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UNLABELLED: Basic Local Alignment Search Tool, (BLAST) allows the comparison of a query sequence/s to a database of sequences and identifies those sequences that are similar to the query above a user-defined threshold. We have developed a user friendly web application, MULTBLAST that runs a series of BLAST searches on a user-supplied list of proteins against one or more target protein or nucleotide databases. The application pre-processes the data, launches each individual BLAST search on the University of Nevada, Reno's-TimeLogic DeCypher® system (available from Active Motif, Inc.) and retrieves and combines all the results into a simple, easy to read output file. The output file presents the list of the query proteins, followed by the BLAST results for the matching sequences from each target database in consecutive columns. This format is especially useful for either comparing the results from the different target databases, or analyzing the results while keeping the identification of each target database separate. AVAILABILITY: The application is available at the URLhttp://blastpipe.biochem.unr.edu/

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To examine the role of striatal mechanisms in cocaine-induced stereotyped licking, we investigated the acute effects of cocaine on striatal neurons in awake, freely moving rats before and after cocaine administration (0, 5, 10, or 20 mg/kg). Stereotyped licking was induced only by the high dose. Relative to control (saline), cocaine reduced lick duration and concurrently increased interlick interval, particularly at the high dose, but it did not affect licking rhythm. Firing rates of striatal neurons phasically related to licking movements were compared between matched licks before and after injection, minimizing any influence of sensorimotor variables on changes in firing. Both increases and decreases in average firing rate of striatal neurons were observed after cocaine injection, and these changes exhibited a dose-dependent pattern that strongly depended on predrug firing rate. At the middle and high doses relative to the saline group, the average firing rates of slow firing neurons were increased by cocaine, resulting from a general elevation of movement-related firing rates. In contrast, fast firing neurons showed decreased average firing rates only in the high-dose group, with reduced firing rates across the entire range for these neurons. Our findings suggest that at the high dose, increased phasic activity of slow firing striatal neurons and simultaneously reduced phasic activity of fast firing striatal neurons may contribute, respectively, to the continual initiation of stereotypic movements and the absence of longer movements.

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Over a quarter of all eukaryotic genes encode proteins with obscure features that lack currently defined motifs or domains (POFs). Interestingly, most of the differences in gene repertoire among species were recently found to be attributed to POFs. A comparison of the Arabidopsis, rice and poplar genomes reveals that Arabidopsis contains 5069 POFs, of which 2045 have no obvious homologs in rice or poplar and are likely to be involved in species- or phylogenetic-specific functions in Arabidopsis. The study of POFs is an important endeavor that will shed much needed light on the genetic properties that make any given plant species unique. Furthermore, with respect to many species-specific features, such studies show that we seem to be limited in what we can expect to learn from a model plant such as Arabidopsis.

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BACKGROUND: Proteins with obscure features (POFs), which lack currently defined motifs or domains, represent between 18% and 38% of a typical eukaryotic proteome. To evaluate the contribution of this class of proteins to the diversity of eukaryotes, we performed a comparative analysis of the predicted proteomes derived from 10 different sequenced genomes, including budding and fission yeast, worm, fly, mosquito, Arabidopsis, rice, mouse, rat, and human. RESULTS: Only 1,650 protein groups were found to be conserved among these proteomes (BLAST E-value threshold of 10(-6)). Of these, only three were designated as POFs. Surprisingly, we found that, on average, 60% of the POFs identified in these 10 proteomes (44,236 in total) were species specific. In contrast, only 7.5% of the proteins with defined features (PDFs) were species specific (17,554 in total). As a group, POFs appear similar to PDFs in their relative contribution to biological functions, as indicated by their expression, participation in protein-protein interactions and association with mutant phenotypes. However, POF have more predicted disordered structure than PDFs, implying that they may exhibit preferential involvement in species-specific regulatory and signaling networks. CONCLUSION: Because the majority of eukaryotic POFs are not well conserved, and by definition do not have defined domains or motifs upon which to formulate a functional working hypothesis, understanding their biochemical and biological functions will require species-specific investigations.

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