By building powerful phylogenetic trees, scientists are able to quickly identify similarities and differences between the make-up of many different organisms, crucial information in the search for treatments to fight anything from the bugs that cause food poisoning to the pathogens that cause life-threatening diseases such as cholera and the plague.
A "tree of life," or phylogenetic tree, is a way to visualize the evolutionary relationships among different biological species that have descended from a common ancestor. The gamma-proteobacteria tree developed by VBI researchers was reconstructed using powerful computers from as many as 30 million data points of bacterial sequence information.
Kelly Williams, Research Investigator at VBI, remarked: "Ribosomal RNA is one of the central components of the ribosome, the protein manufacturing machinery of all living cells. In the past, researchers have often depended on looking at a single ribosomal RNA gene to construct evolutionary relationships for their tree-building efforts. The method we use to make our tree of life uses hundreds of different genes and integrates much more information than can be gleaned from the traditional single gene approach. We firmly believe that the multi-gene or phylogenomics approach should become the standard for tree-building when several genome sequences are available, which is now the case for most bacterial groups."
The researchers selected 108 available genomes from the more than 200 complete and partial sequences available for the gamma-proteobacteria, placing the emphasis on the diversity of the bacterial species and quality of the original sequence data. Allan Dickerman, Assistant Professor at VBI, remarked: "The consensus tree that we have put together for the gamma-proteobacteria is a powerful tool that can be used to predict shared biology and analyze, for example, the novel ways that bacteria have adapted to their living environments. Phylogenomics provides for very accurate reconstructions of inheritance from common ancestors."
The researchers looked at a very large class of bacteria that lack a well-resolved phylogenetic tree. By placing emphasis on searches for single-copy genes, the scientists were able to radically improve the resolution of the evolutionary tree. Said Williams, "Some parts of our tree were still not fully resolved, but we believe that future work will improve our method further to handle these deficiencies."
Bruno Sobral, Director of the CyberInfrastructure Section at VBI, commented: "The work described in this paper was inspired and funded by the needs of our PATRIC 2.0 project. The effort is part of the on-going work of PATRIC 2.0 team members to build a comprehensive, state-of-the-art bioinformatics resource for bacteria that serves the biomedical research community. Because of the exponentially growing number of bacterial genomes that PATRIC needs to handle, we are now in a phase where whole-genome phylogenetic analysis is both possible and necessary. PATRIC is integrating the very latest phylogenomic information and tools, such as those in this paper and a preceding publication that developed a phylogenetic tree for the alpha-proteobacteria**, into our system." He added: "This work is a great example of how PATRIC implements and deploys an infrastructure that will allow any person to develop these results in the future by going to the PATRIC site."
In October 2009, The National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), awarded a 5-year, $27,670,448 contract to Dr. Sobral's CyberInfrastructure Group of VBI to support the biomedical research community's work on infectious diseases. The funding is being used to integrate vital information on pathogens, provide key resources and tools to scientists, and help researchers to analyze genomic, proteomic and other data arising from infectious disease research.###
* Williams KP, Gillespie JJ, Sobral BW, Nordberg EK, Snyder EE, Shallom JM, Dickerman AW (2010) Phylogeny of Gammaproteobacteria. Journal of Bacteriology 192(9): 2305-2314. [PMID: 20207755]
** Williams KP, Sobral BW, Dickerman AW (2007) A robust species tree for the alphaproteobacteria. Journal of Bacteriology 189: 4578-4586. [PMID: 17483224]
The Virginia Bioinformatics Institute (http://www.vbi.vt.edu) at Virginia Tech is a premier bioinformatics, computational biology, and systems biology research facility that uses transdisciplinary approaches to science combining information technology, biology, and medicine. These approaches are used to interpret and apply vast amounts of biological data generated from basic research to some of today's key challenges in the biomedical, environmental, and agricultural sciences. With more than 240 highly trained multidisciplinary, international personnel, research at the institute involves collaboration in diverse disciplines such as mathematics, computer science, biology, plant pathology, biochemistry, systems biology, statistics, economics, synthetic biology, and medicine. The large amounts of data generated by this approach are analyzed and interpreted to create new knowledge that is disseminated to the world's scientific, governmental, and wider communities.
The Cyberinfrastructure Group (CIG) at VBI develops methods, infrastructure, and resources to help enable scientific discoveries in infectious disease research and other research fields. The group applies the principles of cyberinfrastructure to integrate data, computational infrastructure, and people. CIG has developed many public resources for curated, diverse molecular and literature data from various infectious disease systems, and implemented the processes, systems, and databases required to support them. It also conducts research by applying its methods and data to make new discoveries of its own. CIG has developed PATRIC, the PathoSystems Resource Integration Center (http://patricbrc.vbi.vt.edu/portal/portal/patric/Home), which serves as a comprehensive web-based resource for bacterial pathogens, biodefense research, and the study of emerging infectious diseases.
Barry Whyte | EurekAlert!
The birth of a new protein
20.10.2017 | University of Arizona
Building New Moss Factories
20.10.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau
University of Maryland researchers contribute to historic detection of gravitational waves and light created by event
On August 17, 2017, at 12:41:04 UTC, scientists made the first direct observation of a merger between two neutron stars--the dense, collapsed cores that remain...
Seven new papers describe the first-ever detection of light from a gravitational wave source. The event, caused by two neutron stars colliding and merging together, was dubbed GW170817 because it sent ripples through space-time that reached Earth on 2017 August 17. Around the world, hundreds of excited astronomers mobilized quickly and were able to observe the event using numerous telescopes, providing a wealth of new data.
Previous detections of gravitational waves have all involved the merger of two black holes, a feat that won the 2017 Nobel Prize in Physics earlier this month....
Material defects in end products can quickly result in failures in many areas of industry, and have a massive impact on the safe use of their products. This is why, in the field of quality assurance, intelligent, nondestructive sensor systems play a key role. They allow testing components and parts in a rapid and cost-efficient manner without destroying the actual product or changing its surface. Experts from the Fraunhofer IZFP in Saarbrücken will be presenting two exhibits at the Blechexpo in Stuttgart from 7–10 November 2017 that allow fast, reliable, and automated characterization of materials and detection of defects (Hall 5, Booth 5306).
When quality testing uses time-consuming destructive test methods, it can result in enormous costs due to damaging or destroying the products. And given that...
Using a new cooling technique MPQ scientists succeed at observing collisions in a dense beam of cold and slow dipolar molecules.
How do chemical reactions proceed at extremely low temperatures? The answer requires the investigation of molecular samples that are cold, dense, and slow at...
Scientists from the Max Planck Institute of Quantum Optics, using high precision laser spectroscopy of atomic hydrogen, confirm the surprisingly small value of the proton radius determined from muonic hydrogen.
It was one of the breakthroughs of the year 2010: Laser spectroscopy of muonic hydrogen resulted in a value for the proton charge radius that was significantly...
17.10.2017 | Event News
10.10.2017 | Event News
10.10.2017 | Event News
20.10.2017 | Information Technology
20.10.2017 | Materials Sciences
20.10.2017 | Interdisciplinary Research