[
Journal of the American Society for Information Science,
1995]
This research reports an algorithmic approach to the automatic generation of thesauri for electronic community systems. The techniques used included term filtering, automatic indexing, and cluster analysis. The testbed for our research was the Worm Community System, which contains a comprehensive library of specialized community data and literature, currently in use by molecular biologists who study the nematode worm C. elegans. The resulting worm thesaurus included 2709 researchers' names, 798 gene names, 20 experimental methods, and 4302 subject descriptors. On average, each term had about 90 weighted neighboring terms indicating relevant concepts. The thesaurus was developed as an online search aide. We tested the worm thesaurus in an experiment with six worm researchers of varying degrees of expertise and background. The experiment showed that the thesaurus was an excellent "memory-jogging" device and that it supported learning and serendipitous browsing. Despite some occurrences of obvious noise, the system was useful in suggesting relevant concepts for the researchers' queries and it helped improve concept recall. With a simple browsing interface, an automatic thesaurus can become a useful tool for online search and can assist researchers in exploring and traversing a dynamic and complex electronic community system.
[
MicroPubl Biol,
2019]
Several techniques are available for spatiotemporal control of genome recombination and gene expression in the nematode Caenorhabditis elegans. Here we report a novel tool to combine the powerful FLP-Frt and GAL4-UAS systems to increase their versality and to offer additional levels of control.FLP is an enzyme that catalyzes recombination between two short Frt DNA sequences and is frequently used to excise genomic fragments flanked by Frt sites, thereby either activating or knocking out gene expression, depending on the experimental design (Hubbard, 2014). Recently, we generated multiple strains that stably express FLP in different somatic tissues from single-copy transgenes and demonstrated that they in most cases induce recombination in ~100% of the cells of the expected tissue (Munoz-Jimenez et al., 2017). We subsequently constructed a strain for germline recombination to permanently knock out Frt-flanked genes or exons (Macas-Len and Askjaer, 2018).The GAL4-UAS system is based on the Saccharomyces cerevisiae Gal4p transcription factor and its cognate DNA target called upstream activating sequence (UAS). Typically, this bipartite system includes a series of driver strains expressing GAL4 in specific tissues and one or several strains with an effector gene downstream of UAS repeats. Wang and colleagues from the Sternberg laboratory recently optimized the GAL4-UAS system for C. elegans (cGAL) and reported several tissue-specific cGAL drivers (Wang et al., 2017). Moreover, they have developed a split cGAL toolkit where the DNA binding and activation domains are expressed as individual polypeptides, thereby enabling further fine-tuning of spatiotemporal control: only when and where the two components are co-expressed they will activate the UAS::effector transgene (Wang et al., 2018).