Mathematical modeling and parameters estimation of anaerobic fermentation processes

In the paper some problems of the mathematical modeling of anaerobic (methane) fermentation of animal waste in stirred tank bioreactors are considered. Laboratory experiments are carried out with highly concentrated organic pollutants and transient step responses of the control output for continuous methane fermentation are obtained. The dynamic behavior of this process is described by sets of deterministic nonlinear differential equations from 2nd order with different structures. Static characteristics are obtained with these models analytically. Investigations by computer simulation of the methane fermentation are performed with the aim to chose appropriate models for automatic control system design of this process.     

Mitochondrial and microsomal ferric b5 cytochromes exhibit divergent conformational plasticity in the context of a common fold

Native-state hydrogen-deuterium exchange (HDX) monitored by NMR spectroscopy has been used to compare conformational plasticity in ferric rat liver outer mitochondrial membrane cytochrome b5 (rOM b5) and ferric bovine liver microsomal cytochrome b5 (bMc b5). Analysis of the data indicated that rOM b5 is the less conformationally flexible protein on the time scale probed by the HDX experiments. The data also suggest a likely contributor to the much higher kinetic barrier for the release of hemin from OM b5s in comparison to Mc b5s, a characteristic that may be to a large extent the source of their divergent functional properties. Specifically, the data indicate that conformational mobility within helices alpha4 and alpha5, which flank the loop harboring axial ligand His63, is considerably more restricted in rOM b5 than in bMc b5. The lower conformational flexibility of alpha4 and alpha5 in rOM b5 can reasonably be attributed to more extensive hydrophobic packing in that region of the protein, arising from two conserved side chain packing motifs in OM cytochrome b5s [Altuve, A., Wang, L., Benson, D. R., and Rivera, M. (2004) Biochem. Biophys. Res. Commun. 314, 602-609].     

Biochemical,Cellular, and Biophysical Characterization of a Potent Inhibitor of Mutant Isocitrate Dehydrogenase IDH1

Two mutant forms (R132H and R132C) of isocitrate dehydrogenase 1 (IDH1) have been associated with a number of cancers including glioblastoma and acute myeloid leukemia. These mutations confer a neomorphic activity of 2-hydroxyglutarate (2-HG) production, and 2-HG has previously been implicated as an oncometabolite. Inhibitors of mutant IDH1 can potentially be used to treat these diseases. In this study, we investigated the mechanism of action of a newly discovered inhibitor, ML309, using biochemical, cellular, and biophysical approaches. Substrate binding and product inhibition studies helped to further elucidate the IDH1 R132H catalytic cycle. This rapidly equilibrating inhibitor is active in both biochemical and cellular assays. The (+) isomer is active (IC₅₀ = 68 nm), whereas the (−) isomer is over 400-fold less active (IC₅₀ = 29 μm) for IDH1 R132H inhibition. IDH1 R132C was similarly inhibited by (+)-ML309. WT IDH1 was largely unaffected by (+)-ML309 (IC₅₀ >36 μm). Kinetic analyses combined with microscale thermophoresis and surface plasmon resonance indicate that this reversible inhibitor binds to IDH1 R132H competitively with respect to α-ketoglutarate and uncompetitively with respect to NADPH. A reaction scheme for IDH1 R132H inhibition by ML309 is proposed in which ML309 binds to IDH1 R132H after formation of the IDH1 R132H NADPH complex. ML309 was also able to inhibit 2-HG production in a glioblastoma cell line (IC₅₀ = 250 nm) and had minimal cytotoxicity. In the presence of racemic ML309, 2-HG levels drop rapidly. This drop was sustained until 48 h, at which point the compound was washed out and 2-HG levels recovered.     

Robust compensator control of continuous fermentation processes

The paper deals with the robust compensator control of continuous fermentation processes described by a set of three non-linear differential equations. For the design purposes the non-linear model is transformed into linear one with interval parameters. Robust state space compensator is designed by the internal model principle, which ensures robust step-wise set points asymptotic tracking and external disturbances rejection in the wide working range. The effectiveness of the algorithm designed is performed by computer simulation experiments. An important feature of the proposed algorithms is their robustness over parameter uncertainties in the process models.     

A simple and rapid test for differentiation of aerobic from anaerobic bacteria

A rapid qualitative test is proposed for bacterial respiratory type based on 24 h culturing of bacteria in liquid medium supplemented with a redox indicator: methylene blue or resazurin. Five reference bacterial strains with definite respiratory type as well as nine bacterial isolates from a laboratory digester for methane fermentation were used. Results obtained showed that both indicators can be used for distinction of strict aerobes from other bacterial representatives with definite respiration. In addition, the resazurin is able to differentiate strict anaerobes from microaerophiles and other anaerobes. The main advantages of the methylene blue is that it is a cheap, easily accessible dye, wide-used in microbiological practice and the results obtained with it are more stable over time. It was also noticed that the test with both indicators gave reliable results for the bacterial respiration only when an inoculum up to 48 h old was used.     

Non-iminosugar glucocerebrosidase small molecule chaperones

Small molecule chaperones are a promising therapeutic approach for the Lysosomal Storage Disorders (LSDs). Here, we report the discovery of a new series of non-iminosugar glucocerebrosidase inhibitors with chaperone capacity, and describe their structure activity relationship (SAR), selectivity, cell activity phamacokinetics.