X
X
X

Filters:

Fungal Enzymes Team Up to More Efficiently Break Down Cellulose

Cost-effectively breaking down bioenergy crops into sugars that can then be converted into fuel is a barrier to commercially producing sustainable biofuels. Enabled by DOE User Facilities, a team reports that early lineages of fungi can form enzyme complexes capable of degrading plant biomass.

Argonne Scientists Make Vanadium Into a Useful Catalyst for Hydrogenation

In a new study, Argonne chemist Max Delferro boosted and analyzed the unprecedented catalytic activity of an element called vanadium for hydrogenation - a reaction that is used for making everything from vegetable oils to petrochemical products to vitamins.

Printed, Flexible and Rechargeable Battery Can Power Wearable Sensors

Nanoengineers at the University of California San Diego have developed the first printed battery that is flexible, stretchable and rechargeable. The zinc batteries could be used to power everything from wearable sensors to solar cells and other kinds of electronics. The work appears in the April 19, 2017 issue of Advanced Energy Materials.

Neutrons Provide the First Nanoscale Look at a Living Cell Membrane

A research team from the Department of Energy's Oak Ridge National Laboratory has performed the first-ever direct nanoscale examination of a living cell membrane. In doing so, it also resolved a long-standing debate by identifying tiny groupings of lipid molecules that are likely key to the cell's functioning.

How X-Rays Helped to Solve Mystery of Floating Rocks

Experiments at Berkeley Lab's Advanced Light Source have helped scientists to solve a mystery of why some rocks can float for years in the ocean, traveling thousands of miles before sinking.

Special X-Ray Technique Allows Scientists to See 3-D Deformations

In a new study published last Friday in Science, researchers at Argonne used an X-ray scattering technique called Bragg coherent diffraction imaging to reconstruct in 3-D the size and shape of grain defects. These defects create imperfections in the lattice of atoms inside a grain that can give rise to interesting material properties and effects.

Neptune: Neutralizer-Free Plasma Propulsion

The most established plasma propulsion concepts are gridded-ion thrusters that accelerate and emit a larger number of positively charged particles than those that are negatively charged. To enable the spacecraft to remain charge-neutral, a "neutralizer" is used to inject electrons to exactly balance the positive ion charge in the exhaust beam. However, the neutralizer requires additional power from the spacecraft and increases the size and weight of the propulsion system. Researchers are investigating how the radio-frequency self-bias effect can be used to remove the neutralizer altogether, and they report their work in this week's Physics of Plasmas.

Report Sheds New Insights on the Spin Dynamics of a Material Candidate for Low-Power Devices

In a report published in Nano LettersArgonne researchers reveal new insights into the properties of a magnetic insulator that is a candidate for low-power device applications; their insights form early stepping-stones towards developing high-speed, low-power electronics that use electron spin rather than charge to carry information.

Researchers Find Computer Code That Volkswagen Used to Cheat Emissions Tests

An international team of researchers has uncovered the mechanism that allowed Volkswagen to circumvent U.S. and European emission tests over at least six years before the Environmental Protection Agency put the company on notice in 2015 for violating the Clean Air Act. During a year-long investigation, researchers found code that allowed a car's onboard computer to determine that the vehicle was undergoing an emissions test.

Physicists Discover That Lithium Oxide on Tokamak Walls Can Improve Plasma Performance

A team of physicists has found that a coating of lithium oxide on the inside of fusion machines known as tokamaks can absorb as much deuterium as pure lithium can.


Filters:

University of Wisconsin-Milwaukee Joins Energy-Focused National Science Foundation Research Center

The University of Wisconsin-Milwaukee is joining a National Science Foundation-backed research center that will develop new technologies for storing, controlling and distributing energy that could ward off cybersecurity threats and lower energy bills.

Rensselaer Polytechnic Institute Graduates Urged to Embrace Change at 211th Commencement

Describing the dizzying pace of technological innovation, former United States Secretary of Energy Ernest J. Moniz urged graduates to "anticipate career change, welcome it, and manage it to your and your society's benefit" at the 211th Commencement at Rensselaer Polytechnic Institute (RPI) Saturday.

ORNL Welcomes Innovation Crossroads Entrepreneurial Research Fellows

Oak Ridge National Laboratory today welcomed the first cohort of innovators to join Innovation Crossroads, the Southeast region's first entrepreneurial research and development program based at a U.S. Department of Energy national laboratory.

Department of Energy Secretary Recognizes Argonne Scientists' Work to Fight Ebola, Cancer

Two groups of researchers at Argonne earned special awards from the office of the U.S. Secretary of Energy for addressing the global health challenges of Ebola and cancer.

Jefferson Science Associates, LLC Recognized for Leadership in Small Business Utilization

Jefferson Lab/Jefferson Science Associates has a long-standing commitment to doing business with and mentoring small businesses. That commitment and support received national recognition at the 16th Annual Dept. of Energy Small Business Forum and Expo held May 16-18, 2017 in Kansas City, Mo.

Rensselaer Polytechnic Institute President's Commencement Colloquy to Address "Criticality, Incisiveness, Creativity"

To kick off the Rensselaer Polytechnic Institute Commencement weekend, the annual President's Commencement Colloquy will take place on Friday, May 19, beginning at 3:30 p.m. The discussion, titled "Criticality, Incisiveness, Creativity," will include the Honorable Ernest J. Moniz, former Secretary of Energy, and the Honorable Roger W. Ferguson Jr., President and CEO of TIAA, and will be moderated by Rensselaer President Shirley Ann Jackson.

ORNL, University of Tennessee Launch New Doctoral Program in Data Science

The Tennessee Higher Education Commission has approved a new doctoral program in data science and engineering as part of the Bredesen Center for Interdisciplinary Research and Graduate Education.

SurfTec Receives $1.2 Million Energy Award to Develop Novel Coating

The Department of Energy has awarded $1.2 million to SurfTec LLC, a company affiliated with the U of A Technology Development Foundation, to continue developing a nanoparticle-based coating to replace lead-based journal bearings in the next generation of electric machines.

Ames Laboratory Scientist Inducted Into National Inventors Hall of Fame

Iver Anderson, senior metallurgist at Ames Laboratory, has been inducted into the National Inventors Hall of Fame.

DOE HPC4Mfg Program Funds 13 New Projects to Improve U.S. Energy Technologies Through High Performance Computing

A U.S. Department of Energy (DOE) program designed to spur the use of high performance supercomputers to advance U.S. manufacturing is funding 13 new industry projects for a total of $3.9 million.


Filters:

Casting a Wide Net

Designed molecules will provide positive impacts in energy production by selectively removing unwanted ions from complex solutions.

New Software Tools Streamline DNA Sequence Design-and-Build Process

Enhanced software tools will accelerate gene discovery and characterization, vital for new forms of fuel production.

The Ultrafast Interplay Between Molecules and Materials

Computer calculations by the Center for Solar Fuels, an Energy Frontier Research Center, shed light on nebulous interactions in semiconductors relevant to dye-sensitized solar cells.

Supercapacitors: WOODn't That Be Nice

Researchers at Nanostructures for Electrical Energy Storage, an Energy Frontier Research Center, take advantage of nature-made materials and structure for energy storage research.

Groundwater Flow Is Key for Modeling the Global Water Cycle

Water table depth and groundwater flow are vital to understanding the amount of water that plants transmit to the atmosphere.

Finding the Correct Path

A new computational technique greatly simplifies the complex reaction networks common to catalysis and combustion fields.

Opening Efficient Routes to Everyday Plastics

A new material from the Inorganometallic Catalyst Design Center, an Energy Frontier Research Center, facilitates the production of key industrial supplies.

Fight to the Top: Silver and Gold Compete for the Surface of a Bimetallic Solid

It's the classic plot of a buddy movie. Two struggling bodies team up to drive the plot and do good together. That same idea, when it comes to metals, could help scientists solve a big problem: the amount of energy consumed by making chemicals.

Saving Energy Through Light Control

New materials, designed by researchers at the Center for Excitonics, an Energy Frontier Research Center, can reduce energy consumption with the flip of a switch.

Teaching Perovskites to Swim

Scientists at the ANSER Energy Frontier Research Center designed a two-component layer protects a sunlight-harvesting device from water and heat.


Saturday May 20, 2017, 12:05 PM

Rensselaer Polytechnic Institute Graduates Urged to Embrace Change at 211th Commencement

Rensselaer Polytechnic Institute (RPI)

Monday May 15, 2017, 01:05 PM

ORNL, University of Tennessee Launch New Doctoral Program in Data Science

Oak Ridge National Laboratory

Friday April 07, 2017, 11:05 AM

Champions in Science: Profile of Jonathan Kirzner

Department of Energy, Office of Science

Wednesday April 05, 2017, 12:05 PM

High-Schooler Solves College-Level Security Puzzle From Argonne, Sparks Interest in Career

Argonne National Laboratory

Tuesday March 28, 2017, 12:05 PM

Champions in Science: Profile of Jenica Jacobi

Department of Energy, Office of Science

Friday March 24, 2017, 10:40 AM

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

Brookhaven National Laboratory

Wednesday February 15, 2017, 04:05 PM

Middle Schoolers Test Their Knowledge at Science Bowl Competition

Argonne National Laboratory

Friday January 27, 2017, 04:00 PM

Haslam Visits ORNL to Highlight State's Role in Discovering Tennessine

Oak Ridge National Laboratory

Tuesday November 08, 2016, 12:05 PM

Internship Program Helps Foster Development of Future Nuclear Scientists

Oak Ridge National Laboratory

Friday May 13, 2016, 04:05 PM

More Than 12,000 Explore Jefferson Lab During April 30 Open House

Thomas Jefferson National Accelerator Facility

Monday April 25, 2016, 05:05 PM

Giving Back to National Science Bowl

Ames Laboratory

Friday March 25, 2016, 12:05 PM

NMSU Undergrad Tackles 3D Particle Scattering Animations After Receiving JSA Research Assistantship

Thomas Jefferson National Accelerator Facility

Tuesday February 02, 2016, 10:05 AM

Shannon Greco: A Self-Described "STEM Education Zealot"

Princeton Plasma Physics Laboratory

Monday November 16, 2015, 04:05 PM

Rare Earths for Life: An 85th Birthday Visit with Mr. Rare Earth

Ames Laboratory

Tuesday October 20, 2015, 01:05 PM

Meet Robert Palomino: 'Give Everything a Shot!'

Brookhaven National Laboratory

Tuesday April 22, 2014, 11:30 AM

University of Utah Makes Solar Accessible

University of Utah

Wednesday March 06, 2013, 03:40 PM

Student Innovator at Rensselaer Polytechnic Institute Seeks Brighter, Smarter, and More Efficient LEDs

Rensselaer Polytechnic Institute (RPI)

Friday November 16, 2012, 10:00 AM

Texas Tech Energy Commerce Students, Community Light up Tent City

Texas Tech University

Wednesday November 23, 2011, 10:45 AM

Don't Get 'Frosted' Over Heating Your Home This Winter

Temple University

Wednesday July 06, 2011, 06:00 PM

New Research Center To Tackle Critical Challenges Related to Aircraft Design, Wind Energy, Smart Buildings

Rensselaer Polytechnic Institute (RPI)

Friday April 22, 2011, 09:00 AM

First Polymer Solar-Thermal Device Heats Home, Saves Money

Wake Forest University

Friday April 15, 2011, 12:25 PM

Like Superman, American University Will Get Its Energy from the Sun

American University

Thursday February 10, 2011, 05:00 PM

ARRA Grant to Help Fund Seminary Building Green Roof

University of Chicago

Tuesday December 07, 2010, 05:00 PM

UC San Diego Installing 2.8 Megawatt Fuel Cell to Anchor Energy Innovation Park

University of California San Diego

Monday November 01, 2010, 12:50 PM

Rensselaer Smart Lighting Engineering Research Center Announces First Deployment of New Technology on Campus

Rensselaer Polytechnic Institute (RPI)

Friday September 10, 2010, 12:40 PM

Ithaca College Will Host Regional Clean Energy Summit

Ithaca College

Tuesday July 27, 2010, 10:30 AM

Texas Governor Announces $8.4 Million Award to Create Renewable Energy Institute

Texas Tech University

Friday May 07, 2010, 04:20 PM

Creighton University to Offer New Alternative Energy Program

Creighton University

Wednesday May 05, 2010, 09:30 AM

National Engineering Program Seeks Subject Matter Experts in Energy

JETS Junior Engineering Technical Society

Wednesday April 21, 2010, 12:30 PM

Students Using Solar Power To Create Sustainable Solutions for Haiti, Peru

Rensselaer Polytechnic Institute (RPI)

Wednesday March 03, 2010, 07:00 PM

Helping Hydrogen: Student Inventor Tackles Challenge of Hydrogen Storage

Rensselaer Polytechnic Institute (RPI)

Thursday February 04, 2010, 02:00 PM

Turning Exercise into Electricity

Furman University

Thursday November 12, 2009, 12:45 PM

Campus Leaders Showing the Way to a Sustainable, Clean Energy Future

National Wildlife Federation (NWF)

Tuesday November 03, 2009, 04:20 PM

Furman University Receives $2.5 Million DOE Grant for Geothermal Project

Furman University

Thursday September 17, 2009, 02:45 PM

Could Sorghum Become a Significant Alternative Fuel Source?

Salisbury University

Wednesday September 16, 2009, 11:15 AM

Students Navigating the Hudson River With Hydrogen Fuel Cells

Rensselaer Polytechnic Institute (RPI)

Wednesday September 16, 2009, 10:00 AM

College Presidents Flock to D.C., Urge Senate to Pass Clean Energy Bill

National Wildlife Federation (NWF)

Wednesday July 01, 2009, 04:15 PM

Northeastern Announces New Professional Master's in Energy Systems

Northeastern University

Friday October 12, 2007, 09:35 AM

Kansas Rural Schools To Receive Wind Turbines

Kansas State University

Thursday August 17, 2006, 05:30 PM

High Gas Prices Here to Stay, Says Engineering Professor

Rowan University

Wednesday May 17, 2006, 06:45 PM

Time Use Expert's 7-Year Fight for Better Gas Mileage

University of Maryland, College Park




Finding a New Major Gene Expression Regulator in Fungi

Article ID: 674195

Released: 2017-05-04 21:00:45

Source Newsroom: Lawrence Berkeley National Laboratory

  • Credit: ZyGoLife Research Consortium via Flickr, CC BY-SA 2.0

    Linderina pennispora is one of the early-diverging fungi whose genomes were sequenced, annotated and analyzed for the study led by U.S. Department of Energy Joint Genome Institute researchers in the May 8, 2017 issue of Nature Genetics.

Just four letters – A, C, T, and G – make up an organism’s genetic code. Changing a single letter, or base, can lead to changes in protein structures and functions, impacting an organism’s traits. In addition, though, subtler changes can and do happen, involving modifications of the DNA bases themselves. The best-known example of this kind of change is a methylation of the base cytosine at the 5th position on its carbon ring (5mC). In eukaryotes, a less-well known modification involves adding a methyl group to base 6 of adenine (6mA).

In the May 8, 2017 issue of Nature Genetics, a team led by scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, report the prevalence of 6mA modifications in the earliest branches of the fungal kingdom. Though fungi have been around for a billion years and collectively are capable of degrading nearly all naturally-occurring polymers and even some human-made ones, most of the species that have been studied belong to just two phyla, the Ascomycota and Basidiomycota. The remaining 6 groups of fungi are classified as “early diverging lineages,” the earliest branches in fungal genealogy. They comprise a little-explored realm of fungi, providing a repertoire of important and valuable gene products for DOE missions in bioenergy and environment.

“By and large, early-diverging fungi are very poorly understood compared to other lineages. However, many of these fungi turn out to be important in a variety of ways,” said study first author and DOE JGI analyst Stephen Mondo. “Consider the Neocallimastigomycetes - these fungi are one of the most powerful degraders of plant biomass currently known and have a tremendous arsenal of plant cell wall degrading enzymes which may be useful for bioenergy production. They are a good example of how exploring these understudied lineages leads to valuable biological and technological insights.”

Many of the fungal genomes used in the study were sequenced as part of the DOE JGI’s 1000 Fungal Genomes initiative aimed at producing at least one reference genome for every family of fungi. For the study, the team used 16 fungal genomes sequenced at the DOE JGI using the Pacific Biosciences sequencing platform. While the technology was used with the goal of attaining very high quality genome assemblies, DOE JGI scientists have now additionally taken advantage of this sequencing platform to explore epigenetic (5mC, 6mA) modifications.  They discovered very high levels of 6mA in fungi, where up to 2.8% of all adenines were methylated,  confirming these findings using multiple independent methods. The previous record holder for genomic 6mA, noted Mondo, is the alga Chlamydomonas reinhardtii (sequenced and annotated by the DOE JGI), in which just 0.4% of adenines were methylated.

“This is one of the first direct comparisons of 6mA and 5mC in eukaryotes, and the first 6mA study across the fungal kingdom,” said DOE JGI Fungal Genomics head and senior author Igor Grigoriev. “6mA has been shown to have different functions depending on the organism. For example, in animals it is involved in suppressing transposon activity, while in algae it is positively associated with gene expression. Our analysis has shown that 6mA modifications are associated with expressed genes and is preferentially deposited based on gene function and conservation, revealing 6mA as a marker of expression for important functionally-relevant genes.”

In addition to 6mA performing what seems to be the opposite role of 5mC (which suppresses expression), the team found that the presence of 5mC and 6mA are inversely correlated. Specifically, while 5mC is found at repetitive regions of the genome, the methylated adenines were clustered into dense “methylated adenine clusters” (MACs) at gene promoters. 6mA was also found consistently on both strands of DNA, which may enable propagation of methylation through cell division.

“Using genomics, we explore the diversity of fungi to develop catalogs of genes, enzymes, and pathways - parts lists for bio-based economy and bioenergy applications,” said Grigoriev. “A lot of this is encoded in early diverging fungi. In these fungi, we found that majority of expressed genes have 6mA MACs. Thus, the discovery of DNA methylation in early diverging fungi helps the research community better understand regulation of genes that encode the parts for bio-based economy and bioenergy applications.”

Mondo described the identification and proposed role of 6mA in early diverging fungi at the 2017 Genomics of Energy & Environment Meeting. Watch his talk on the DOE JGI’s YouTube channel at http://bit.ly/JGI2017Mondo.

***

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.