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FEMS Microbiol Lett, 2005, 248(1):93-100

For many microbial processes, the complexity of the metabolisms and the responses to transient and realistic conditions are difficult to capture in mechanistic models. The cells seem to have an innate intelligence that enables them to respond optimally to environmental changes. Some "intelligent" models have therefore been proposed and compared with a mechanistic model for fed-batch cultures of Ralstonia eutropha.

Isoprenoids, also known as terpenoids, are a large and highly diverse class of natural organic chemicals with many functions in plant primary and secondary metabolism. Most are multicyclic structures that differ from one another not only in functional groups but also in their basic carbon skeletons. Isoprenoids are synthesized from common prenyl diphosphate precursors through the action of terpene synthases and terpene-modifying enzymes such as cytochrome P450 monooxygenases. Plant terpenoids are used extensively for their aromatic qualities. They play a role in traditional herbal remedies and are under investigation for antibacterial, antineoplastic, and other pharmaceutical functions. Much effort has been directed toward their production in microbial hosts.

Appl Microbiol Biotechnol,1998, 49(3):258-266

Appl Environ Microbiol, 2006, 72(11):7394-7397

Microbiology, 2001, 147(Pr12):3353-3358

Isolation and identification of granule-associated proteins relevant for poly(3-hydroxyalkanoic acid) biosynthesis in Chromatium vinosum D[J].FEMS MicrobiolLett, 1992, 78(2-3):227-232

24 Aug 2005.

3. Gold Medal (with special acknowledgement from the jury) for the invention of Novel Eco-Friendly Probe For On-Site Determination of Microbial Activity in Biological Waste Water Treatment Systems.

Microbial degradation of polyhydroxyalkanoates[J].

for Marine Microbiology, Germany

Selected recent honours and awards
1. Gold Medal for the production of biodegradable polymer with superior properties from palm kernel oil.

Annu Rev Microbiol, 2002, 56(1):403-432

Polyhydroxyalkanoates (PHAs) constitute a family of natural polyesters that various microorganisms synthesize as intracellular granules to store carbon and reducing equivalents (, , , , ). When nutrient supplies are starved or imbalanced, it is advantageous for microorganisms to store excess nutrients in the form of PHAs for survival at a relatively low maintenance cost. Many microorganisms have evolved the ability to degrade and utilize these storage materials within their cells. PHAs extracted from microbial cells have attractive practical applications, since their properties can be similar to those of polypropylene. Because of their thermoprocessibility, biodegradability, and biocompatibility, they have received much attention as prime candidates for commodity and specialty production of commercial bioplastics ().

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Arch Microbiol, 2000, 174(1-2):42-49

Appl Environ Microbiol, 2009, 75(7):2012-2016

The superiority of intelligent approaches such as the neural and cybernetic methods under realistic conditions points both to the limitations of mechanistic models and to the complexity of cellular responses to environment changes. However, the cybernetic and neural methods also have both weaknesses and strengths, suggesting the possibility of developing intelligent hybrid descriptions that combine more than one kind of intelligent model with a segment of mechanistic modeling. Recent successes with hybrid neural models, i.e. combinations of mechanistic and neural models, indicate the feasibility of a hybrid neural-cybernetic-mechanistic approach for microbial kinetics. While this is the subject of future work, an exploratory analysis [] has provided a road map for the development of such models.

Appl Environ Microbiol, 2014, 80(8):2526-2535

This study has explored the relative merits of cybernetic, neural and mechanistic descriptions of microbial kinetics in terms of their ability to optimize PHB production by R. eutropha in fed-batch cultures. To mimic a large nonideal bioreactor the degree of dispersion of the fermentation broth was set at Pe = 20, shown earlier [] to be the best value.

Appl Microbiol Biotechnol, 2011, 89(5):1423-1433

PhaR from Paracoccus denitrificans functions as a repressor or autoregulator of the expression of genes encoding phasin protein (PhaP) and PhaR itself, both of which are components of polyhydroxyalkanoate (PHA) granules (A. Maehara, S. Taguchi, T. Nishiyama, T. Yamane, and Y. Doi, J. Bacteriol. 184:3992-4002, 2002). PhaR is a unique regulatory protein in that it also has the ability to bind tightly to an effector molecule, PHA polyester. In this study, by using a quartz crystal microbalance, we obtained direct evidence that PhaR binds to the target DNA and poly[(R)-3-hydroxybutyrate] [P(3HB)], one of the PHAs, at the same time. To identify the PhaR amino acid residues responsible for DNA binding, deletion and PCR-mediated random point mutation experiments were carried out with the gene encoding the PhaR protein. PhaR point mutants with decreased DNA-binding abilities were efficiently screened by an in vivo monitoring assay system coupled with gene expression of green fluorescent protein in Escherichia coli. DNA-binding abilities of the wild-type and mutants of recombinant PhaR expressed in E. coli were evaluated using a gel shift assay and a surface plasmon resonance analysis. These experiments revealed that basic amino acids and a tyrosine in the N-terminal region, which is highly conserved among PhaR homologs, are responsible for DNA binding. However, most of the mutants with decreased DNA-binding abilities were unaffected in their ability to bind P(3HB), strongly suggesting that PhaR has two separate domains capable of binding to the target DNA and P(3HB).

Microbiology, 2002, 148(8):2413-2426

To be able to express all the relevant features of a microbial system under different conditions, cybernetic models tend to be quite complex. For instance, Ferraz et al.'s [] model has 53 parameters and 11 dependent variables. Two other difficulties with these models are: (a) the inability to establish a correspondence between the key enzymes in a model and the enzymes in the actual metabolic network and (b) the possibility of more than one cybernetic goal meeting the desired objective equally well.

Appl Environ Microbiol, 2009, 75(14):4668-4675

The assay was highly reproducible when analytical standards dissolved in dodecane were used. This indicates that when the assay is applied to culture extracts, variation observed between replicate samples is due to differences between fermentations rather than some technical aspect of the DPPH assay. Reactions containing different concentrations of monoterpenes could be ranked by calculating the slope of the curve where the reaction rate was linear, and also by directly observing the kinetic plot of the assay (e.g. Figure A). Ideally it would be possible to compare assay results directly to a standard curve, but caution should be exercised here as incubation of dodecane with live microbial cultures may affect the background reaction rate, preventing direct comparison to standards prepared with fresh dodecane. Appropriate pre-testing and controls should therefore always be included, and the reagents used in each experiment (particularly DPPH and dodecane) should be sourced from a single production batch in order to minimise variability (since the ratios of DPPH crystalline forms may be variable between batches and since dodecane may have different background rates between batches). Furthermore, it became more difficult to capture the true initial reaction rate as the concentration of monoterpene increased due to the time lag between reads in the microplate reader. Although different monoterpene concentrations could still be easily ranked simply by observing the raw data, the delay between reads prevented the construction of a linear standard curve other than across a narrow range of concentrations close to the hit identification threshold. In the event that highly reactive monoterpenes or high concentrations prevent the comparison of initial reaction rates, we propose that samples are simply diluted further in dodecane. Alternately, reactions that rapidly run to completion could be ranked according to T50% (the time taken to deplete 50% of the initial concentration of DPPH). Comparison of T50% values is an established method for ranking antioxidant capacities of complex mixtures[].

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