Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Study analyzes role of PARP enzyme in eukaryotes

09.03.2011
OSU's Lamb leverages supercomputer to study protein's evolution

An Ohio State University molecular biologist leveraged a supercomputer to help better define the family tree of a group of enzymes that have been implicated in a wide range of human diseases and are important targets for anti-cancer therapies.

Along with several OSU colleagues, Rebecca S. Lamb, Ph.D., an assistant professor of Molecular Genetics, recently analyzed the evolutionary history of the poly(ADP-ribose)polymerase (PARP) superfamily.

These proteins are found in eukaryotes, a wide range of organisms – animals, plants, molds, fungi, algae and protozoa –whose cells contain complex structures enclosed within membranes. While PARP proteins can be found with any of these “supergroups,” they have been most extensively studied in mammals.

“In these organisms, PARPs have key functions in DNA repair, genome integrity and epigenetic regulation,” said Lamb. “More recently it has been found that proteins within the PARP superfamily have a broader range of functions that initially predicted.”

The researchers used computers to identify 236 PARP proteins from 77 species across five of the six supergroups. Lamb then accessed the Glen Cluster at the Ohio Supercomputer Center (OSC) to perform extensive phylogenetic analyses of the identified PARP regions.

“This is computationally intensive work that would have been impossible without the computer resources provided at OSC,” Lamb said. “In particular, the ability to try a variety of tools that require a great deal of CPU and memory capabilities was essential for success.”

Amongst other tools, she employed the PhyML3.0 software package, which fit a statistical model to the aligned sequence data and provided estimates for the model’s parameters.

“Dr. Lamb’s project is an excellent example of a scientist running a very domain-specific software package on our state-of-the-art systems,” said Ashok Krishnamurthy, Ph.D., interim co-executive director of OSC. “While the center maintains a large collection of licensed and open-source software, there are occasions where very specialized or customized applications are required. Our staff mdembers are very good at working with researchers to modify these codes to get them installed, running and delivering results.”

Access to powerful OSC systems allowed the researchers to experiment with a wide variety of options and parameters, in order to achieve the best results, Lamb noted.

“PARPs are found in all eukaryotic supergroups for which sequence is available, but some individual lineages within supergroups have independently lost these genes,” said Lamb. “The PARP superfamily can be subdivided into six branches or ‘clades.’ Two of these clades were likely found in the last common eukaryotic ancestor. In addition, we have identified PARPs in organisms in which they have not previously been described.”

Three main conclusions were drawn from the study. First, the broad distribution and pattern of representation of PARP genes indicated to the researchers that the ancestor of all existing eukaryotes encoded proteins of this type. Second, the ancestral PARP proteins had different functions and activities. One of these proteins likely functioned in DNA damage response. Third, the diversity of the PARP superfamily is larger than previously documented, suggesting as more eukaryotic genomes become available, this gene family will grow in both number and type.

The study, “Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes,” was authored by Lamb and OSU colleagues Matteo Citarelli and Sachin Teotia and appeared in a recent issue of the journal BMC Evolutionary Biology. The work was supported by a grant from the Ohio Plant Biotechnology Consortium and by funds from the Ohio State University.

The Ohio Supercomputer Center (OSC) is a catalytic partner of Ohio universities and industries that provides reliable advanced computational infrastructure and services for academic and industry research. OSC is funded by the Ohio Board of Regents to provide advanced computation, research and educational resources to a diverse statewide community, including higher education, K-12, and industry. More information is available at www.osc.edu.

Mr. Jamie Abel | EurekAlert!
Further information:
http://www.osc.edu

Further reports about: ADP-ribose DNA OSC Supercomputer advanced computation evolutionary history

More articles from Life Sciences:

nachricht Cnidarians remotely control bacteria
21.09.2017 | Christian-Albrechts-Universität zu Kiel

nachricht Immune cells may heal bleeding brain after strokes
21.09.2017 | NIH/National Institute of Neurological Disorders and Stroke

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Highly precise wiring in the Cerebral Cortex

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...

Im Focus: Tiny lasers from a gallery of whispers

New technique promises tunable laser devices

Whispering gallery mode (WGM) resonators are used to make tiny micro-lasers, sensors, switches, routers and other devices. These tiny structures rely on a...

Im Focus: Ultrafast snapshots of relaxing electrons in solids

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...

Im Focus: Quantum Sensors Decipher Magnetic Ordering in a New Semiconducting Material

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...

Im Focus: Fast, convenient & standardized: New lab innovation for automated tissue engineering & drug

MBM ScienceBridge GmbH successfully negotiated a license agreement between University Medical Center Göttingen (UMG) and the biotech company Tissue Systems Holding GmbH about commercial use of a multi-well tissue plate for automated and reliable tissue engineering & drug testing.

MBM ScienceBridge GmbH successfully negotiated a license agreement between University Medical Center Göttingen (UMG) and the biotech company Tissue Systems...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

“Lasers in Composites Symposium” in Aachen – from Science to Application

19.09.2017 | Event News

I-ESA 2018 – Call for Papers

12.09.2017 | Event News

EMBO at Basel Life, a new conference on current and emerging life science research

06.09.2017 | Event News

 
Latest News

Comet or asteroid? Hubble discovers that a unique object is a binary

21.09.2017 | Physics and Astronomy

Cnidarians remotely control bacteria

21.09.2017 | Life Sciences

Monitoring the heart's mitochondria to predict cardiac arrest?

21.09.2017 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>