The Systems Biology Institute

Tokyo, Japan

The Systems Biology Institute

Tokyo, Japan

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News Article | November 17, 2016
Site: www.eurekalert.org

Half of all coral species in the Caribbean went extinct between 1 and 2 million years ago, probably due to drastic environmental changes. Which ones survived? Scientists working at the Smithsonian Tropical Research Institute (STRI) think one group of survivors, corals in the genus Orbicella, will continue to adapt to future climate changes because of their high genetic diversity. "Having a lot of genetic variants is like buying a lot of lottery tickets," said Carlos Prada, lead author of the study and Earl S. Tupper Post-doctoral Fellow at STRI. "We discovered that even small numbers of individuals in three different species of the reef-building coral genus Orbicella have quite a bit of genetic variation, and therefore, are likely to adapt to big changes in their environment." "The implications of these findings go beyond basic science," said Monica Medina, research associate at STRI and the Smithsonian's National Museum of Natural History and associate professor at Pennsylvania State University. "We can look forward to using similar approaches to predict demographic models to better manage the climate change threatened Orbicella reefs of today." To look back in time, the team of researchers working at the Smithsonian's Bocas del Toro Research Station and Naos Molecular and Marine Laboratories collected fossils from ancient coral reefs and used high-resolution geologic dating methods to determine their ages. They compared the numbers of fossilized coral species at different time points. One of the best-represented groups in the fossil collections were species in the genus Orbicella. In addition to the fossil collections, they also used whole genome sequencing to estimate current and past numbers of several Orbicella species. Within a single individual there are two copies of their genetic material, in some instances, one copy is different than the other and is called a genetic variant. The authors first assembled the full genomic sequence of an individual from Florida and then, using it as an anchor, reconstructed the genetic variation contained within single individuals. Depending on the amount of the genetic variation at certain intervals across the genome, the authors were able to recover the population sizes of each species at different times in the past. Between 3.5 to 2.5 million years ago, numbers of all coral species increased in the Caribbean. But from 2 to 1.5 million years ago, a time when glaciers moved down to cover much of the northern hemisphere and sea surface temperatures plunged, the number of coral species in the Caribbean also took a nosedive. Sea levels fell, eliminating much of the original shallow, near-shore habitat. "Apart from the species that exist today, all species of Orbicella that survived until 2 million years ago suddenly went extinct," write the authors. When huge numbers of species die out, it makes room for other species to move in and for new species to develop to occupy the space the others held. Two species that grow best in shallow water doubled in number at about the same time that their sister species and competitor, the organ pipe Orbicella (O. nancyi) disappeared. When a species declines during an extinction event, it loses more and more genetic variation, and sometimes does not have much to work with during the recovery period. Scientists call this a genetic bottleneck. Orbicella was able to recover after the bottleneck. "It's incredible how predictions from genetic data correlated so well with observations from the fossil and environmental record," said Michael DeGiorgio (assistant professor of biology at Pennsylvania State University). "We see hope in our results that Orbicella species survived a dramatic environmental variation event," said Prada. "It is likely that surviving such difficult times made these coral populations more robust and able to persist under future climatic change." "The in-depth analysis of population size in a now ESA-threatened coral, as well as the release of its genome and that of its close relatives (which are also threatened) would be of great interest to coral reef researchers addressing conservation issues," said Nancy Knowlton, senior scientist emeritus at STRI, currently at the National Museum of Natural History. Authors are from STRI, the National Museum of Natural History, Pennsylvania State University, University of Iowa, U.S. National Oceanic and Atmospheric Administration, Hudson Alpha Institute of Biotechnology, Universidad Nacional Autónoma, Australian Research Council Centre of Excellence for Coral Reef Studies and University of Queensland School of Biological Sciences, Florida State University, Natural History Museum, The Systems Biology Institute. The Smithsonian Tropical Research Institute, headquartered in Panama City, Panama, is a unit of the Smithsonian Institution. The Institute furthers the understanding of tropical nature and its importance to human welfare, trains students to conduct research in the tropics and promotes conservation by increasing public awareness of the beauty and importance of tropical ecosystems. Website: http://www. . Prada, C., Hanna, B., Budd, A.F., et al. 2016. Empty niches after extinctions increase population sizes of modern corals. Current Biology


Patent
Okinawa Institute of Science, Technology and The Systems Biology Institute | Date: 2013-07-11

A simulation system includes an interface component connected to a public or shared network that has less restrictive access than networks inside the firewall, generating a simulation job and registering the simulation job in a database, a job control component accessing said database to retrieve the simulation job and scheduling the simulation job for execution, and a simulation execution component receiving the simulation job from the job control component, creating executable codes for numerical and parallel computing algorithms and distributing computing processes to multiple computers to execute the simulation job.


Patent
Okinawa Institute of Science, Technology and The Systems Biology Institute | Date: 2013-06-13

The present invention acquires compound structure data and candidate protein structure data on a candidate protein serving as a candidate for interaction with the compound. The present invention calculates a binding strength between the candidate protein and the compound using a docking simulation method, determines a predicted binding strength corresponding to the binding strength predicted by making a comprehensive evaluation of the binding strength, and determines a predicted protein corresponding to the candidate protein predicted to interact with the compound. The present invention calculates an interaction strength using a binding strength simulation method and determines a predicted interaction strength corresponding to the interaction strength predicted by making the comprehensive evaluation of the interaction strength.


Patent
The Systems Biology Institute, Okinawa Institute of Science and Technology | Date: 2011-03-31

The present invention sets, for each cells or each condition, a production output of the cells or the biomass based on the measured data and a variable indicating an extent of variation of the production output, calculates a variable range of the production output and the variable in case of combining the multiple cells or conditions based on the production output and the variable set, and calculates an optimum combination within the variable range by using an optimization method.


Patent
The Systems Biology Institute, Okinawa Institute of Science and Technology | Date: 2011-03-31

The present invention involves retrieving edges that do not constitute a designated network model which is a network model designated by a user and are linked to nodes that constitute the designated network model, displaying retrieval results that include the retrieved edges and network model IDs corresponding to the edges in a selectable manner, and generating an integrated network model in which, when the retrieval results are selected by the user, the edges that are included in the selected retrieval results and the nodes that do not constitute the designated network model and are linked to the edges, are integrated into the designated network model.


Patent
Okinawa Institute of Science, Technology, SBX Corporation and The Systems Biology Institute | Date: 2013-11-07

In a plurality of data analysis apparatuses communicatively coupled to one another, a database is accessed at a given access level. Based on the data acquired from the database, an application program is executed to perform data analysis. Communication control is performed to allow transmission and reception of a data analysis result with respect to another data analysis apparatus at a different access level.


Patent
Okinawa Institute of Science, Technology and The Systems Biology Institute | Date: 2013-08-07

The present invention involves retrieving edges that do not constitute a designated network model which is a network model designated by a user and are linked to nodes that constitute the designated network model, displaying retrieval results that include the retrieved edges and network model IDs corresponding to the edges in a selectable manner, and generating an integrated network model in which, when the retrieval results are selected by the user, the edges that are included in the selected retrieval results and the nodes that do not constitute the designated network model and are linked to the edges, are integrated into the designated network model.


Patent
Okinawa Institute of Science, Technology, SBX Corporation and The Systems Biology Institute | Date: 2015-09-16

According to the present invention, in a plurality of data analysis apparatuses communicatively coupled to one another, a database is accessed at a given access level. Based on the data acquired from the database, an application program is executed to perform data analysis. Communication control is performed to allow transmission and reception of a data analysis result with respect to another data analysis apparatus at a different access level.


Patent
Okinawa Institute of Science, Technology and The Systems Biology Institute | Date: 2013-04-10

The present invention sets, for each cells or each condition, a production output of the cells or the biomass based on the measured data and a variable indicating an extent of variation of the production output, calculates a variable range of the production output and the variable in case of combining the multiple cells or conditions based on the production output and the variable set, and calculates an optimum combination within the variable range by using an optimization method.


Patent
Okinawa Institute of Science, Technology and The Systems Biology Institute | Date: 2015-04-22

The present invention acquires compound structure data and candidate protein structure data on a candidate protein serving as a candidate for interaction with the compound. The present invention calculates a binding strength between the candidate protein and the compound using a docking simulation method, determines a predicted binding strength corresponding to the binding strength predicted by making a comprehensive evaluation of the binding strength, and determines a predicted protein corresponding to the candidate protein predicted to interact with the compound. The present invention calculates an interaction strength using a binding strength simulation method and determines a predicted interaction strength corresponding to the interaction strength predicted by making the comprehensive evaluation of the interaction strength.

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