Bioassay data sets

Is the proper comparator data for evaluating performance human or rodent bioassay data It should be kept in mind that there are sets of rodent bioassay... 

Effects of different C. truncatum and A. cassiae spore concentrations on seedling stem collapse bioassay of hemp sesbania and sicklepod, respectively. Solid lines for each data set = predicted trends for C. truncatum/hemp sesbania and for A. cass/ ae/sicklepod interactions, respectively, based on the exponential decay model described in the text. Triangles = recorded values and closed circles = recorded values for A. cass/ ae/sicklepod and C. truncatum/hemp sesbania, respectively. (From Hoagland, R. E. 1995, Biocontrol Sci. Techno ., 5, 251-259. With permission.)... 

Subsequently, shallow water collections of Lyngbya majuscula from Puerto Rico and the Dry Tortugas yielded additional supplies of ATX as well as a new congener termed antillatoxin B (Figure 6.10) [149]. The structure of the new metabolite was determined largely by comparison with the spectroscopic data set for ATX, and stereochemistry deduced by Marfey s analysis for L-alanine while the i-N-methyl homophenylalanine was proposed based on nuclear Overhauser effect (nOe) and bioassay results. Substitution of i-N-methyl homo-phenylalanine, an intriguing amino acid of quite rare occurrence in natural products, for i-N-methyl valine... 

In addition to automated sample injection, considerable effort has been directed towards the development of automated sample evaluation. The final goal is a set of programs and file formats which accompany a collection of compounds from the automated synthesis via the automated analysis to the final evaluation of a bioassay. In order to minimize time losses incurred by the conversion of files, file formats and software programs must be fully compatible. Data sets should contain complete information about each single compound (structure, HPLC/MS analysis, biological activity, etc.). 

Beyond a summary description, one would like to view, analyze, and display the actual bioassay data. PubChem provides an integrated suite of tools, each presented as an individual tab, for this purpose. One would use the bioactivity summary tool to, at a glance, be able to examine an overview of the bioassays tested for a list of substances or compounds. To be able to subset and analyze substances or compounds tested in a set of bioassays, one would use the structure-activity analysis tool. To view the actual bioassay outcomes, one would use the data table tool. 

Metatree The metatree organizes the metatables for the set of structure collections and research projects into a single hierarchical tree that is a representation of the users natural models of how the data interrelate. The hierarchical relationships may be explicit in the underlying data sources but are often implicit. For example, the Mobius metatree organizes in vitro bioassay data in three alternative views ... 

Figure 13.1 hERG compound data obtained from PubChem BioAssay AID 376. Upper line Conventional hERG blockers. Lower line Atypical hERG blockers which do not contain the conventional pharmacophore of a basic nitrogen, decorated by a set of lipophilic rings, (also see Chapter 16). 

As part of this field study, relevant quality assurance/quality control (QA/QC) criteria and guidelines (SETAC, 1993 JAMP, 1998a,b) have to be set to insure the quality of data generated during the assessments. The development of QA/QC criteria for this study involved conducting a series of replicate bioassays with each of the methods. Samples tested included a control sediment, contaminated sediments and reference toxicants. Based on the results of the bioassay replicates, the variability associated with the tests was quantified and we were able to determine what we considered acceptable QA/QC criteria for these methods. 

---