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The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
  • 2018-04-25 15:05:34
  • Article ID: 693378

A Novel Method for Comparing Plant Genes

Researchers develop a method of identifying gene expression patterns in drought-resistant plants.

  • Credit: Image courtesy of Oak Ridge National Laboratory

    A map of gene expression correlation triangles with positive correlations (blue edges) between Kalanchoƫ genes (dark green nodes) and pineapple genes (yellow nodes) and negative correlations (red edges) between Kalanchoƫ or pineapple genes and Arabidopsis genes (light green nodes).

The Science

During normal photosynthesis, plants open their stomata (microscopic pores in the plant epidermis that permit the flow of gases and water vapor) during the day to take in carbon dioxide needed for carbohydrate production. But a small percentage of plants open their stomata to capture carbon dioxide only at night, thereby conserving water. This form of photosynthesis is called crassulacean acid metabolism (CAM). In this study, scientists created a new method to analyze this conservation by comparing genes of CAM plants with each other and with the genes of plants possessing a more common type of photosynthesis called C3. They found a collection of gene “triangles”—and a new method of studying time-related patterns of gene expression across species.

The Impact

The study provides insights into CAM mechanisms. The research will serve scientists across the biological and chemical science domains who have a long-term goal of engineering CAM into bioenergy and food crops, so they will be more tolerant to drought. The team said this newly developed Fisher triangle enrichment method could be applied to study any mechanism across species. The team believes the method may even have potential applications in human clinical genomics studies, such as those related to diseased versus nondiseased populations.

Summary

The water-saving characteristics developed by CAM plants allow for survival in arid climates. Plant species such as orchid, pineapple, and Kalanchoë use CAM photosynthesis to conserve water by keeping their stomata, or pores, shut during the day and open at night to collect carbon dioxide. In studying the building blocks of CAM, scientists open doors to bioengineering the metabolic processes of water-intensive crops such as rice, wheat, and soybeans to accelerate their adaptation to more arid environments.

In this study, a team developed a new method of comparing genes of CAM plants with genes of C3 plants that will provide scientists with a detailed understanding of the mechanisms behind CAM. The team compared plant data that described the abundance of expressed (activated) genes throughout the day based on sequenced RNA molecules in each plant’s tissue. The team searched for gene families in which an Arabidopsis gene (1) had an opposite expression pattern to genes of pineapple and Kalanchoë, both CAM plants, and (2) shared the same expression patterns with pineapple and Kalanchoë. Arabidopsis belongs to the cress family of plants—it was the first plant to have its genome sequenced and is the domain standard for studying gene expression in plants. The scientists ended up with a collection of gene triangles that detailed the similarities among CAM genes and a method of comparing genes of CAM versus non-CAM plants. The team’s results also enabled scientists at Oak Ridge National Laboratory to identify 54 genes that showed convergent regulatory patterns in CAM species, providing insight into CAM mechanisms that may prove useful for bioengineering plants that use water more efficiently.

Funding

This research was supported by the Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research Genomic Science Program; the United Kingdom Biotechnology and Biological Sciences Research Council; the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory (ORNL); and the DOE Joint Genome Institute. This research used resources of the Oak Ridge Leadership Computing Facility and the Compute and Data Environment for Science at ORNL.

Publication

X. Yang, R. Hu, H. Yin, et al., “The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.” Nature Communications 8, 1899 (2017). [DOI: 10.1038/s41467-017-01491-7]

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No Longer Whistling in the Dark: Scientists Uncover a Little-Understood Source of Waves Generated Throughout the Universe

Scientists at the U.S. Department of Energy's Princeton Plasma Physics Laboratory (PPPL) and other laboratories, using data from a NASA four-satellite mission that is studying reconnection, have developed a method for identifying the source of waves that help satellites determine their location in space.

New biofuel production system powered by a community of algae and fungi

MSU scientists have a new proof of concept for a biofuel production platform that uses two species of marine algae and soil fungi. It lowers cultivation and harvesting costs and increases productivity, factors that currently hold back biofuels from being widely adopted.

Multimodal Imaging Shows Strain Can Drive Chemistry in a Photovoltaic Material

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Neutrons Produce First Direct 3D Maps of Water During Cell Membrane Fusion

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Nucleation a boon to sustainable nanomanufacturing

Young-Shin Jun, professor of energy, environmental & chemical engineering in the School of Engineering & Applied Science, and Quingun Li, a former doctoral student in her lab, are the first to measure the activation energy and kinetic factors of calcium carbonate's nucleation, both key to predicting and controlling the process.

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Department of Energy Announces $218 Million for Quantum Information Science

The U.S. Department of Energy (DOE) announced $218 million in funding for 85 research awards in the important emerging field of Quantum Information Science (QIS).

Energy Secretary awards researchers for global threat reduction

Seven employees from the U.S. Department of Energy's (DOE) Argonne National Laboratory were among those presented with a Secretary of Energy Achievement Award at the Secretary's Honors Awards ceremony in Washington, D.C., on August 29.

University of Minnesota to lead $5.3 million federal grant to improve electronic circuit design

The University of Minnesota announced today that it has received a four-year, $5.3 million grant from the Defense Advanced Research Projects Agency (DARPA), an agency of the U.S. Department of Defense, to lead an effort that could spark the next wave of U.S. semiconductor innovation and broaden the competitive field for circuit design.

Berkeley Lab to Build an Advanced Quantum Computing Testbed

Lawrence Berkeley National Laboratory (Berkeley Lab) will receive $30 million over five years from the U.S. Department of Energy to build and operate an Advanced Quantum Testbed (AQT) allowing researchers to explore superconducting quantum processors to advance scientific research

Cheng wins Midwest Energy News' 40 Under 40 Award

Lei Cheng, an assistant chemist in the Materials Science division at the U.S. Department of Energy's (DOE) Argonne National Laboratory, has received a Midwest Energy News 40 Under 40 Award.

JCESR renewed for another five years

The U.S. Department of Energy (DOE) today announced its decision to renew the Joint Center for Energy Storage Research (JCESR), a DOE Energy Innovation Hub led by Argonne National Laboratory and focused on advancing battery science and technology.

Binghamton designated as NextFlex New York Node for flexible hybrid electronics initiative

NextFlex has designated Binghamton University to be the New York "Node" for its flexible hybrid electronics (FHE) initiative. As the NextFlex New York Node, Binghamton will design, develop and manufacture tools; process materials and products for flexible hybrid electronics; and attract, train and employ an advanced manufacturing workforce, building on the region's existing electronics manufacturing base.

First Particle Tracks Seen in Prototype for International Neutrino Experiment

The largest liquid-argon neutrino detector in the world has just recorded its first particle tracks, signaling the start of a new chapter in the story of the international Deep Underground Neutrino Experiment (DUNE). DUNE's scientific mission is dedicated to unlocking the mysteries of neutrinos, the most abundant (and most mysterious) matter particles in the universe.

Tais Gorkhover Wins LCLS Young Investigator Award for Pioneering Novel X-ray Imaging Methods

Tais Gorkhover, a principal investigator with the Stanford PULSE Institute, will receive the 2018 LCLS Young Investigator Award, granted to early-career scientists in recognition of exceptional research using the Linac Coherent Light Source (LCLS) X-ray free-electron laser at the Department of Energy's SLAC National Accelerator Laboratory.

ORNL, United Kingdom Lab Partner on Nuclear Energy Research

The United Kingdom's National Nuclear Laboratory and the U.S. Department of Energy's Oak Ridge National Laboratory have agreed to cooperate on a wide range of nuclear energy research and development efforts that leverage both organizations' unique expertise and capabilities.


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Breaking the Symmetry Between Fundamental Forces

Scientists improve our understanding of the relationship between fundamental forces by re-creating the earliest moments of the universe.

Water Plays Unexpected Role in Forming Minerals

Water molecules line up tiny particles to attach and form minerals; understanding how this happens impacts energy extraction and storage along with waste disposal.

Heavy Particles Get Caught Up in the Flow

First direct measurement show how heavy particles containing a charm quark get caught up in the flow of early universe particle soup.

Seeing Between the Atoms

New detector enables electron microscope imaging at record-breaking resolution.

Scaling Up Single-Crystal Graphene

New method can make films of atomically thin carbon that are over a foot long.

Discovered: Optimal Magnetic Fields Suppress Instabilities in Tokamak Plasmas

U.S. and Korean scientists show how to find and use beneficial 3-D field perturbations to stabilize dangerous edge-localized modes in plasma.

New Electron Glasses Sharpen Our View of Atomic-Scale Features

A new approach to atom probe tomography promises more precise and accurate measurements vital to semiconductors used in computers, lasers, detectors, and more.

Getting an Up-Close, 3-D View of Gold Nanostars

Scientists can now measure 3-D structures of tiny particles with properties that hold promise for advanced sensors and diagnostics.

Small, Short-Lived Drops of Early Universe Matter

Particle flow patterns suggest even small-scale collisions create drops of early universe quark-gluon plasma.

Tuning Terahertz Beams with Nanoparticles

Scientists uncover a way to control terahertz radiation using tiny engineered particles in a magnetic field, potentially opening the doors for better medical and environmental sensors.


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