• Last Updated: 08/17/2007

News

Canadian researchers have promised to squeeze "decades" of cancer research into just two years by harnessing the power of a global PC grid.

From ITNews:

"The team will use the grid to analyse the results of experiments on proteins using data collected by scientists at the Hauptman-Woodward Medical Research Institute in Buffalo, New York. The researchers estimate that this analysis would take conventional computer systems 162 years to complete. Dr Jurisica anticipates that the analysis could be finished in one to two years..."

Sequence of genome of Fusarium graminearum

From the University of Minnesota News Service http://www1.umn.edu/umnnews/news_details.php?release=070906_3489&page=NS

"Scientists led by a team from the University of Minnesota have sequenced the genome of the fungal
pathogen that causes the deadly grain disease Fusarium Head Blight (FHB). Their findings [were] published in Science (Cuomo et al, "The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization," vol. 317, 7 September 2007, 1400-1402).

The disease can have devastating effects on wheat and barley crops, because it creates toxins that can sicken humans and livestock who consume infected grain. It is one of the most significant plant pathogens worldwide...Fungicides are costly and not always effective.

The FHB pathogen has about 13,000 genes. However, "(because of the sequencing breakthrough), now we can look at the genes in detail, in terms of their ability to allow the pathogen to cause disease and produce toxin," said H. Corby Kistler, an adjunct professor of plant pathology at the U of M and a research geneticist for the U.S.
Department of Agriculture's Agricultural Research Service.

According to Kistler, sequencing the genome will help researchers determine how the disease operates at a genetic level and eventually, how to prevent it. The research could also help fight other plant diseases."

The research was a multinational effort, with the participation of university researchers in Germany, Spain, Netherlands, Austria, UK, Canada, France, and the Ukraine, along with U.S.-based groups (Broad Institute of MIT and Harvard, Purdue, Michigan State, Cornell, Pacific Northwest National Laboratory, St. Louis University, Universities of Arizona and Tennessee, and the USDA). Further analyses of gene products also will prove to be data-intensive.

More e-science at the University of Minnesota

Cedar Creek Natural History Area http://www.cedarcreek.umn.edu/ is an NSF-sponsored Long-Term Ecological Research (LTER) site. There are 4 major themes to this research:

*Theme 1:* What are the impacts of major perturbations -- especially climatic variation, N deposition, land use history, changes in fire frequency, elevated CO2, exotic species, and changes in trophic structure --on species composition, diversity and ecosystem functioning?
*Theme 2:* What processes, interactions and positive and negative feedbacks control species abundances, community assembly, and community composition, diversity and dynamics in Cedar Creek grasslands and savanna?
*Theme 3:* How do composition and biodiversity directly and indirectly impact ecosystem functioning?
*Theme 4:* What general principles allow integration across scales ranging from ecophysiological and population processes to ecosystem functioning; from single trophic levels to whole foodwebs; from single plots to landscapes; and from snapshots in time to long time series?

"We are pursuing these four themes in five inter-related types of long-term studies that form the heart of the Cedar Creek LTER. Each is guided by our research philosophy and each addresses several themes. LTER funding supports this core long-term work and the research infrastructure of Cedar Creek (computer network, analytical chemistry laboratory, herbarium and insect collections, data management and software development, and shared research equipment)."

The Long Term Ecological Research (LTER) Network is a collaborative effort involving more than 1800 scientists and students investigating ecological processes over long time periods and broad geographical scales. The Network promotes synthesis and comparative research across sites and ecosystems and among other related national and international research programs. The 26 sites that constitute the Network represent diverse ecosystems and research emphases. http://www.lternet.edu/

UMN has 11 principal investigators working on the LTER at Cedar Creek, mostly faculty from Ecology, Evolution, and Behavior, with one from Plant Biology and two from Forest Resources. There are a couple dozen additional UMN faculty involved (see http://www.cedarcreek.umn.edu/people/currentstaff.php)

HarvestChoice http://www.harvestchoice.org/ Funded by the Gates Foundation. (Phil Pardey, et al.)

"Over the coming three years, HarvestChoice and its growing number of partners will deliver a series of databases, tools, analyses, findings, and syntheses designed to improve strategic investment and policy decisions. The overriding objective is to accelerate and enhance the performance of those crops and cropping systems most likely to bring significant benefits to the world's poor and undernourished."

There are a several collaborative NSF plant/crop genome mapping research projects involving the University of Minnesota.

Nevin Young (Plant Pathology/Plant Biology) has an NSF grant to sequence the model legume Medicago Truncatula http://www.medicago.org/genome/ Project goals include: Genome Sequencing: Complete, high quality genome sequence for all eight chromosomes of Medicago.

Informatics: An integrated database of clone, map, assembly, and sequence information combined with coordinated, automated annotation of the Medicago genome sequence.
Project Organization: This NSF project is coordinated with partners in the EU who receive funding from the 6th Framework Programme, BBSRC in the UK and ANR in France. EU partners
come from the UK, France, Germany, Netherlands, and Belgium

Ronald Philips (CFANS) has an NSF grant to work on mapping the corn genome http://corn.ccgb.umn.edu/

Goals include:
* To produce an efficient means to map genes of corn, our major cereal crop.
* To implement a system analogous to one used in the mapping of human genes, where special Chinese hamster cell lines containing portions of the human genome are used. We will use oat lines containing portions of the corn genome.
* To complete the series of the 10 different oat-corn chromosome addition lines and, for each chromosome, produce a series of approximately 100 radiation hybrid lines.
* Arrays of DNA samples ultimately will be available to researchers for mapping any gene or DNA fragment to a small region of a given chromosome.

Electronic laboratory notebooks

Declan Butler discusses the development, applications, and advantages of e-notebooks in his article, "A New Leaf" (Nature, vol.436, 7 July 2005, 20-21). An editorial in Nature, dated approximately two years later, further emphasizes the benefits of e-notebooks, but notes that "academic acceptance of e-notebooks will not improve unless universities promote their use and recognize that e-notebooks can help them fulfill their responsibilities as the owners of most grant-funded data...Institutions therefore need to show leadership in this area, and funding agencies should provide additional infrastructure support earmarked for the development and upkeep of electronic notebook systems" (vol.447, 3 May 2007, 1-2).

Pharmaceutical companies routinely use e-notebooks to document their proprietary research; the U. S. Food and Drug Administration accepts e-notebook records during a drug's evaluation and approval processes.

The University of Minnesota provides some guidelines about the 'use of electronic records' in "Guidelines for Maintaining Laboratory Notebooks" (http://www.research.umn.edu/techcomm/licensingcenter/documents/labnotes.pdf); however, the document emphasizes record-keeping in a paper format.

Universities, as well as businesses, continue to develop e-notebook software. A selected list follows, with brief descriptions.

ELN (Electronic Laboratory Notebook) from the EMSL Collaboratory, Pacific Northwest National Laboratory (http://collaboratory.emsl.pnl.gov/software/eln). The software, available for download at the EMSL site, is "a shared web-based version of the traditional paper laboratory notebook. Each notebook page shows data and time-stamped entries that include static information such as text and images, as well as dynamic information ranging from animated GIF images and video clips to rotatable 3-D protein structures and X-Y graphs of spectra that support zoom and other capabilities."

The NeuroSys Project from Montana State University (http://neurosys.cns.montana.edu), "provides a set of easy to use tools for data sharing by the scientific community. Neurosys enables users to construct and store a coherent description of their data, according to the hierarchical organizational scheme that makes the most sense for their specific set of applications; allows users to design and construct their own custom GUI screens for data entry, data query and retrieval, combined with automated links to external analytical software tools; automatically creates a controlled vocabulary, and supports the extension and/or migration of that vocabulary to whatever standard might be chosen at a later date..."

The Smart Tea Project (http://www.smarttea.org), based at the University of Southampton and part of the Combechem eScience Research Initiative. Its "first phase will support the complete life cycle of chemists' interactions with the lab; the next phase will integrate the lab aether with the larger network of chemistry on the grid for shared information services." A related project is the "myTea Project" (http://mytea.org.uk), which focuses on "improving capture of experiments for bioinformatics practitioners."

CERF (Collaborative Electronic Research Framework) - The Electronic Lab Notebook for Biology and Multidisciplinary Life Sciences (http://www.rescentris.com/products.html) developed by Rescentris, Ltd. It is an "enterprise scientific information system designed specifically for managing and sharing information in life sciences research organizations. CERF combines a full-featured electronic lab notebook with scientific content management, and extensible knowledge and data integration framework, and a science-driven informatics platform....The CERF server provides a central management of data storage, system functions, projects, organization of experiments, content, annotations, and rich metadata."

Biometerology and Micrometerology

http://www.biometeorology.umn.edu/Biomet_welcome.php
Heat and mass transfer between the biosphere and atmosphere can have important consequences for the climate system. We use biometeorological techniques to better understand the processes and feedback mechanisms that control heat and mass transfer near the Earth's surface from ecosystem to regional scales. Measurement technologies have been developed that allow rapid and continuous measurement of atmospheric properties, such as turbulence and trace gases, providing an opportunity to answer important questions related to the cycles of energy, water, carbon, and many other scalars.

There is access to real-time data, plus archived data (in cooperation with USDA-Agricultural Research Service).