Use of SELDI MS to discover and identify potential biomarkers of toxicity in InnoMed PredTox: a multi-site, multi-compound study
A serious bottleneck in the drug development pipeline is the inability of current pre-clinical toxicology evaluation methods to predict early on, and with good accuracy, that a drug candidate will have to be removed from development due to toxicology/safety issues. The InnoMed PredTox consortium attempted to address this issue by assessing the value of using molecular profiling techniques (proteomics, transcriptomics, and metabonomics), in combination with conventional toxicology measurements, on decision making earlier in pre-clinical safety evaluation. In this study, we report on the SELDI-TOF-MS proteomics component of the InnoMed PredTox project. In this large scale, multi-site, multi-compound study, tissue and plasma samples from 14-day in vivo rat experiments conducted for 16 hepato- and nephro-toxicants with known toxicology endpoints (including 14 proprietary compounds and 2 reference compounds) were analyzed by SELDI-TOF-MS. We have identified seven plasma proteins and four liver proteins which were shown to be modulated by treatment, and correlated with histopathological evaluations and can be considered potential biomarker candidates for the given toxicology endpoints. In addition, we report on the intra- and inter-site variations observed based on measurements from a reference sample, and steps that can be taken to minimize this variation. Read Article

Impact of adenylyltransferase GlnE on nitrogen starvation response in Corynebacterium glutamicum
Adenylyltransferases regulate glutamine synthetase activity in enterobacteria and actinomycetes such as Streptomyces coelicolor, Mycobacterium tuberculosis and Corynebacterium glutamicum. In this study the effects of a mutation of the glnE gene, coding for adenylyltransferase, on transcriptome and metabolome profiles of C. glutamicum was investigated. As expected, the glnE deletion led to a loss of activity regulation of glutamine synthetase. Astonishingly, additionally the glnE  mutation caused a nitrogen limitation response on the transcript level as well. Interestingly, induction of the nitrogen starvation response in the mutant strain was unusually weak and GlnK was present in adenylylated form even without nitrogen starvation. The results obtained might hint to a moonlighting function of adenylyltransferase and might be explained by protein interaction of adenylyltransferase and an unknown interaction partner of the nitrogen regulatory network. Read Article

Microarray analysis of the moss Physcomitrella patens reveals evolutionarily conserved transcriptional regulation of salt stress and abscisic acid signalling
Regulatory networks of salt stress and abscisic acid (ABA) responses have previously been analyzed in seed plants. Here, we report microarray expression profiles of 439 genes encoding transcription-associated proteins (TAPs) in response to salt stress and ABA in the salt-tolerant moss Physcomitrella patens. Fourteen and 56 TAP genes were differentially expressed within 60 min of NaCl and ABA treatment, respectively, indicating that these responses are regulated at the transcriptional level. Overlapping expression profiles, as well as the up-regulation of ABA biosynthesis genes, suggest that ABA mediates the salt stress responses in P. patens. Comparison to public gene expression data of Arabidopsis thaliana  and phylogenetic analyses suggest that the role of DREB-like, Dof, and bHLH TAPs in salt stress responses have been conserved during embryophyte evolution, and that the function of ABI3-like, bZIP, HAP3, and CO-like TAPs in seed development and flowering emerged from pre-existing ABA and light signalling pathways. Read Article

Transcriptome and proteome analysis of Chinese hamster ovary cells under low temperature and butyrate treatment
Recombinant Chinese hamster ovary (CHO) cells selected for high productivity are capable of secreting immunoglobulin G (IgG) molecules at a level that rivals plasma cells in vivo. Following butyrate treatment at 33 degrees C, further increases in productivity are observed. To better understand the mechanisms by which this increased productivity is incurred, the transcriptional response of an antibody-producing cell line undergoing these treatments was investigated using oligo-DNA microarrays. Using distance calculations, more than 900 genes were identified as kinetically differentially expressed between the butyrate-treated 33 degrees C culture and the untreated culture. Furthermore, transcript levels of the heavy and light chain IgG genes increased following treatment. Using stable isotope labeling (SILAC), the secretion rate of IgG was investigated by tracking the decay of the isotope label upon switching to unlabeled medium. Both treated and untreated cultures exhibited very similar IgG secretion kinetics. In contrast, the intracellular IgG content was found to be elevated following treatment. This result suggests that increased productivity under treatment is attributable to elevated cellular secretory capacity, rather than shorter holding times in the secretory pathway. This hypothesis is further supported by the results of gene set enrichment analysis (GSEA), which revealed that elements of the secretory pathway, including Golgi apparatus, cytoskeleton protein binding and small GTPase-mediated signal transduction are enriched and thus may play a role in the increased recombinant protein production observed under butyrate treatment at 33 degrees C.
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