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!
A Map of the Cell’s Power Station
18.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau
On the way to developing a new active ingredient against chronic infections
18.08.2017 | Deutsches Zentrum für Infektionsforschung
Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.
As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...
Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.
Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...
For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.
While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...
An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.
The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...
A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.
Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...
16.08.2017 | Event News
04.08.2017 | Event News
26.07.2017 | Event News
18.08.2017 | Life Sciences
18.08.2017 | Physics and Astronomy
18.08.2017 | Materials Sciences