SpotWhatR: a user-friendly microarray data analysis system

SpotWhatR is a user-friendly microarray data analysis tool that runs under a widely and freely available R statistical language (http://www.r-project.org) for Windows and Linux operational systems. The aim of SpotWhatR is to help the researcher to analyze microarray data by providing basic tools for data visualization, normalization, determination of differentially expressed genes, summarization by Gene Ontology terms, and clustering analysis. SpotWhatR allows researchers who are not familiar with computational programming to choose the most suitable analysis for their microarray dataset. Along with well-known procedures used in microarray data analysis, we have introduced a stand-alone implementation of the HTself method, especially designed to find differentially expressed genes in low-replication contexts. This approach is more compatible with our local reality than the usual statistical methods. We provide several examples derived from the Blastocladiella emersonii and Xylella fastidiosa Microarray Projects. SpotWhatR is freely available at http://blasto.iq.usp.br/~tkoide/SpotWhatR, in English and Portuguese versions. In addition, the user can choose between [quot ]single experiment[quot ] and [quot ]batch processing[quot ] versions.

Antitrypanosomal effects of traditional Chinese herbal medicines on bloodstream forms of Trypanosoma brucei rhodesiense in vitro.

The antitrypanosomal activity of traditional Chinese herbal medicines and these crude drug ingredients were determined using axenic cultured bloodstream forms of Trypanosoma b. rhodesiense which is one of the two causative agents of African sleeping sickness in man. The drugs tested were 8 traditional Chinese herbal medicines and these 14 crude drug ingredients. Of these traditional Chinese medicines examined, san'o-shasin-to and oren-gedoku-to showed most potent antitrypanosomal effect. The minimal effective concentration (MEC) which killed all bloodstream form populations within 24 hours of both drug exposure was 125 microg/ml. The 50% effective concentration (EC50) of san'o-shashin-to and oren-gedoku-to was 63 and 74 microg/ml, respectively. In the crude drug ingredients tested, Scutellaria baicalensis G. and Coptis japonica M. which are the main components of san'o-shasin-to and oren-gedoku-to, showed the most powerful antitrypanosomal activity. The MEC and EC50 value of these crude drug ingredients were 30 and 60 microg/ml, and 20 and 36 microg/ml.

Continuous growth of bloodstream forms of Trypanosoma brucei brucei in an axenic culture system containing a low concentration of serum.

An effective axenic culture system for bloodstream forms of Trypanosoma brucei brucei GUT at 3.1 containing a low concentration of serum is described. Bloodstream forms routinely maintained in Iscove's modification of Dulbecco's medium supplemented with 100 microM hypoxanthine, 30 microM thymidine, 40 microM adenosine, 1 mM sodium pyruvate, 50 microM L-glutamine, 100 microM 2-mercaptoethanol and 20% FBS for more than one year were grown in the same medium supplemented with 5% FBS without reducing their growth rate. Then culture adapted trypanosomes in the culture medium containing 5% FBS were transferred into the modified medium supplemented with 0.5% FBS. For the constant growth of bloodstream forms in the medium containing 0.5% FBS, the culture medium was further supplemented with 200 microM L-alanine, 100 microM glycine, 10 microM L-oruithine hydrochloride and 10 microM L-citrullin. The trypanosomes propagated in this culture system for one year retained their infectivity for mice. This culture system was also shown to be useful for cloning of T.b. brucei GUT at 3.1 which is important for separation of mutants.