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 Complete skin regeneration system of fish unraveled
24.04.2018 | Tokyo Institute of Technology

nachricht Scientists generate an atlas of the human genome using stem cells
24.04.2018 | The Hebrew University of Jerusalem

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: BAM@Hannover Messe: innovative 3D printing method for space flight

At the Hannover Messe 2018, the Bundesanstalt für Materialforschung und-prüfung (BAM) will show how, in the future, astronauts could produce their own tools or spare parts in zero gravity using 3D printing. This will reduce, weight and transport costs for space missions. Visitors can experience the innovative additive manufacturing process live at the fair.

Powder-based additive manufacturing in zero gravity is the name of the project in which a component is produced by applying metallic powder layers and then...

Im Focus: Molecules Brilliantly Illuminated

Physicists at the Laboratory for Attosecond Physics, which is jointly run by Ludwig-Maximilians-Universität and the Max Planck Institute of Quantum Optics, have developed a high-power laser system that generates ultrashort pulses of light covering a large share of the mid-infrared spectrum. The researchers envisage a wide range of applications for the technology – in the early diagnosis of cancer, for instance.

Molecules are the building blocks of life. Like all other organisms, we are made of them. They control our biorhythm, and they can also reflect our state of...

Im Focus: Spider silk key to new bone-fixing composite

University of Connecticut researchers have created a biodegradable composite made of silk fibers that can be used to repair broken load-bearing bones without the complications sometimes presented by other materials.

Repairing major load-bearing bones such as those in the leg can be a long and uncomfortable process.

Im Focus: Writing and deleting magnets with lasers

Study published in the journal ACS Applied Materials & Interfaces is the outcome of an international effort that included teams from Dresden and Berlin in Germany, and the US.

Scientists at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) together with colleagues from the Helmholtz-Zentrum Berlin (HZB) and the University of Virginia...

Im Focus: Gamma-ray flashes from plasma filaments

Novel highly efficient and brilliant gamma-ray source: Based on model calculations, physicists of the Max PIanck Institute for Nuclear Physics in Heidelberg propose a novel method for an efficient high-brilliance gamma-ray source. A giant collimated gamma-ray pulse is generated from the interaction of a dense ultra-relativistic electron beam with a thin solid conductor. Energetic gamma-rays are copiously produced as the electron beam splits into filaments while propagating across the conductor. The resulting gamma-ray energy and flux enable novel experiments in nuclear and fundamental physics.

The typical wavelength of light interacting with an object of the microcosm scales with the size of this object. For atoms, this ranges from visible light to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Invitation to the upcoming "Current Topics in Bioinformatics: Big Data in Genomics and Medicine"

13.04.2018 | Event News

Unique scope of UV LED technologies and applications presented in Berlin: ICULTA-2018

12.04.2018 | Event News

IWOLIA: A conference bringing together German Industrie 4.0 and French Industrie du Futur

09.04.2018 | Event News

 
Latest News

Complete skin regeneration system of fish unraveled

24.04.2018 | Life Sciences

Scientists create innovative new 'green' concrete using graphene

24.04.2018 | Materials Sciences

BAM@Hannover Messe: innovative 3D printing method for space flight

24.04.2018 | Trade Fair News

VideoLinks
Science & Research
Overview of more VideoLinks >>>