U.S. National Science Foundation awards grants to seed plant systems biology - biofuel and bioeconomy-centered projects
The wealth of genomics tools and sequence resources developed over the past ten years of the PGRP have opened up exciting, new comparative approaches in plant biology. PGRP researchers continue to uncover gene networks that regulate plant development and growth in concert with environmental signals, such as temperature, light, disease and pests.
Amongst the projects of immediate interest to the emerging biofuels and bioeconomy are:
A four-year, $5.5 million project to make a comparative analysis of C3 and C4 leaf development in rice, sorghum and maize, led by Timothy Nelson, which involves Yale University, Boyce Thompson Institute, Cornell University and Iowa State University:
C4-type plants such as maize, sorghum and several promising biofuel feedstocks possess a set of complex traits that greatly enhance their efficiency of carbon-fixation, water and nitrogen use, and performance in high temperatures and light intensities, in comparison to C3-type plants such as rice and many temperate grasses. The key C4 traits are (1) specialization and cooperation of two leaf photosynthetic cell types (mesophyll and bundle sheath) for carbon fixation and photosynthesis, (2) enhanced movement of metabolites between cooperating cells, and (3) very high density of leaf venation. These C4 traits appear to be regulatory enhancements of features already present in less-efficient C3 plants, but regulated in different patterns. Although C4 plants have evolved at least 50 times independently in various taxonomic groups, the molecular basis of key C4 traits is insufficiently understood to permit their introduction into important C3 plants to enhance their performance as agricultural or biofuel feedstocks.
This project will compare the leaves of rice (a C3 grass), maize (a moderate C4 grass) and sorghum (an extreme C4 grass). The abundance and spectrum of gene transcripts, proteins and metabolites will be compared along a developmental gradient from immature tissues at leaf base to mature tissues at the leaf tip. To align the gradients of the three species, markers for developmental time points in gene expression, protein accumulation, sink-source transition and cell wall specialization will be employed. Mesophyll and bundle sheath cells will be obtained from each leaf stage by laser microdissection, and their whole genome RNA transcripts, proteomes (including modifications), and selected metabolites (related to photosynthesis) will be profiled and compared. Two hypotheses will be tested by the comparative analysis of the corresponding C3 and C4 plant datasets: (1) To produce C4 traits, plants use networks of genes, proteins, and metabolites that are already present in C3 plants, and (2) C4 features are plastic and expressed in a degree that depends on environment and developmental stage. This analysis should identify the regulatory points that are potential targets for the production of C4 traits in C3 species.
A four-year, $4.6 million grant to a project led by John Browse at Washington State University to continue research that uses biochemical genomics to reveal components of biosynthesis pathways necessary to produce novel fatty acids in oilseeds:
The goal of this project is to use genomics to access the network of genes and proteins that operate chemical factories to synthesize and accumulate novel fatty acids in seeds. Evolution of new enzyme functions, together with the co-evolution of additional biochemical and cell biological traits, has provided hundreds of potentially useful chemicals in seed oils, including the hydroxylated, conjugated and cyclopropane fatty acids to be studied in this project.
Providing a detailed description of genes and proteins required for optimal pathway function will require the integrated deployment of four strategies: a) Investigate and optimize the activities of enzymes for unusual fatty acid synthesis using bioinformatics and protein engineering. b) Carry out extensive sequencing of seeds sampled through the period of oil synthesis, and use functional genomic screens to identify co-evolved enzymes (and other protein functions) required for incorporation of the novel fatty acid into the oil. c) Perform biochemical analysis of the identified proteins and quantify their contributions to the accumulation of unusual fatty acids through expression in transgenic plants. d) Analyze protein-protein interactions in membranes to gain insight how these pathways are physically organized. Finally, the accumulated knowledge will be tested through experiments to reconstruct the native pathways in transgenic plants using expression of multiple genes and pathway engineering. The discoveries that result from this project will yield an understanding of the underlying principles of how pathways evolved for the synthesis of novel seed oils.
The basic knowledge from this project will enable the design of a new generation of specialty crops that will become the green factories of the future, providing for the production of industrial lubicants, solvent oils and biodiesel.
A four-year, $1.7 million grant to a University of Alaska Fairbanks and University of Minnesota-Twin Cities project led by Matthew Olson to study population genomics of cold adaptation in poplar:
Populus species are economically, ecologically, and environmentally important; they are harvested for paper pulp and particle board production, and hold potential for playing important roles in CO2 biosequestration and biofuel production:
energy :: sustainability ::biomass :: bioenergy :: biofuels :: bioproducts :: bioeconomy :: energy crops :: systems biology :: genomics ::
Populus also is the model organism for hardwood tree genomics and physiology. Population genetic tools are increasingly useful for identifying genes that underlie variation in ecologically and economically important traits, but are not presently available in Populus. This project will develop these tools for Populus balsamifera, use them to identify the genetic basis for phenotypic variation in bud set (an important determinant of cold adaptation and growth rate). This research also will test whether the same genes responsible for variation and adaptive evolution of bud set in North American P. balsamifera and European P. tremula.
These objectives will be accomplished through collaboration with Canadian researchers who are establishing long-term common gardens of P. balsamifera. These common gardens will be maintained as a long term resource and are available to the wider scientific community; therefore, the data we generate will greatly facilitate future genotype-phenotype association analyses on additional economically and ecologically important traits (wood density, drought tolerance, etc.). The comparative population genomic analyses of adaptation to northern latitudes will be accomplished through collaboration with colleagues at the University of Umea, Sweden, who are conducting complementary research in European aspen (P. tremula).
A three-year, $2.5 million grant to The Grass Regulome Initiative which will focus on integrating control of gene expression and agronomic traits across the grasses; the project is led by Erich Grotewold and involves the Ohio State University and the University of Toledo (earlier a similar project led by Gronewold - "Engineering phenolic metabolism in the grasses using transcription factors"- received a grant from the U.S. Department of Energy):
An emerging theme in plant systems biology is establishing the architecture of regulatory networks and linking system components to agronomic traits. The goal of this project is to provide a concerted effort to perform comparative transcriptional genomics across several grass crops (maize, sorghum, sugarcane and rice), combining the development of experimental tools and bioinformatic resources to discover and display regulatory motifs. The Grass Regulatory Information Service (GRASSIUS) will be implemented as a public web resource that integrates sequence and expression information on transcription factors (TFs), their DNA-binding properties, TF binding sites in the genome, the genes that TFs target for regulation and the regulatory motifs in which they participate.
A method for the in vivo identification of direct targets for TFs, which should be applicable even in the absence of a complete genome sequence, will be developed and applied towards the identification of direct targets for a small subset of maize, rice, sorghum and sugarcane TFs. Together with the generation of a large centralized collection of plasmids harboring open reading frames for several TFs and antibodies to a subset of them, this project will facilitate the community-wide identification of protein-DNA interactions, essential for establishing the grass regulatory map. The experimental and computational integration of regulatory motifs with QTLs will provide an accelerated translation of findings derived from these studies to issues of agronomic relevance.
Benefiting from the increasing amount of genome sequence available, this proposal integrates genetics, molecular biology, biochemistry, statistics, bioinformatics and computer sciences in establishing the architecture of the regulatory networks that control plant gene expression, in a pioneering effort to launch the comparative transcriptional genomics field to important grass crops.
And 4 major projects on maize genomics (maize artificial chromosomes; functional genomics of maize gametophytes; construction of comprehensive sequence indexed transposon resources for maize; cell fate acquisition in maize).
Plant biologists continue to exploit genomics tools and sequence resources in new and innovative ways. It's exciting to see research involving biologists and mathematicians, computer scientists and engineers, all working to address major unanswered questions in plant biology. These latest projects will also have a significant impact on how we train the next generation of plant scientists to carry out research at the cutting edge of the biological sciences. - James Collins, NSF assistant director for biological sciences.PGRP is also continuing to support the development of tools to enable researchers to make breakthroughs in understanding the structure and function of economically important plants - from the gene level to the whole plant. Example projects include:
- A multidisciplinary team of investigators at the University of Wisconsin-Madison will develop cutting-edge technology using cameras, robotics and computational tools to enable high-throughput analysis of traits in mutant or naturally varying plant populations.
- A project led by the Dana-Farber Cancer Institute is using Arabidopsis and rice genomic resources to produce a plant "interactome," a map of all protein-protein interactions. This map will provide scientists with testable predictions of how genes and the proteins they encode interact to carry out complex functions within a plant cell.
References:
National Science Foundation: NSF Awards 26 New Grants to Seed Plant Systems Biology - October 11, 2007.
National Science Foundation: overview of 2007 PGRP Awards.
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Saturday, October 13, 2007
European project finds nitrogen damages biodiversity - biomass stripping coupled to bioenergy could offer conservation strategy
Key research
Gowing was one of Carly Stevens' PhD supervisors at The Open University in the UK. When Stevens finished her thesis in 2004, her findings were so significant they were published in Science (abstract). Not only that, they were selected as contributing to one of the top ten scientific breakthroughs of that year – quite something for a PhD student. Stevens had found the first evidence that nitrogen deposition from the atmosphere was depleting numbers of plant species in British grasslands. Gowing and Stevens say "there was experimental evidence that this could happen, but we were the first to show the effect is real and happening now".
Stevens studied acid grasslands – upland pastures with relatively infertile soils. She found that in places where more nitrogen is deposited, there are fewer plant species. The gradient was so pronounced that one species has been lost for each additional 2.5 kg of nitrogen per hectare deposited every year. Nitrogen from man-made sources, like intensive farming and cars, causes significant air pollution in the UK, and some is deposited from the air on to the land. Deposition is highest in densely-populated areas, and in Britain ranges from about 5 to 35 kg of nitrogen per hectare per year.
The approach to protecting wildlife from nitrogen pollution is to calculate critical load values for different ecosystems – how much nitrogen a system can accumulate every year before damage occurs. Infertile habitats, like heathlands and bogs, are the most vulnerable. But Stevens’ research showed that species are being lost even where deposition is ‘beneath’ the critical load for grasslands.
Europe-wide effect
So last year, Stevens, her UK colleagues Gowing, Nancy Dise and Owen Mountford, and a team of experts from Germany, the Netherlands and France, embarked on a Europe wide project titled 'Biodiversity of European grasslands – the impact of atmospheric nitrogen deposition (BEGIN)', part of the ESF's EuroDIVERSITY Programme. The project’s aim is to see if the effects are the same on a wider range of grasslands, across the entire Atlantic side of Europe. "The low countries and northern Germany are the epicentre of European nitrogen deposition," says Gowing.
70 new grasslands in at least nine countries have been added to the picture, including different types of grassland. So far, the first year’s field results seem to adhere to the pattern, showing that species loss is directly related to long term deposition of nitrogen:
energy :: sustainability :: fossil fuels :: air pollution :: nitrogen :: biodiversity :: grasslands :: biomass :: bioenergy :: Europe ::
The team has started experiments to see if they can establish how extra nitrogen has these effects. They hope to predict what will happen in the future.
What should be done?
Gowing and his team are hoping for a clear signal that we can maintain species richness under nitrogen deposition by biomass stripping. That means extra mowing and grazing. This could offer a management strategy for nature conservation.
Biopact asked Gowing how the technique of biomass stripping fits into such a strategy and whether there are any concrete uses for the harvested material.
Gowing confirmed that the stripped biomass could be used for bioenergy production. But he pointed at several barriers:
Decentralised and mobile bioconversion technologies might help tackle some of these barriers. Small, modular and mobile fast-pyrolysis plants that convert the biomass into bio-oil (earlier post) and mobile pellet plants (more here) are currently under development. The concept behind these technologies is simple: convert the bulky biomass into a higher density product close to the place where it is harvested and then transport it more efficiently to a central biofuel production facility or a power plant.
Biopact thinks that, instead of converting existing ecosystems into monocultures of energy crops, it might be more interesting to look into ways to couple bioenergy production to conservation strategies first. An example of such an approach is the Tallgrass Prairie Center's grassland restoration effort currently underway in the U.S. (previous post). A similar approach might be applied to managing Europe's nitrogen poisoned grasslands.
First results of the BEGIN project were presented at the first EuroDIVERSITY conference, held in Paris from 3-5 October 2007. BEGIN is funded under the European Science Foundation’s (ESF) EuroDIVERSITY Programme, which fosters pan-European collaborative research on biodiversity.
The project involves scientists from the Open University, UK; the University of Bordeaux, France; Utrecht University, the Netherlands; the University of Bremen, Germany; Manchester Metropolitan University, UK and the Norwegian Institute for Nature Research, Norway. Associated projects are run by the Centre for Ecology and Hydrology, UK; the University of Lund, Sweden; Katholieke University, Leuven, Belgium; the University of Metz, France; the University of Sheffield, UK; The Institute of Ecosystem Studies, Millbrook, USA; Radboud University of Nijmegen, Netherlands; the University of Minnesota, USA and the University of Bergen, Norway.
Picture: Ox-eye daisies and other wildflowers are dotted around the acidic grassland of Ifton Meadows, Shropshire, UK. Wildflowers and other broad-leaved species, rather than grasses, are hit hardest by nitrogen deposition.
References:
Stevens, C.J., Dise, N.B., Mountford, J.O. and Gowing, D.G., "Impact of nitrogen deposition on the species richness of grasslands" Science, 19 March 2004: Vol. 303. no. 5665, pp. 1876 - 1879 DOI: 10.1126/science.1094678
Stevens, C.J., Dise, N.B. Gowing, D.G. and Mountford, J.O. "Loss of forb diversity in relation to nitrogen deposition in the UK: regional trends and potential controls." Global Change Biology, Volume 12, Number 10, October 2006 , pp. 1823-1833(11)
Open University, Research group on Ecohydrology and Nutrient Cycling: profile of Carly Stevens describing her work on Ecosystem Properties of Acidic Grasslands; profile of prof David Gowing.
European Science Foundation: Nitrogen – the silent species eliminator - October 12, 2007.
European Science Foundation: Biodiversity of European Grasslands the Impact of Atmospheric Nitrogen Deposition (BEGIN).
Biopact: Mobile pyrolysis plant converts poultry litter into bio-oil - August 20, 2007
Biopact: The mobile pellet plant - April 29, 2007
Biopact: Dynamotive begins construction of modular fast-pyrolysis plant in Ontario - December 19, 2006
Biopact: Tallgrass Prairie Center to implement Tilman's mixed grass findings - September 02, 2007
Wildflowers and other broad-leaved species, rather than grasses, are the hardest hit.
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posted by Biopact team at 5:06 PM 0 comments links to this post