The EADGENE Microarray Data Analysis Workshop (Open Access publication)

Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays from a direct comparison of two treatments (dye-balanced). While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful in facilitating interaction between scientists with a diverse background but a common interest in microarray analyses

Expresión diferencial de proteínas por rhodobacter capsulatus b10s en respuesta a la presencia de 2,4-dinitrofenol.

Los compuestos nitrofenólicos son utilizados como intermediarios en la producción de fármacos, colorantes, pesticidas, conservantes de la madera y explosivos. El 2,4-dinitrofenol (2,4-DNP) es un compuesto tóxico y persistente considerado contaminante prioritario por la Agencia de Protección Ambiental de los Estados Unidos (EPA). Se ha seleccionado la cepa bacteriana Rhodobacter capsulatus B10S, perteneciente al grupo de las bacterias rojas fotosintéticas (Rhodospirillales), este microorganismo fotorreduce el 2,4-dinitrofenol a 2-amino-4- nitrofenol (ANP) en anaerobiosis, mediante una actividad nitrofenol reductasa que se induce en presencia de nitrofenoles y se reprime en células cultivadas con amonio. El 2,4-DNP es un desacoplante energético que inhibe fuertemente la fijación de nitrógeno en R. capsulatus. De hecho, esta bacteria sólo puede crecer diazotróficamente (condiciones de fijación de nitrógeno), cuando el 2,4-DNP se ha transformado casi en su totalidad en ANP. El objetivo del presente estudio es determinar la expresión diferencial de proteínas (inducción, represión, sobreexpresión) mediante electroforesis bidimensional en R. capsulatus B10S, en presencia de 2,4-DNP, en células cultivadas en amonio y en condiciones daizotróficas

Regulation and Characterization of Two Nitroreductase Genes, nprA and nprB, of Rhodobacter capsulatus

Among photosynthetic bacteria, strains B10 and E1F1 of Rhodobacter capsulatus photoreduce 2,4-dinitrophenol (DNP), which is stoichiometrically converted into 2-amino-4-nitrophenol by a nitroreductase activity. The reduction of DNP is inhibited in vivo by ammonium, which probably acts at the level of the DNP transport system and/or physiological electron transport to the nitroreductase, since this enzyme is not inhibited by ammonium in vitro. Using the complete genome sequence data for strain SB1003 of R. capsulatus, two putative genes coding for possible nitroreductases were isolated from R. capsulatus B10 and disrupted. The phenotypes of these mutant strains revealed that both genes are involved in the reduction of DNP and code for two major nitroreductases, NprA and NprB. Both enzymes use NAD(P)H as the main physiological electron donor. The nitroreductase NprA is under ammonium control, whereas the nitroreductase NprB is not. In addition, the expression of the nprB gene seems to be constitutive, whereas nprA gene expression is inducible by a wide range of nitroaromatic and heterocyclic compounds, including several dinitroaromatics, nitrofuran derivatives, CB1954, 2-aminofluorene, benzo[a]pyrene, salicylic acid, and paraquat. The identification of two putative mar/sox boxes in the possible promoter region of the nprA gene and the induction of nprA gene expression by salicylic acid and 2,4-dinitrophenol suggest a role in the control of the nprA gene for the two-component MarRA regulatory system, which in Escherichia coli controls the response to some antibiotics and environmental contaminants. In addition, upregulation of the nprA gene by paraquat indicates that this gene is probably a member of the SoxRS regulon, which is involved in the response to stress conditions in other bacteria