The PlaNet Consortium: A Network of European Plant Databases Connecting Plant Genome Data in an Integrated Biological Knowledge Resource

The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network. Objectives are the implementation of infrastructure and data sources to capture plant genomic information into a comprehensive, integrated platform. This will facilitate the systematic exploration of Arabidopsis and other plants. New methods for data exchange, database integration and access are being developed to create a highly integrated, federated data resource for research. The connection between the individual resources is realized with BioMOBY. BioMOBY provides an architecture for the discovery and distribution of biological data through web services. While knowledge is centralized, data is maintained at its primary source without a need for warehousing. To standardize nomenclature and data representation, ontologies and generic data models are defined in interaction with the relevant communities.Minimal data models should make it simple to allow broad integration, while inheritance allows detail and depth to be added to more complex data objects without losing integration. To allow expert annotation and keep databases curated, local and remote annotation interfaces are provided. Easy and direct access to all data is key to the project

The impact of free convection on late morning ozone decreases on an Alpine foreland mountain summit

Exceptional patterns in the diurnal course of ozone mixing ratio at a mountain top site (998 m a.s.l.) were observed during a field experiment (September 2005). They manifested themselves as strong and sudden decreases of ozone mixing ratio with a subsequent return to previous levels. The evaluation of corresponding long-term time series (2000–2005) revealed that such events occur mainly during summer, and affect the mountain top site on about 18% of the summer days. Combining (a) surface layer measurements at mountain summit and at the foot of the mountain, (b) in-situ (tethered balloon) and remote sensing (SODAR-RASS) measurements within the atmospheric boundary layer, the origin of these events of sudden ozone decrease could be attributed to free convection. The free convection was triggered by a rather frequently occurring wind speed minimum around the location of the mountain

Conference Review The PlaNet consortium: a network of European plant databases connecting plant genome data in an integrated biological knowledge resource

Abstract The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network. Objectives are the implementation of infrastructure and data sources to capture plant genomic information into a comprehensive, integrated platform. This will facilitate the systematic exploration of Arabidopsis and other plants. New methods for data exchange, database integration and access are being developed to create a highly integrated, federated data resource for research. The connection between the individual resources is realized with BioMOBY. BioMOBY provides an architecture for the discovery and distribution of biological data through web services. While knowledge is centralized, data is maintained at its primary source without a need for warehousing. To standardize nomenclature and data representation, ontologies and generic data models are defined in interaction with the relevant communities. Minimal data models should make it simple to allow broad integration, while inheritance allows detail and depth to be added to more complex data objects without losing integration. To allow expert annotation and keep databases curated, local and remote annotation interfaces are provided. Easy and direct access to all data is key to the project

Protocolos de Micropropagação de Plantas. I-Batata.

bitstream/item/44084/1/documento-317.pd

Micropropagação de batata 'BRS Ana': produção de material básico com alta sanidade.

bitstream/item/60642/1/CIRCULAR-118.pd

Direct Formation of Supermassive Black Holes via Multi-Scale Gas Inflows in Galaxy Mergers

Observations of distant bright quasars suggest that billion solar mass supermassive black holes (SMBHs) were already in place less than a billion years after the Big Bang. Models in which light black hole seeds form by the collapse of primordial metal-free stars cannot explain their rapid appearance due to inefficient gas accretion. Alternatively, these black holes may form by direct collapse of gas at the center of protogalaxies. However, this requires metal-free gas that does not cool efficiently and thus is not turned into stars, in contrast with the rapid metal enrichment of protogalaxies. Here we use a numerical simulation to show that mergers between massive protogalaxies naturally produce the required central gas accumulation with no need to suppress star formation. Merger-driven gas inflows produce an unstable, massive nuclear gas disk. Within the disk a second gas inflow accumulates more than 100 million solar masses of gas in a sub-parsec scale cloud in one hundred thousand years. The cloud undergoes gravitational collapse, which eventually leads to the formation of a massive black hole. The black hole can grow to a billion solar masses in less than a billion years by accreting gas from the surrounding disk.Comment: 26 pages, 4 Figures, submitted to Nature (includes Supplementary Information

MIPS: analysis and annotation of proteins from whole genomes in 2005

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein–protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server ()

Observation of Multi-Tev Diffuse Gamma Rays from the Galactic Plane with the Tibet Air Shower Array

Data from the Tibet-III air shower array (with energies around 3 TeV) and from the Tibet-II array (with energies around 10 TeV) have been searched for diffuse gamma rays from the Galactic plane. These arrays have an angular resolution of about 0.9 degrees. The sky regions searched are the inner Galaxy, 20 degrees <= l <= 55 degrees, and outer Galaxy, 140 degrees <= l <= 225 degrees, and |b| <= 2 degrees or <= 5 degrees. No significant Galactic plane gamma-ray excess was observed. The 99% confidence level upper limits for gamma-ray intensity obtained are (for |b| <= 2 degrees) 1.1 times 10^{-15} cm^{-2}s^{-1}sr^{-1}MeV^{-1} at 3 TeV and 4.1 times 10^{-17} cm^{-2}s^{-1}sr^{-1}MeV^{-1} at 10 TeV for the inner Galaxy, and 3.6 times 10^{-16} cm^{-2}s^{-1}sr^{-1}MeV^{-1} at 3 TeV and 1.3 times 10^{-17} cm^{-2}s^{-1}sr^{-1}MeV^{-1} at 10 TeV for the outer Galaxy, assuming a differential spectral index of 2.4. The upper limits are significant in the multi-TeV region when compared to those from Cherenkov telescopes in the lower energy region and other air shower arrays in the higher energy region; however, the results are not sufficient to rule out the inverse Compton model with a source electron spectral index of 2.0.Comment: 22 pages, 8 figures, Accepted for publication in Ap

Fitting the Gamma-Ray Spectrum from Dark Matter with DMFIT: GLAST and the Galactic Center Region

We study the potential of GLAST to unveil particle dark matter properties with gamma-ray observations of the Galactic center region. We present full GLAST simulations including all gamma-ray sources known to date in a region of 4 degrees around the Galactic center, in addition to the diffuse gamma-ray background and to the dark matter signal. We introduce DMFIT, a tool that allows one to fit gamma-ray emission from pair-annihilation of generic particle dark matter models and to extract information on the mass, normalization and annihilation branching ratios into Standard Model final states. We assess the impact and systematic effects of background modeling and theoretical priors on the reconstruction of dark matter particle properties. Our detailed simulations demonstrate that for some well motivated supersymmetric dark matter setups with one year of GLAST data it will be possible not only to significantly detect a dark matter signal over background, but also to estimate the dark matter mass and its dominant pair-annihilation mode.Comment: 37 pages, 16 figures, submitted to JCA