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BEESPACE: AN INTERACTIVE ENVIRONMENT FOR ANALYZING NATURE AND NURTURE IN SOCIETAL ROLES
How much of social behavior is determined by genes and how much influenced by environments?
One of the most hotly debated questions in biology concerns the origins of behavior: Nature or nurture? Are genes (nature) or environment (nurture) the primary reason a person or other animal does what it does? The debate centers around the ethical implications of genetic determinism, which assumes that any role for genes automatically diminishes the role of the environment.
The BeeSpace project, led by Bruce Schatz at the University of Illinois, Urbana-Champaign, is working to help forge a deeper understanding of the relationship between genes and behavior that transcends the nature-nurture debate. Using genomic biology, the project's multidisciplinary team is exploring the idea that DNA is both genetically inherited and environmentally responsive.
This project will analyze social behavior as it relates to an entire genome, using as its target the honey bee an animal living in a complex society where different individuals perform different jobs.
On the project team, biologists will create databases that describe the gene activity in the brain associated with each societal role. Information scientists will develop an interactive computer environment that integrates the recently sequenced bee genome, genomic and proteomic databases, as well as the complete scientific literature relevant to behavioral biology and honey bees. New text-mining software will create a bee-focused thesaurus, or "concept space," to help navigate through the diverse database and literature sources.
The resulting BeeSpace system will enable many kinds of biologists to interact with all the knowledge relevant to bees and genes from many points of view, including the perspectives of molecular biology, neuroscience and evolutionary biology. Information technology similar to that used in BeeSpace may also serve as a model for the evolution of cyberspace beyond the Internet and help to create the "Interspace," a universal library where all the worlds knowledge can be easily analyzed across many sources.
Total estimated funding through August 2009: $5 million.
Lead principal investigator:
Bruce Schatz, University of Illinois, Urbana-Champaign (UIUC), 217-244-0651, schatz@uiuc.edu
Participating Researchers:
Gene Robinson, ChengXiang Zhai, Sandra Rodriguez-Zas, Bertram Bruce, UIUC
Susan Fahrbach, Wake Forest University
Media contacts:
Jim Barlow, UIUC, 217-333-5802, jebarlow@uiuc.edu
Web site:
BeeSpace: http://www.beespace.uiuc.edu/
Award abstract:
http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0425852
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ECOLOGICAL GENOMICS AND HERITABILITY: CONSEQUENCES OF EXTENDED PHENOTYPES
What are the genetic forces that draw members of an ecological community together?
The emerging field of ecological genomics studies the genetic basis for formation of a functional community, including the genetic linkages among species, complex communities and whole ecosystems. Scientists do not yet know the extent of these linkages, but in today's world they are clearly being disrupted at an increasing rate. Human disturbances, habitat fragmentation and the introduction of exotic species are being felt by ecosystems that have evolved over millions of years. Understanding and mitigating these effects will require defining the fundamental forces that give rise to ecological communities and which tie them together. The goal in this FIBR project is to define the genetic linkages that drive the formation, structure and fate of whole ecological communities.
The research team, led by Tom Whitham of Northern Arizona University, is composed of 30 researchers spanning disciplines ranging from molecular genetics to ecology and biogeography and specializing in organisms ranging from microbes to plants and insects. The team will study communities formed around cottonwoods, a dominant tree of a threatened habitat type and an organism whose complete genome sequence will soon be available.
In collaboration with federal agencies working to restore endangered stream-side habitat in the arid Southwest, the researchers will plant experimental forests at restoration sites to quantify aspects of community genetics, addressing key scientific questions and restoring habitat simultaneously. For example, the researchers will examine how genetic diversity in a dominant tree affects the biodiversity of the rest of the community. Another set of experimental forests will be used to examine whether the trees and key organisms that depend on the trees for survival evolve as a community.
They will also use old and new restoration sites to examine whether community structure, biodiversity and ecosystem processes can be inherited. For example, they will try to determine whether an individual tree inherits from its parents the community of microbes, insects and birds that the tree supports. A genetic component to community structure may ultimately result in community evolution over time.
Such studies have major implications for establishing the genetic foundations of communities and ecosystems, for quantifying the impacts of newly introduced organisms on the rest of the community and for making informed decisions about environmental policy and management.
Total estimated funding through August 2009: $5 million.
Lead principal investigator:
Tom Whitham, Northern Arizona University, 928-523-7215, Thomas.Whitham@nau.edu
Participating Researchers:
Steve Shuster, Catherine Gehring, Gery Allan, Jane Marks, Steve Hart, Paul Keim, Northern Arizona University
Rick Lindroth, University of Wisconsin
Stephen DiFazio, University of Tennessee
Brad Potts, University of Tasmania
Media contacts:
Lisa Nelson, Northern Arizona University, 928-523-6123, Lisa.Nelson@nau.edu
Terry Devitt, University of Wisconsin, Madison, 608-262-8282, trdevitt@wisc.edu
Web sites:
NAU Cottonwood Ecology Group: http://www.poplar.nau.edu/
NAU Merriam-Powell Center for Environmental Research: http://www.mpcer.nau.edu/
Award abstract:
http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0425908
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HOW ORGANISMS ADAPT TO NEW ENZYMES AND PATHWAYS
How do organisms adapt to opportunities for 'sudden' evolution?
When Charles Darwin proposed his model for the evolution of species, he assumed that a species evolved by gradually accumulating mutations, resulting in progressive adaptations through successive generations. In this era of massive genome sequencing, we now know what Darwin could not: As many as a quarter of all genes in many organisms were acquired not through a process of continuous inheritance across generations, but through the transfer of DNA between unrelated organisms. Thus, in addition to the gradual process envisioned by Darwin, evolution can also proceed quickly, requiring an organism to adjust rapidly to newfound capabilities and functions.
This process of acquiring DNA from an unrelated source, called "gene capture" or horizontal gene transfer, can even involve whole sets of genes moving from one organism to another. Gene capture is what enables drug resistance to spread rapidly from one bacterial population to another, causes a harmless species to suddenly become pathogenic to humans or allows an organism to suddenly thrive in a new environment or in the presence of a toxin. This same mechanism performed in the lab (and then called "genetic engineering") is used to create microbes that eat pollutants or produce useful materials.
But the process of gene capture poses fundamental biological questions that this project will attempt to answer. How does an organism react when a new, fully functioning enzyme or pathway is suddenly introduced? What aspects of its own genetic machinery does the organism change to accommodate the new chemistry that it can now carry out? How does the organism learn to control the new genes and modify them so that they function optimally in their new host?
To find the answers, Gregory Petsko and Dagmar Ringe of Brandeis University will lead an interdisciplinary team of microbial geneticists and physiologists, molecular biologists, enzymologists, structural biologists and experts in systems biology and bioinformatics. These researchers will take a well-understood metabolic pathway from a soil bacterium and introduce it into the familiar intestinal bacterium E. coli, which must then adjust to the presence of both the new pathway and the new and unproductive compounds it produces.
The team will study how E. coli copes with this challenge and how the response changes as the pathway is modified to produce compounds that are productive and allow the bacterium to grow. The team will use a comprehensive combination of experimental and modeling approaches to determine how cells adjust the dynamic balance among regulatory circuits and metabolic pathways so as to accommodate new flux and how new pathways are modulated to allow the cell to regain metabolic control. The project will lead to fundamental new information on how living cells adapt and evolve, as well as information that may lead to the engineering of microbes with new capabilities for industrial and environmental uses.
Total estimated funding through August 2009: $4.25 million.
Lead principal investigator:
Gregory Petsko, Brandeis University, 781-736-4903, petsko@brandeis.edu
Participating Researchers:
Dagmar Ringe (co-PI), Brandeis University
Michael McLeish, George Kenyon, University of Michigan
James Collins, Boston University
Media contacts:
Cristin Carr, Brandeis University, 781-736-4203, carr@brandeis.edu
Web site:
Petsko-Ringe Lab: http://www.rose.brandeis.edu/PRLab/main.html
Award abstract:
http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0425719
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MOLECULAR EVOLUTIONARY ECOLOGY OF DEVELOPMENTAL SIGNALING PATHWAYS IN COMPLEX ENVIRONMENTS
To bloom or not to bloom: How do plants weigh the cues of seasonal change to time choices that are right for their climate?
Timing is everything for plants in their natural environment. For starters, they must flower during favorable seasonal conditions to reproduce successfully. To flower at the right time, plants integrate information from environmental cues such as day length, growth temperature and past winter chilling -- and different responses to these cues are favored in different climatic regions. This capacity for integration in plants illustrates an important capacity of many biological systems: the ability to assess multiple signals in responding to complex challenges.
This project will identify mechanisms underlying this intriguing capability by exploring how plants integrate environmental signals and how the genetic pathways underlying their responses evolve in different climates. The research team will examine natural genetic variation in flowering responses in the model species Arabidopsis thaliana, an annual weed closely related to crops such as canola and cabbage. The team will collect molecular, genetic and ecological data for a core set of inbred lines of Arabidopsis originating from a wide range of climates, from Mediterranean to subarctic, across the native European range of the species.
Led by evolutionary ecologist Johanna Schmitt of Brown University, the team includes molecular biologists, evolutionary geneticists, plant modelers and computer scientists. Working together, the team will dissect the molecular mechanisms underlying natural variation in environmental signal integration. Variation in specific genes that control flowering responses will be analyzed to uncover the evolutionary forces shaping genetic signaling networks. Mapping methods similar to those used to identify genes contributing to human disease will be used to test whether natural variation in these particular genes contributes to variation in flowering responses.
These experimental efforts will be complemented by powerful modeling and simulation analyses. Computer scientists will develop a model to simulate and predict how variation in these genes affects the overall pathway function and consequent flowering responses to different environments. Evolutionary ecologists will test -- at six sites in Spain, Germany, England and Finland, in collaboration with seven leading European Arabidopsis laboratories -- the prediction that geographic climate variation favors different flowering responses in different regions.
The answers to these questions are important for understanding the molecular mechanisms controlling flowering responses in crops and wild plants, as well as how natural variation in these mechanisms may allow plants to inhabit diverse geographic regions and respond to ongoing climate change. This work will also shed light on the essential capacity of biological systems to respond to complex signals in making critical adjustments in patterns of behavior, development, physiology and metabolism, and other essential functions.
Total estimated funding through August 2009: $5 million.
Lead principal investigator:
Johanna Schmitt, Brown University, 401-863-3435, Johanna_Schmitt@brown.edu
Participating Researchers:
Tonia Korves, Brown University
Stephen Welch, William Hsu, Sanjoy Das, Judith Roe, Kansas State University
Michael Purugganan, North Carolina State University
Richard Amasino, University of Wisconsin
Detlef Weigel, Max Planck Institute for Developmental Biology
Media contacts:
Wendy Lawton, Brown University, 401-863-2476, wendy_lawton@brown.edu
Mary Lou Peter, Kansas State University, 785-532-1164, mlpeter@oznet.ksu.edu
Terry Devitt, University of Wisconsin, Madison, 608-262-8282, trdevitt@wisc.edu
Web sites:
Schmitt Lab: http://www.brown.edu/Departments/EEB/schmitt/
Ecological Genomics in Kansas: http://www.ksu.edu/ecogen/modeling.html
Purugganan Lab: http://purugganan.gnets.ncsu.edu/
Award abstract:
http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0425759
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NEUROMECHANICAL SYSTEMS BIOLOGY
How exactly do animals move?
Despite many discoveries over the past 50 years, scientists still know very little about how animals move. Although movement can be broken down into a series of general steps -- brain activates muscles, muscles move skeleton, skeleton carries body along -- no single model exists to explain the complex signals and feedbacks among neurons, muscles, the skeleton and the whole body that make movement possible and prevent animals from falling over.
Robert Full of the University of California, Berkeley, is leading a team to tackle this challenge, and they will start with a cockroach -- a robot cockroach. They will tweak the robot to tease apart the complexities in the neural and muscular networks in insects. At the same time, they will conduct biomechanical and neurological experiments on insects and develop mathematical models to improve the robot. This multi-pronged approach will allow them to uncover the neural and muscular control and feedback loops that lead to the remarkably similar patterns of whole-body motion in animals as diverse as crabs, cockroaches, lizards, dogs and humans.
The problem, a new field that Full has coined "neuromechanical systems biology," demands a multidisciplinary approach to integrate data across mathematical models, numerical simulations, robot models and biological experiments.
The team includes researchers with expertise in studying running insects as they cross virtual terrains. Add to that researchers who have learned to read and even rewrite the neural code in insects while measuring motion, forces and neuromuscular signals. Mathematicians will use the data to analyze and simulate mathematical models. The models will, in turn, provide feedback to the six-legged robot cockroach, which will serve as a controlled experiment, easier to manipulate than real animals but able to tackle real-world challenges.
The project is designed to elicit fundamental principles for how animals move, and the implications of these principles are expected to extend well beyond the immediate goals of the research. In the biological sciences, this work can provide an intellectual framework for describing the behaviors of other complex biological systems and control networks. In engineering, the results may provide the basis for novel controller architectures, lead to new strategies for tuned materials and artificial muscles and enable the design of highly mobile robots.
Total estimated funding through August 2009: $5 million.
Lead principal investigator:
Robert Full, University of California, Berkeley, 510-642-9896, rjfull@socrates.berkeley.edu
Participating Researchers:
John Miller, Montana State University
Daniel Koditschek, University of Michigan
Philip Holmes, Princeton University
John Guckenheimer, Cornell University
Media contacts:
Bob Sanders, UC Berkeley, 510-643-6998, rls@pa.urel.berkeley.edu
Web sites:
Poly-PEDAL Lab: http://polypedal.berkeley.edu/
Award abstract:
http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0425878
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A SYSTEMS APPROACH TO STUDY REDOX REGULATION OF FUNCTIONS OF PHOTOSYNTHETIC ORGANISMS
How do whole molecular networks serve as modular units for function, regulation and evolution?
The operation and control of complex biological processes such as photosynthesis and respiration involve a large number of molecules operating together as a discrete, functional network. An interdisciplinary team of investigators led by Himadri Pakrasi of Washington University in St. Louis will examine fundamental questions about how such networks arise, persist and evolve as modular units.
The networks to be studied by this team center around the oxidation and reduction (redox) reactions essential to many cellular processes in all organisms. These reactions, which are crucial in transferring energy via the loss and gain of electrons, can also have damaging effects when they affect the wrong molecules. As a result, cells have evolved a variety of responses to maintain the balance between essential and destructive redox reactions.
In particular, plants, algae and cyanobacteria rely on a redox chain reaction for photosynthesis, the process that converts water, carbon dioxide and sunlight into oxygen and carbohydrates. Over the course of biogeological time, the processes of photosynthesis have dramatically increased the oxygen concentration in the atmosphere and changed the chemical environment in the biosphere in a fundamental way.
To survive under such profoundly altered conditions, cyanobacteria and plants have evolved elaborate protective and regulatory networks, both at the genetic and metabolic levels. A central goal of this FIBR project is to unravel the networks that help maintain redox balance in cyanobacteria and plants.
The researchers will initially focus on the cyanobacterium Synechocystis 6803, which has a completely sequenced genome that can easily be manipulated. Despite the detailed inventory of the genes and proteins from Synechocystis, scientists still don't understand how the complex functions of this organism are organized.
The expertise of the project team spans molecular genetics, biochemistry, proteomics, computational biology, systems engineering and other disciplines. The team has worked with well-established model systems in cyanobacteria, flowering plants and mosses, so they will work to apply the insights gained from Synechocystis to the plant Arabidopsis and the moss Physcomitrella. Furthermore, the team's approach will highlight how these processes were conserved during the evolution of land plants. The overall goal of this work is to provide a framework for understanding the origins and properties of modular, functional networks in biological systems.
Total estimated funding through August 2009: $5 million.
Lead principal investigator:
Himadri B. Pakrasi, Washington University, 314-935-6853, pakrasi@wustl.edu
Participating Researchers:
Ralph S. Quatrano, Bijoy K. Ghosh, Rajeev Aurora, Victoria L. May, Washington University
Kenneth D. Belanger, Colgate University
Richard D. Smith, Pacific Northwest National Laboratories
Yukako Hihara, Saitama University (Japan)
Media contacts:
Tony Fitzpatrick, Washington University, 314-935-5272, tony_fitzpatrick@wustl.edu
Web sites:
Pakrasi Lab: http://sysbio.wustl.edu/
Award abstract:
http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0425749
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