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Scientists Set Record Resolution for Drawing at the One-Nanometer Length Scale

Using a specialized electron microscope outfitted with a pattern generator, scientists turned an imaging instrument into a lithography tool that could be used to create and study materials with new properties.

For First Time, Researchers Measure Forces That Align Crystals and Help Them Snap Together

For the first time, researchers have measured the force that draws tiny crystals together and visualized how they swivel and align. Called van der Waals forces, the attraction provides insights into how crystals self-assemble, an activity that occurs in a wide range of cases in nature, from rocks to shells to bones.

Video Captures Bubble-Blowing Battery in Action

PNNL researchers have created a unique video that shows oxygen bubbles inflating and later deflating inside a tiny lithium-air battery. The knowledge gained from the video could help make lithium-air batteries that are more compact, stable and can hold onto a charge longer.

Study Offers New Theoretical Approach to Describing Non-Equilibrium Phase Transitions

Two physicists at Argonne offered a way to mathematically describe a particular physics phenomenon called a phase transition in a system out of equilibrium. Such phenomena are central in physics, and understanding how they occur has been a long-held and vexing goal; their behavior and related effects are key to unlocking possibilities for new electronics and other next-generation technologies.

Berkeley Lab Scientists Discover New Atomically Layered, Thin Magnet

Berkeley Lab scientists have found an unexpected magnetic property in a 2-D material. The new atomically thin, flat magnet could have major implications for a wide range of applications, such as nanoscale memory, spintronic devices, and magnetic sensors.

Stabilizing Molecule Could Pave Way for Lithium-Air Fuel Cell

Lithium-oxygen fuel cells boast energy density levels comparable to fossil fuels and are thus seen as a promising candidate for future transportation-related energy needs.

Scientists Identify Chemical Causes of Battery "Capacity Fade"

Researchers at Argonne National Laboratory identified one of the major culprits in capacity fade of high-energy lithium-ion batteries.

Modeling Reveals How Policy Affects the Adoption of Solar Energy Photovoltaics in California

Researchers at the University of California, Riverside, inspired by efforts to promote green energy, are exploring the factors driving commercial customers in Southern California, both large and small, to purchase and install solar photovoltaic (PV) systems. As the group reports this week in the Journal of Renewable and Sustainable Energy, they built a model for commercial solar PV adoption to quantify the impact of government incentives and solar PV costs.

Machine Learning Dramatically Streamlines Search for More Efficient Chemical Reactions

A catalytic reaction may follow thousands of possible paths, and it can take years to identify which one it actually takes so scientists can tweak it and make it more efficient. Now researchers at the Department of Energy's SLAC National Accelerator Laboratory and Stanford University have taken a big step toward cutting through this thicket of possibilities.

Freezing Lithium Batteries May Make Them Safer and Bendable

Columbia Engineering Professor Yuan Yang has developed a new method that could lead to lithium batteries that are safer, have longer battery life, and are bendable, providing new possibilities such as flexible smartphones. His new technique uses ice-templating to control the structure of the solid electrolyte for lithium batteries that are used in portable electronics, electric vehicles, and grid-level energy storage. The study is published online April 24 in Nano Letters.


OU Engineering Professor Receives National Science Foundation Early CAREER Award

A University of Oklahoma Gallogly College of Engineering professor, Steven P. Crossley, is the recipient of a five-year, National Science Foundation Early CAREER Award in the amount of $548,829 for research that can be used to understand catalysts that are important for a broad range of chemical reactions ranging from the production of renewable fuels and chemicals for natural gas processing. The research will be integrated with educational and outreach programs intended for American Indian students, emphasizing the importance of sustainable energy.

3 Small Energy Firms to Collaborate with PNNL

Pacific Northwest National Laboratory is collaborating with three small businesses to address technical challenges concerning hydrogen for fuel cell cars, bio-coal and nanomaterial manufacturing.

ORNL to Collaborate with Five Small Businesses to Advance Energy Tech

Five small companies have been selected to partner with the Department of Energy's Oak Ridge National Laboratory to move technologies in commercial refrigeration systems, water power generation, bioenergy and battery manufacturing closer to the marketplace.

U.S. Department of Energy's INCITE Program Seeks Advanced Computational Research Proposals for 2018

The Department of Energy's INCITE program will be accepting proposals for high-impact, computationally intensive research campaigns in a broad array of science, engineering, and computer science domains.

New Berkeley Lab Project Turns Waste Heat to Electricity

A new Berkeley Lab project seeks to efficiently capture waste heat and convert it to electricity, potentially saving California up to $385 million per year. With a $2-million grant from the California Energy Commission, Berkeley Lab scientists will work with Alphabet Energy to create a cost-effective thermoelectric waste heat recovery system.

New SLAC Theory Institute Aims to Speed Research on Exotic Materials at Light Sources

A new institute at the Department of Energy's SLAC National Accelerator Laboratory is using the power of theory to search for new types of materials that could revolutionize society - by making it possible, for instance, to transmit electricity over power lines with no loss.

Lenvio Inc. Exclusively Licenses ORNL Malware Behavior Detection Technology

Virginia-based Lenvio Inc. has exclusively licensed a cyber security technology from the Department of Energy's Oak Ridge National Laboratory that can quickly detect malicious behavior in software not previously identified as a threat.

Argonne Scientist and Nobel Laureate Alexei Abrikosov Dies at 88

Alexei Abrikosov, an acclaimed physicist at the U.S. Department of Energy's Argonne National Laboratory who received the 2003 Nobel Prize in Physics for his work on superconducting materials, died Wednesday, March 29. He was 88.

Jefferson Lab Accomplishes Critical Milestones Toward Completion of 12 GeV Upgrade

The Continuous Electron Beam Accelerator Facility (CEBAF) at the U.S. Department of Energy's Thomas Jefferson National Accelerator Facility has achieved two major commissioning milestones and is now entering the final stretch of work to conclude its first major upgrade. Recently, the CEBAF accelerator delivered electron beams into two of its experimental halls, Halls B and C, at energies not possible before the upgrade for commissioning of the experimental equipment currently in each hall. Data were recorded in each hall, which were then confirmed to be of sufficient quality to allow for particle identification, a primary indicator of good detector operation.

Valerie Taylor Named Argonne National Laboratory's Mathematics and Computer Science Division Director

Computer scientist Valerie Taylor has been appointed as the next director of the Mathematics and Computer Science division at Argonne, effective July 3, 2017.


Uncrowded Coils

A new fast and robust algorithm for computing stellarator coil shapes yields designs that are easier to build and maintain.

Fast Electrons and the Seeds of Disruption

Physicists measured fast electron populations. They achieved this first-of-its-kind result by seeing the effect of the fast electrons on the ablation rate of small frozen argon pellets.

Plasma Turbulence Generates Flow in Fusion Reactors

Heating the core of fusion reactors causes them to develop sheared rotation that can improve plasma performance.

The Roadmap to Quark Soup

Scientists discover new signposts in the quest to determine how matter from the early universe turned into the world we know today.

Neutrons Play the Lead to Protons in Dance Around "Double-Magic" Nucleus

Electric and magnetic properties of a radioactive atom provide unique insight into the nature of proton and neutron motion.

Ultrafast Imaging Reveals the Electron's New Clothes

Scientists use high-speed electrons to visualize "dress-like" distortions in the atomic lattice. This work reveals the vital role of electron-lattice interactions in manganites. This material could be used in data-storage devices with increased data density and reduced power requirements.

One Small Change Makes Solar Cells More Efficient

For years, scientists have explored using tiny drops of designer materials, called quantum dots, to make better solar cells. Adding small amounts of manganese decreases the ability of quantum dots to absorb light but increases the current produced by an average of 300%.

Electronic "Cyclones" at the Nanoscale

Through highly controlled synthesis, scientists controlled competing atomic forces to let spiral electronic structures form. These polar vortices can serve as a precursor to new phenomena in materials. The materials could be vital for ultra-low energy electronic devices.

In a Flash! A New Way for Making Ceramics

A new process controllably but instantly consolidates ceramic parts, potentially important for manufacturing.

Deciphering Material Properties at the Single-Atom Level

Scientists determine the precise location and identity of all 23,000 atoms in a nanoparticle.


Friday April 07, 2017, 11:05 AM

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Argonne National Laboratory

Tuesday March 28, 2017, 12:05 PM

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Great Neck South High School Wins Regional Science Bowl at Brookhaven Lab

Brookhaven National Laboratory

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Middle Schoolers Test Their Knowledge at Science Bowl Competition

Argonne National Laboratory

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Oak Ridge National Laboratory

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Internship Program Helps Foster Development of Future Nuclear Scientists

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Unveiled: Earth's Viral Diversity

Article ID: 659162

Released: 2016-08-15 20:30:15

Source Newsroom: Lawrence Berkeley National Laboratory

  • Credit: Graphic by Zosia Rostomian, Berkeley Lab

    DOE JGI researchers utilized the largest collection of assembled metagenomic datasets from around the world to uncover over 125,000 partial and complete viral genomes, the majority of them infecting microbes.

The number of microbes in, on, and around the planet – on the order of a nonillion, or 1030 – is estimated to outnumber the stars in the Milky Way. Microbes are known to play crucial roles in regulating carbon fixation, as well as maintaining global cycles involving nitrogen, sulfur, and phosphorus and other nutrients, but the majority of them remain uncultured and unknown. The U.S. Department of Energy (DOE) is targeting this “microbial dark matter” to better understand the planet’s microbial diversity and glean from nature lessons that can be applied toward energy and environmental challenges.

Plumbing the Earth’s microbial diversity, though, requires learning more about the poorly-studied relationships between microbes and the viruses that infect them, viruses that impact the microbes’ abilities to regulate global cycles. Although the number of viruses is estimated to be at least two orders of magnitude more than the microbial cells on the planet, there are currently less than 2,200 sequenced DNA virus genomes, compared to the approximately 50,000 bacterial genomes, in sequence databases. In a study published online August 17, 2016 in Nature, researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, utilized the largest collection of assembled metagenomic datasets from around the world to uncover over 125,000 partial and complete viral genomes, the majority of them infecting microbes. This single effort increases the number of known viral genes by a factor of 16, and provides researchers with a unique resource of viral sequence information.

“It is the first time that someone has looked systematically across all habitats and across such a large compendium of data,” said study senior author and DOE JGI Prokaryote Super Program head Nikos Kyrpides. “A key to uncover all these novel viruses was the sensitive computational approach we have developed along this work.”

"A key to uncover novel viruses"

That approach, explained first author and postdoctoral fellow David Paez-Espino, involved using a non-targeted metagenomic approach, referencing both isolate viruses and manually curated viral protein models, and what he described as “the largest and most diverse dataset to date.” The team analyzed over 5 trillion bases (Terabases or Tb) of sequence available in the DOE JGI’s Integrated Microbial Genomes with Microbiome Samples (IMG/M) system collected from 3,042 samples around the world from 10 different habitat types. Their efforts to sift through the veritable haystack of datasets yielded over 125,000 viral sequences containing 2.79 million proteins.

The team matched viral sequences against multiple samples in multiple habitats. For example, one viral group they identified was found in 95 percent of all samples in the ocean’s twilight zone – a region located between 200 and 1,000 meters below the ocean surface where insufficient sunlight penetrates for microorganisms to perform photosynthesis.

By analyzing a CRISPR-Cas system – an immune mechanism in bacteria that confers resistance to foreign genetic elements by incorporating short sequences from infecting viruses and phages – the team was able to generate a database of 3.5 million spacer sequences in IMG. These spacers, fragments of phage genetic sequences retained by the host, can then be used to explore viral and phage metagenomes for where the fragments may have originally come from. Also, using mainly this approach, the team computationally identified the host for nearly 10,000 viruses. “The majority of these connections were previously unknown, and include the identification of organisms serving as viral hosts from 16 prokaryotic phyla for which no viruses have previously been identified,” they reported.

Beacons for CRISPR-Cas proteins

Jan-Fang Cheng, head of the DOE JGI’s Functional Genomics group, said the work being done by Kyrpides’ group in identifying new viral sequences will help the Synthetic Biology group develop novel promoters that can work in many bacterial hosts. “We are constantly searching for regulatory DNA parts that will work across many different phyla, and that would allow us to build genes and pathways that can express in many different hosts.”

Cheng also anticipated that the expanded viral sequence space generated by Kyrpides’ team will allow researchers to look for other genetic sequences known as proto-spacer adjacent motifs (PAMs). These sequences lie next to spacer sequencers in phages and are used as beacons by CRISPR-Cas proteins, triggering actions such as editing or regulating a gene. “People are looking for new PAM sequences and new Cas9s, and with this new information, if you can map the spacer sequence back to the same phage and align them and see what’s in common in neighboring sequences, then you could ID new PAM sequences.”

“We believe that the finding of many large phages including the longest phage genome reported thus far points to the limitations of conventional virome enrichment and sequencing strategies which may bias the studies against the highly novel viruses with unusual properties”, said Natalia Ivanova, group lead in the Super Program and co-author of this study.

“One of the most important aspects of this study is that we did not focus on a single habitat type. Instead, we explored the global virome and examined the flow of viruses across all ecosystems," said Kyrpides. "We have increased the number of viral sequences by 50x, and 99 percent of the virus families identified are not closely related to any previously sequenced virus. This provides an enormous amount of new data that would be studied in more detail in the years to come. We have more than doubled the number of microbial phyla that serve as hosts to viruses, and have created the first global viral distribution map. The amount of analysis and discoveries that we anticipate will follow this dataset cannot be overstated.”

The work used resources at the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory.

***

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.