Biomedical subjects

Oliver Sorgenfrei

Publications and source records attributed to Oliver Sorgenfrei.

3 recordsLinked to original sources

PubMed2005

Laser microdissection in CNS research.

The complexity of the brain makes the investigation of anatomically defined regions using manual dissection techniques problematic. With these manual dissection techniques, only a mixture of many different cell types can be obtained. This leads to averaging the contents of all the different cell types, making it nearly impossible to observe effects that are specific to one type of cell. Laser microdissection enables individual cell-types to be dissected accurately from the brain for subsequent analysis of the genome, proteome or, most frequently, the transcriptome. Investigating only functionally relevant cells with high specificity provides unambiguous data, resulting in faster identification of potential targets, the elucidation of drug mode-of-action, as well as aiding identification of biomarkers for diagnostics use.

Animals↗

PubMed2004

In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome.

An in-depth analysis of the intracellular metabolite concentrations, metabolic fluxes, and gene expression (metabolome, fluxome, and transcriptome, respectively) of lysine-producing Corynebacterium glutamicum ATCC 13287 was performed at different stages of batch culture and revealed distinct phases of growth and lysine production. For this purpose, 13C flux analysis with gas chromatography-mass spectrometry-labeling measurement of free intracellular amino acids, metabolite balancing, and isotopomer modeling were combined with expression profiling via DNA microarrays and with intracellular metabolite quantification. The phase shift from growth to lysine production was accompanied by a decrease in glucose uptake flux, the redirection of flux from the tricarboxylic acid (TCA) cycle towards anaplerotic carboxylation and lysine biosynthesis, transient dynamics of intracellular metabolite pools, such as an increase of lysine up to 40 mM prior to its excretion, and complex changes in the expression of genes for central metabolism. The integrated approach was valuable for the identification of correlations between gene expression and in vivo activity for numerous enzymes. The glucose uptake flux closely corresponded to the expression of glucose phosphotransferase genes. A correlation between flux and expression was also observed for glucose-6-phosphate dehydrogenase, transaldolase, and transketolase and for most TCA cycle genes. In contrast, cytoplasmic malate dehydrogenase expression increased despite a reduction of the TCA cycle flux, probably related to its contribution to NADH regeneration under conditions of reduced growth. Most genes for lysine biosynthesis showed a constant expression level, despite a marked change of the metabolic flux, indicating that they are strongly regulated at the metabolic level. Glyoxylate cycle genes were continuously expressed, but the pathway exhibited in vivo activity only in the later stage. The most pronounced changes in gene expression during cultivation were found for enzymes at entry points into glycolysis, the pentose phosphate pathway, the TCA cycle, and lysine biosynthesis, indicating that these might be of special importance for transcriptional control in C. glutamicum.

Amino Acids↗

PubMed2002

Genome-wide transcription profiling of Corynebacterium glutamicum after heat shock and during growth on acetate and glucose.

To monitor the global gene expression of Corynebacterium glutamicum we established two formats of DNA-arrays on nylon membranes. We produced an ordered DNA-array of PCR fragments from a shotgun library of C. glutamicum representing a threefold coverage of the genome. With this format we studied genome-wide transcriptional changes after heat shock. Sequence and subsequent BLAST analysis of PCR fragments with elevated expression after heat shock revealed PCR fragments harboring genes that encode several proteins of the heat shock family, proteins of the oxidative stress response and proteins with unknown function. DNA-arrays based on PCR fragments representing 2804 annotated ORFs of C. glutamicum were used to monitor the transcript levels during growth on acetate and glucose. We determined minimal detectable ratios and compared labeling approaches with random hexamers and ORF-specific primers. ORF-based DNA-array analysis with different labeling approaches showed similar results: e.g. increased mRNA levels of the pta-ack operon, aceA, aceB and genes encoding phosphoenolpyruvate carboxykinase and enzymes of the citric acid cycle during growth on acetate and elevated mRNA levels of some enzymes of the glycolytic pathway and lactate dehydrogenase upon growth on glucose. These results demonstrate that shotgun DNA-arrays and ORF-based DNA-arrays are appropriate tools to study physiology of microorganism.

Acetates↗