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8 by windows of the 2DE map, significant changes of the expression patterns can be ascertained at different time points of the fermentation. One of the often encountered difficulties in proteomic analysis with 2-DE is the accurate identification of the spots on the gels. Peptide mass fingerprinting (PMF) by MALDI-TOF MS is the widely used technique for protein identification. This approach relies, however, on the presence of the proteins studied in publicly-accessible protein databases or the availability of annotated genome sequences for the organism.

The classical method of metabolic engineering, alleviating the network bottleneck by enzyme overexpression, has only limited practical success [48]. One possible reason is that the target gene is controlled by other genes, thus more gene copies does not mean more enzyme proteins expressed. The long history of strain improvement practice has shown that modifying the regulatory relationships (reducing or removing the inhibiting or activating effect) is more efficient in screening improved strains for the overproduction of objective products.

FHWA-RD-98-174; April 1999. N. T. Yang, Production of galacto-oligosaccharides from lactose by Aspergillus oryzae E-galactosidase immobilized on cotton cloth, Biotechnol. , 77 (2002) 819. T. M. B. Min, Xanthan gum fermentation by Xanthomonas campestris immobilized in a novel centrifugal fibrous-bed bioreactor, Biotechnol. Progress, 12 (1996) 630637. C. Bro, B. Regenberg, J. Forster, and J. Nielsen, In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production.

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