BioQuery: an object framework for building queries to biomedical databases.

SUMMARY: BioQuery is an application that helps scientists automate database searches. Users can build and store queries to public biomedical databases, and receive periodic updates on the results of those queries when new data is available. The application is implemented on a portable object framework that can provide database-searching capability to other applications. This framework is easily extensible, allowing users to develop plug-ins that provide access to new databases. BioQuery thus provides end-users with a complete database searching interface and updating service, and gives developers a toolkit to provide database-searching capability to their applications. AVAILABILITY: Free to all users: http://www.bioquery.org.

Delivering bioinformatics training: bridging the gaps between computer science and biomedicine.

Biomedical researchers have always sought innovative methodologies to elucidate the underlying biology in their experimental models. As the pace of research has increased with new technologies that 'scale-up' these experiments, researchers have developed acute needs for the information technologies which assist them in managing and processing their experiments and results into useful data analyses that support scientific discovery. The application of information technology to support this discovery process is often called bioinformatics. We have observed a 'gap' in the training of those individuals who traditionally aid in the delivery of information technology at the level of the end-user (e.g. a systems analyst working with a biomedical researcher) which can negatively impact the successful application of technological solutions to biomedical research problems. In this paper we describe the roots and branches of bioinformatics to illustrate a range of applications and technologies that it encompasses. We then propose a taxonomy of bioinformatics as a framework for the identification of skills employed in the field. The taxonomy can be used to assess a set of skills required by a student to traverse this hierarchy from one area to another. We then describe a curriculum that attempts to deliver the identified skills to a broad audience of participants, and describe our experiences with the curriculum to show how it can help bridge the 'gap'.

Differential modulation of nucleus accumbens synapses.

The nucleus accumbens (NAcc) is a brain region involved in functions ranging from motivation and reward to feeding and drug addiction. The NAcc is typically divided into two major subdivisions, the shell and the core. The primary output neurons of both of these areas are medium spiny neurons (MSNs), which are quiescent at rest and depend on the relative input of excitatory and inhibitory synapses to determine when they fire action potentials. These synaptic inputs are, in turn, regulated by a number of neurochemical signaling agents that can ultimately influence information processing in the NAcc. The present study characterized the ability of three major signaling pathways to modulate synaptic transmission in NAcc MSNs and compared this modulation across different synapses within the NAcc. The opioid [Met](5)enkephalin (ME) inhibited excitatory postsynaptic currents (EPSCs) in shell MSNs, an effect mediated primarily by micro-opioid receptors. Forskolin, an activator of adenylyl cyclase, potentiated shell EPSCs. An analysis of miniature EPSCs indicated a primarily presynaptic site of action, although a smaller postsynaptic effect may have also contributed to the potentiation. Adenosine and an adenosine A(1)-receptor agonist inhibited shell EPSCs, although no significant tonic inhibition by endogenous adenosine was detected. The effects of these signaling agents were then compared across four different synapses in the NAcc: glutamatergic EPSCs and GABAergic inhibitory postsynaptic currents (IPSCs) in both the core and shell subregions. ME inhibited all four of these synapses but produced a significantly greater inhibition of shell IPSCs than the other synapses. Forskolin produced an increase in transmission at each of the synapses tested. However, analysis of miniature IPSCs in the shell showed no sign of a postsynaptic contribution to this potentiation, in contrast to the shell miniature EPSCs. Tonic inhibition of synaptic currents by endogenous adenosine, which was not observed in shell EPSCs, was clearly present at the other three synapses tested. These results indicate that neuromodulation can vary between the different subregions of the NAcc and between the different synapses within each subregion. This may reflect differences in neuronal interconnections and functional roles between subregions and may contribute to the effects of drugs acting on these systems.

Increase in adenosine sensitivity in the nucleus accumbens following chronic morphine treatment.

There is a growing body of evidence suggesting that the neuromodulator adenosine is involved in drug addiction and withdrawal and that adenosine signaling pathways may offer new targets for therapeutic treatments of addiction. Recent studies have suggested that chronic exposure to drugs of abuse may alter adenosine metabolism in the nucleus accumbens, a brain region critically involved in drug addiction and withdrawal. The present study examined the effects of chronic morphine treatment on the ability of adenosine to inhibit excitatory postsynaptic currents in nucleus accumbens medium spiny neurons. It was found that chronic morphine treatment via subcutaneous implantation of morphine pellets in rats for 1 wk did not alter the level of adenosine-mediated tonic inhibition of nucleus accumbens excitatory synapses. However, chronic morphine treatment did induce a leftward shift in the adenosine dose-response curve, indicating an increase in the sensitivity of synaptic currents to exogenously applied adenosine. This shift was not due to a change in adenosine receptors or their effectors, because chronic morphine treatment had no effect on the dose-response relationship of a nonmetabolized adenosine receptor agonist. When adenosine transport was blocked, the ability of chronic morphine to shift the adenosine dose-response curve was eliminated. These experiments suggest that the increase in the sensitivity of nucleus accumbens synapses to the inhibitory effects of adenosine may be due to a decrease in adenosine transport. The identification of these changes in the adenosine system after chronic drug exposure may help identify new therapeutic strategies aimed at easing withdrawal from opioids.