Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily

The nucleotide binding site (NBS) is a characteristic domain of many plant resistance gene products. An increasing number of NBS-encoding sequences are being identified through gene cloning, PCR amplification with degenerate primers, and genome sequencing projects. The NBS domain was analyzed from 14 known plant resistance genes and more than 400 homologs, representing 26 genera of monocotyledonous, dicotyle-donous and one coniferous species. Two distinct groups of diverse sequences were identified, indicating divergence during evolution and an ancient origin for these sequences. One group was comprised of sequences encoding an N-terminal domain with Toll/Interleukin-1 receptor homology (TIR), including the known resistance genes, N, M, L6, RPP1 and RPP5. Surprisingly, this group was entirely absent from monocot species in searches of both random genomic sequences and large collections of ESTs. A second group contained monocot and dicot sequences, including the known resistance genes, RPS2, RPM1, I2, Mi, Dm3, Pi-B, Xa1, RPP8, RPS5 and Prf. Amino acid signatures in the conserved motifs comprising the NBS domain clearly distinguished these two groups. The Arabidopsis genome is estimated to contain approximately 200 genes that encode related NBS motifs; TIR sequences were more abundant and outnumber non-TIR sequences threefold. The Arabidopsis NBS sequences currently in the databases are located in approximately 21 genomic clusters and 14 isolated loci. NBS-encoding sequences may be more prevalent in rice. The wide distribution of these sequences in the plant kingdom and their prevalence in the Arabidopsis and rice genomes indicate that they are ancient, diverse and common in plants. Sequence inferences suggest that these genes encode a novel class of nucleotide-binding protein

PATRIC: The VBI PathoSystems Resource Integration Center

The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource for selected NIAID priority pathogens, specifically proteobacteria of the genera Brucella, Rickettsia and Coxiella, and corona-, calici- and lyssaviruses and viruses associated with hepatitis A and E. The goal of the project is to provide a comprehensive bioinformatics resource for these pathogens, including consistently annotated genome, proteome and metabolic pathway data to facilitate research into counter-measures, including drugs, vaccines and diagnostics. The project's curation strategy has three prongs: ‘breadth first’ beginning with whole-genome and proteome curation using standardized protocols, a ‘targeted’ approach addressing the specific needs of researchers and an integrative strategy to leverage high-throughput experimental data (e.g. microarrays, proteomics) and literature. The PATRIC infrastructure consists of a relational database, analytical pipelines and a website which supports browsing, querying, data visualization and the ability to download raw and curated data in standard formats. At present, the site warehouses complete sequences for 17 bacterial and 332 viral genomes. The PATRIC website () will continually grow with the addition of data, analysis and functionality over the course of the project

APSTNG: Neutron interrogation for detection of nuclear and CW weapons, explosives, and drugs

A recently developed neutron diagnostic probe system has the potential to satisfy a significant number of van-mobile and fixed- portal requirements for nondestructive verification of sealed munitions and detection of contraband explosives and drugs. The probe is based on a unique associated-particle sealed-tube neutron generator (APSTNG) that interrogates the object of interest with a low-intensity beam of 14-MeV neutrons generated from the deuterium-tritium reaction and that detects the alpha-particle associated with each neutron. Gamma-ray spectra of resulting neutron inelastic scattering and fission reactions identify nuclides associated with all major chemicals in chemical warfare agents, explosives, and drugs, as well as many pollutants and fissile and fertile special nuclear material. Flight times determined from determined from detection times of the gamma-rays and alpha-particles yield a separate tomographic image of each identified nuclide. The APSTNG also forms the basis for a compact fast-neutron transmission imaging system that can be used along with or instead of the emission imaging system; a collimator is not required since scattered neutrons are removed by ``electronic collimation`` (detected neutrons not having the proper flight time to be uncollided are discarded). The small and relatively inexpensive APSTNG exhibits high reliability and can be quickly replaced. Proof-of-concept experiments have been performed under laboratory conditions for simulated nuclear and chemical warfare munitions and for explosives and drugs