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 Discovery of a Key Regulatory Gene in Cardiac Valve Formation
24.05.2017 | Universität Basel

nachricht Carcinogenic soot particles from GDI engines
24.05.2017 | Empa - Eidgenössische Materialprüfungs- und Forschungsanstalt

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: A quantum walk of photons

Physicists from the University of Würzburg are capable of generating identical looking single light particles at the push of a button. Two new studies now demonstrate the potential this method holds.

The quantum computer has fuelled the imagination of scientists for decades: It is based on fundamentally different phenomena than a conventional computer....

Im Focus: Turmoil in sluggish electrons’ existence

An international team of physicists has monitored the scattering behaviour of electrons in a non-conducting material in real-time. Their insights could be beneficial for radiotherapy.

We can refer to electrons in non-conducting materials as ‘sluggish’. Typically, they remain fixed in a location, deep inside an atomic composite. It is hence...

Im Focus: Wafer-thin Magnetic Materials Developed for Future Quantum Technologies

Two-dimensional magnetic structures are regarded as a promising material for new types of data storage, since the magnetic properties of individual molecular building blocks can be investigated and modified. For the first time, researchers have now produced a wafer-thin ferrimagnet, in which molecules with different magnetic centers arrange themselves on a gold surface to form a checkerboard pattern. Scientists at the Swiss Nanoscience Institute at the University of Basel and the Paul Scherrer Institute published their findings in the journal Nature Communications.

Ferrimagnets are composed of two centers which are magnetized at different strengths and point in opposing directions. Two-dimensional, quasi-flat ferrimagnets...

Im Focus: World's thinnest hologram paves path to new 3-D world

Nano-hologram paves way for integration of 3-D holography into everyday electronics

An Australian-Chinese research team has created the world's thinnest hologram, paving the way towards the integration of 3D holography into everyday...

Im Focus: Using graphene to create quantum bits

In the race to produce a quantum computer, a number of projects are seeking a way to create quantum bits -- or qubits -- that are stable, meaning they are not much affected by changes in their environment. This normally needs highly nonlinear non-dissipative elements capable of functioning at very low temperatures.

In pursuit of this goal, researchers at EPFL's Laboratory of Photonics and Quantum Measurements LPQM (STI/SB), have investigated a nonlinear graphene-based...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Marine Conservation: IASS Contributes to UN Ocean Conference in New York on 5-9 June

24.05.2017 | Event News

AWK Aachen Machine Tool Colloquium 2017: Internet of Production for Agile Enterprises

23.05.2017 | Event News

Dortmund MST Conference presents Individualized Healthcare Solutions with micro and nanotechnology

22.05.2017 | Event News

 
Latest News

Physicists discover mechanism behind granular capillary effect

24.05.2017 | Physics and Astronomy

Measured for the first time: Direction of light waves changed by quantum effect

24.05.2017 | Physics and Astronomy

Marine Conservation: IASS Contributes to UN Ocean Conference in New York on 5-9 June

24.05.2017 | Event News

VideoLinks
B2B-VideoLinks
More VideoLinks >>>