols.

    This research was primarily funded by the DOE Office of Science.

    See the full article here.

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  • richardmitnick 11:49 am on August 4, 2015 Permalink | Reply
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    From LBL: “Atomic View of Microtubules” 

    Berkeley Logo

    Berkeley Lab

    August 4, 2015
    Lynn Yarris (510) 486-5375

    1
    Microtubules are hollow cylinders with walls made up of tubulin proteins – alpha (green) and beta (blue) – plus EB proteins (orange) that can either stabilize or destabilize the structure of the tubulin proteins.

    Microtubules, hollow fibers of tubulin protein only a few nanometers in diameter, form the cytoskeletons of living cells and play a crucial role in cell division (mitosis) through their ability to undergo rapid growth and shrinkage, a property called “dynamic instability.” Through a combination of high-resolution cryo-electron microscopy (cryo-EM) and a unique methodology for image analysis, a team of researchers with Berkeley Lab and the University of California (UC) Berkeley has produced an atomic view of microtubules that enabled them to identify the crucial role played by a family of end-binding (EB) proteins in regulating microtubule dynamic instability.

    During mitosis, microtubules disassemble and reform into spindles that are used by the dividing cell to move chromosomes. For chromosome migration to occur, the microtubules attached to them must disassemble, carrying the chromosomes in the process. The dynamic instability that makes it possible for microtubules to transition from a rigid polymerized or “assembled” nucleotide state to a flexible depolymerized or “disassembled” nucleotide state is driven by guanosine triphosphate (GTP) hydrolysis in the microtubule lattice.

    “Our study shows how EB proteins can either facilitate microtubule assembly by binding to sub-units of the microtubule, essentially holding them together, or else cause a microtubule to disassemble by promoting GTP hydrolysis that destabilizes the microtubule lattice,” says Eva Nogales, a biophysicist with Berkeley Lab’s Life Sciences Division who led this research.

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    Gregory Alushin and Eva Nogales studying images of microtubule structures. (Photo by Roy Kaltschmidt)

    Nogales, who is also a professor of biophysics and structural biology at UC Berkeley and investigator with the Howard Hughes Medical Institute, is a leading authority on the structure and dynamics of microtubules. In this latest study, she and her group used cryo-EM, in which protein samples are flash-frozen at liquid nitrogen temperatures to preserve their natural structure, to determine microtubule structures in different nucleotide states with and without EB3. With cryo-EM and their image analysis methodology, they achieved a resolution of 3.5 Angstroms, a record for microtubules. For perspective, the diameter of a hydrogen atom is about 1.0 Angstroms.

    “We can now study the atomic details of microtubule polymerization and depolymerization to develop a complete description of microtubule dynamics,” Nogales says.

    Beyond their importance to our understanding of basic cell biology, microtubules are a major target for anticancer drugs, such as Taxol, which can prevent the transition from growing to shrinking nucleotide states or vice versa.

    3
    Rui Zhang is the lead author of a Cell paper describing the record 3.5 Angstroms resolution imaging of microtubules

    “A better understanding of how microtubule dynamic instability is regulated could open new opportunities for improving the potency and selectivity of existing anti-cancer drugs, as well as facilitate the development of novel agents,” Nogales says.

    Nogales is the corresponding author of a paper describing this research in the journal Cell. The paper is entitled Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins. Co-authors are Rui Zhang, Gregory Alushin and Alan Brown.

    This work was funded by a grant from NIH’s National Institute of General Medical Sciences.

    See the full article here.

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  • richardmitnick 5:30 pm on August 3, 2015 Permalink | Reply
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    From LBL: “Notes from the Particle Physics Underground” 

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    Berkeley Lab

    August 3, 2015
    Kate Greene 913-634-1611

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    Temp 0

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    Temp 0

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    Temp 0

    The Black Hills region in western South Dakota is known for its rich stores of gold and silver. In fact, 41 million ounces of gold and 9 million ounces of silver were pulled from Homestake Mine in Lead, SD between the 1870s and early 2000s. During that time, 370 miles of mine tunnels were created, reaching depths of 8,000 feet. But in 2006 science took over: Sanford Underground Research Facility (Sanford Lab) is an underground particle physics research complex housed in the former mine, using the earth and rock to shield experiments from cosmic rays. The better the shielding, the more likely the scientists will detect neutrinos and suspected dark matter particles called WIMPs. Earlier this summer, Lead celebrated the ribbon-cutting of a new visitor center that highlights the history of the old mine and the current and future science at Sanford Lab.

    The U.S. Department of Energy’s Lawrence Berkeley National Lab (Berkeley Lab) is a key player in the creation of Sanford Lab and in the operation of some of its current and future experiments, including the dark matter experiment called LUX and a neutrino experiment called the MAJORANA DEMONSTRATOR. Berkeley Lab is also managing the Berkeley Low Background Facility and the forthcoming LUX-ZEPLIN (LZ) dark matter project, which builds on the accomplishments of LUX.

    LUX Dark matter
    LUX

    Majorano Demonstrator Experiment
    MAJORANA DEMONSTRATOR

    Lux Zeplin project
    LUX-ZEPLIN (LZ)

    As a science writer for Berkeley Lab, I was able to catch a ride on one of the mine’s elevators, called a cage, and descend 4,850 feet down to learn more about the science and the scientists who work on these projects.

    The above slideshow illustrates what it’s like to go underground. The short video below shows the last few seconds of the cage ride and our exit into the space called the Davis Campus, completed in 2012 and home to the MAJORANA DEMONSTRATOR, the LUX experiment, and other facilities.

    The cage operator communicates with an operator on the surface at the start and end of the ride. There are no lights in the cage or shaft other than headlamps.

    The Black Hills region in western South Dakota is known for its rich stores of gold and silver. In fact, 41 million ounces of gold and 9 million ounces of silver were pulled from Homestake Mine in Lead, SD between the 1870s and early 2000s. During that time, 370 miles of mine tunnels were created, reaching depths of 8,000 feet. But in 2006 science took over: Sanford Underground Research Facility (Sanford Lab) is an underground particle physics research complex housed in the former mine, using the earth and rock to shield experiments from cosmic rays. The better the shielding, the more likely the scientists will detect neutrinos and suspected dark matter particles called WIMPs. Earlier this summer, Lead celebrated the ribbon-cutting of a new visitor center that highlights the history of the old mine and the current and future science at Sanford Lab.

    The U.S. Department of Energy’s Lawrence Berkeley National Lab (Berkeley Lab) is a key player in the creation of Sanford Lab and in the operation of some of its current and future experiments, including the dark matter experiment called LUX and a neutrino experiment called the MAJORANA DEMONSTRATOR. Berkeley Lab is also managing the Berkeley Low Background Facility and the forthcoming LUX-ZEPLIN (LZ) dark matter project, which builds on the accomplishments of LUX.

    As a science writer for Berkeley Lab, I was able to catch a ride on one of the mine’s elevators, called a cage, and descend 4,850 feet down to learn more about the science and the scientists who work on these projects.

    The above slideshow illustrates what it’s like to go underground. The short video below shows the last few seconds of the cage ride and our exit into the space called the Davis Campus, completed in 2012 and home to the MAJORANA DEMONSTRATOR, the LUX experiment, and other facilities.

    It takes about ten minutes to ride the cage down to the 4,850 level where LUX and the MAJORANA DEMONSTRATOR are located. This video captures the last few seconds of the cage ride and the entry into the Davis Campus.

    In addition to checking out the MAJORANA DEMONSTRATOR and LUX projects, I joined a tour given to a group of esteemed scientists (including Berkeley Lab’s Eric Linder) who were in the nearby town of Deadwood, SD for a conference on particle physics and cosmology. As part of the tour, we traveled through unlit tunnels, visited construction sites of a future experiment, and walked through the refuge chamber, a shelter equipped with water, meal bars, and canisters of breathable air in case a fire or other disaster strikes.

    I went underground at 7:30 a.m. and came back up at noon. My four and a half hours of being shielded from daylight and cosmic rays was pleasant enough, but when I stepped outside, above ground, I was glad to see a bright sun and feel the breeze on my skin.

    All photo and video credits: Kate Greene.

    On the full article is a slideshow that details the underground experiments. The short video that follows gives a sense of what it’s like to travel through the tunnels.

    See the full article here.

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  • richardmitnick 2:41 pm on July 24, 2015 Permalink | Reply
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    From LBL: “Unlocking the Rice Immune System” 

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    Berkeley Lab

    July 24, 2015
    Lynn Yarris (510) 486-5375

    1
    Rice is a staple for half the world’s population and the model plant for grass-type biofuel feedstocks (Photo by Roy Kaltschmidt, Berkeley Lab

    A bacterial signal that when recognized by rice plants enables the plants to resist a devastating blight disease has been identified by a multi-national team of researchers led by scientists with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) and the University of California (UC) Davis.

    The research team discovered that a tyrosine-sulfated bacterial protein called “RaxX,” activates the rice immune receptor protein called “XA21.” This activation triggers an immune response against Xanthomonas oryzaepv.oryzae (Xoo), a pathogen that causes bacterial blight, a serious disease of rice crops.

    “Our results show that RaxX, a small, previously undescribed bacterial protein, is required for activation of XA21-mediated immunity to Xoo,” says Pamela Ronald, a plant geneticist for both JBEI and UC Davis who led this study. “XA21 can detect RaxX and quickly mobilize its defenses to mount a potent immune response against Xoo. Rice plants that do not carry the XA21 immune receptor or other related immune receptors are virtually defenseless against bacterial blight.”

    Ronald, who directs JBEI’s grass genetics program and is a professor in the UC Davis Department of Plant Pathology, is one of two corresponding authors of a paper describing this research in Science Advances, along with Benjamin Schwessinger, a grass geneticist with JBEI’s Feedstocks Division at the time of this study and now with the Australian National University. The paper is titled The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium. (See end of story for a complete list of authors.)

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    Pamela Ronald is a leading authority on plant genetics who holds joint appointments with the Joint BioEnergy Institute and the University of California at Davis. (Photo by John Stumbos, UC Davis)

    Rice is a staple food for half the world’s population and a model plant for perennial grasses, such as Miscanthus and switchgrass, which are prime feedstock candidates for the production of clean, green and renewable cellulosic biofuels. Just as bacterial blight poses a major threat to rice crops, bacterial infections of grass-type fuel plants could present major problems for the future production of advanced biofuels. However, the mechanisms by which bacteria infect such grasses is poorly understood.

    “Pathogens of grass-type biofuel crops that would reduce the yield of fuel-producing biomass likely use similar infection mechanisms to Xoo,” says Schwessinger. “Having identified the activator of XA21, we will be able to study the rice immune system in far greater detail than ever before. As rice is the model for grass-type biofuel feedstocks, this might help in the future engineering of more disease-resistant grass-type biofuel crops.”

    Most plants and many animals can only defend themselves against a given disease if they carry specialized immune receptors that sense the invading pathogen behind the disease. In 2009, Ronald and her group identified a small bacterial protein they named “Ax21” as the molecular key that binds to the XA21 receptor to activate a rice plant’s immune response. Diligent follow-up research by her group led to Ronald retracting these results and continuing the search for the true key.

    “We were ecstatic with our results in 2009 because identifying the molecule that XA21 recognizes provides an important piece to the puzzle of how the rice plant is able to respond to infection,” Ronald says, “but then it was back to the drawing board. Now we have the real XA21 activator.”

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    Benjamin Schwessinger and Rory Pruitt were co-lead authors of a Science Advances paper that described the identification of a bacterial signaling molecule which triggers immunity response in rice. (Photo by Daniel Caddell)

    To uncover the true XA21 activator, Ronald and her collaborators studied mutations around an operon known as “RaxSTAB.” Operons are small groups of genes with related functions that are co-transcribed in a single strand of messenger RNA.

    “We hypothesized that the activator of XA21 might be encoded in the proximity of the molecular machinery that we already knew was involved in production of the activator,” says Rory Pruitt, a member of Ronald’s research group and a co-lead author with Schwessinger of the Science Advances paper. “One of these bacterial mutants had a deletion of a then unknown gene, now called raxX.”

    Adds Schwessinger, “When we looked more closely in this operon region we identified raxX as a potentially expressed gene. This small gene stuck out as it was very well conserved in other Xanthomonas that encode RaxSTAB but not conserved in any other bacteria that miss this operon.”

    In addition to its implications for future grass-type biofuel feedstocks, the revelation of RaxX as the bacterial molecule that triggers the XA21-mediated immune response also holds important implications for the worldwide supply of rice. The research team has shown that a number of strains of the blight bacteria can evade XA21-mediated immunity because they encode a variant of raxX alleles.

    “Like prescribing the best vaccination for the flu each season by monitoring which flu strains are going to be the most prevalent, it should be possible to screen wild Xoo populations in the rice-growing regions of Asia and Africa for whether they encode RaxX alleles that are recognized by XA21,” says Schwessinger. “We can then inform farmers which rice varieties will be resistant to those bacterial populations.”

    Schwessinger also notes that several major human diseases involve tyrosine-sulfated proteins, including HIV. However the precise role of tyrosine sulfation in receptor binding and cell invasion is not understood.

    “Understanding the RaxX/XA21 ligand-receptor pair might help medical researchers better understand the role of tyrosine sulfation for receptor binding in human disease,” Schwessinger says. “This could lead to the development of novel components that block the binding of specific tyrosine-sulfated proteins.”

    This research was supported by both the DOE Office of Science, the National Institutes of Health, and the Human Frontier Science Program.

    In addition to Ronald, Schwessinger and Pruitt, other co-authors of the Science Advances paper were Anna Joe, Nicholas Thomas, Furong Liu, Markus Albert, Michelle Robinson, Leanne Chan, Dee Dee Luu, Huamin Chen, Ofir Bahar, Arsalan Daudi, David De Vleesschauwer, Daniel Caddell,Weiguo Zhang, Xiuxiang Zhao, Xiang Li, Joshua Heazlewood, Deling Ruan, Dipali Majumder, Mawsheng Chern, Hubert Kalbacher, Samriti Midha, Prabhu Patil, Ramesh Sonti, Christopher Petzold, Chang Liu, Jennifer Brodbelt and Georg Felix.

    See the full article here.

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