"Sequencing used to be like locating a golf ball by searching only on the fairway, but not the rough," said IGSB Director Kevin White. "It used to be that only species that could be cultivated, or grown in pure culture, could be sequenced. The capabilities of the new Roche 454 FLEX and Illumina Solexa Genome Sequencer now allow scientists that use the machines to skip the cultivation step. Eliminating that step will save time and speed up the research process, while maintaining accurate sequencing results."
The 454 FLEX is ideally suited for studying microbial communities by de novo sequencing. It provides 400,000 DNA fragments of about 250 base pairs each – or 100 million base pairs per run – that represent either a significant part of the genome of a single organism or a random snapshot of parts of multiple genomes.
The Solexa Genome Sequencer is targeted at resequencing. Compared to the Roche 454 FLEX, it generates more but shorter reads, creating 40 million reads with a current read length of 18 to 36 base pairs – or about 1 billion base pairs per run – depending on the application.
The machines were purchased to facilitate research for three Argonne Laboratory-Directed Research and Development projects. A project led by Michael Miller, a terrestrial ecologist, and Folker Meyer, a computational biologist in IGSB, will enhance our understanding of soil CO2 sequestration capability on the microbial level.
In another project, Argonne's soil ecology group is using metagenome sequencing to study the microbial population in chronoseries plots at DOE's Fermi National Accelerator Laboratory. In a third project, Argonne's environmental remediation program is studying the role played by microbial communities in subsurface remediation of inorganic contaminates using metagenome sequencing.
IGSB's sequencing group plays an active role in the design and optimization of experiments using DNA sequencing technology, such as developing and optimizing protocols for DNA isolation from environment as diverse as subsurface soil and plant leaves. The group also works with researchers to develop protocols for DNA extraction and to conduct downstream bioinformatics analyses.
The new machines are also open to other Argonne and University of Chicago researchers who need genetic samples sequenced. In the near future, the sequencing instruments will be available to select peer-reviewed proposals from researchers from other organizations.
Argonne's genomics research is primarily funded DOE's Office of Science, which supports research that provides a fundamental scientific understanding of plants and microbes necessary to develop strategies for sequestering carbon gases, producing biofuels and cleaning up waste.
Argonne National Laboratory brings the world's brightest scientists and engineers together to find exciting and creative new solutions to pressing national problems in science and technology. The nation's first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities and federal, state and municipal agencies to help them solve their specific problems, advance America's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy's Office of Science.
Angela Hardin | newswise
Rainbow colors reveal cell history: Uncovering β-cell heterogeneity
22.09.2017 | DFG-Forschungszentrum für Regenerative Therapien TU Dresden
The pyrenoid is a carbon-fixing liquid droplet
22.09.2017 | Max-Planck-Institut für Biochemie
Plants and algae use the enzyme Rubisco to fix carbon dioxide, removing it from the atmosphere and converting it into biomass. Algae have figured out a way to increase the efficiency of carbon fixation. They gather most of their Rubisco into a ball-shaped microcompartment called the pyrenoid, which they flood with a high local concentration of carbon dioxide. A team of scientists at Princeton University, the Carnegie Institution for Science, Stanford University and the Max Plank Institute of Biochemistry have unravelled the mysteries of how the pyrenoid is assembled. These insights can help to engineer crops that remove more carbon dioxide from the atmosphere while producing more food.
A warming planet
Our brains house extremely complex neuronal circuits, whose detailed structures are still largely unknown. This is especially true for the so-called cerebral cortex of mammals, where among other things vision, thoughts or spatial orientation are being computed. Here the rules by which nerve cells are connected to each other are only partly understood. A team of scientists around Moritz Helmstaedter at the Frankfiurt Max Planck Institute for Brain Research and Helene Schmidt (Humboldt University in Berlin) have now discovered a surprisingly precise nerve cell connectivity pattern in the part of the cerebral cortex that is responsible for orienting the individual animal or human in space.
The researchers report online in Nature (Schmidt et al., 2017. Axonal synapse sorting in medial entorhinal cortex, DOI: 10.1038/nature24005) that synapses in...
Whispering gallery mode (WGM) resonators are used to make tiny micro-lasers, sensors, switches, routers and other devices. These tiny structures rely on a...
Using ultrafast flashes of laser and x-ray radiation, scientists at the Max Planck Institute of Quantum Optics (Garching, Germany) took snapshots of the briefest electron motion inside a solid material to date. The electron motion lasted only 750 billionths of the billionth of a second before it fainted, setting a new record of human capability to capture ultrafast processes inside solids!
When x-rays shine onto solid materials or large molecules, an electron is pushed away from its original place near the nucleus of the atom, leaving a hole...
For the first time, physicists have successfully imaged spiral magnetic ordering in a multiferroic material. These materials are considered highly promising candidates for future data storage media. The researchers were able to prove their findings using unique quantum sensors that were developed at Basel University and that can analyze electromagnetic fields on the nanometer scale. The results – obtained by scientists from the University of Basel’s Department of Physics, the Swiss Nanoscience Institute, the University of Montpellier and several laboratories from University Paris-Saclay – were recently published in the journal Nature.
Multiferroics are materials that simultaneously react to electric and magnetic fields. These two properties are rarely found together, and their combined...
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