Chemical Engineering

Nanoparticles dispersed in polymer melts have recently been shown to decrease the bulk viscosity. This contradicts expectations based on Einstein's well-known theory for effective viscosity of dilute, random dispersions of rigid spheres in Newtonian fluids. In this paper, we examine a continuum hydrodynamic model where a layer of polymer at the nanoparticle–polymer interface has a different viscosity and density than the bulk polymer.

Embedding colloidal particles in polymeric hydrogels often endows the polymer skeleton with appealing characteristics for microfluidics and biosensing applications. This theoretical study provides a rigorous foundation for interpreting active electrical microrheology and electroacoustic experiments on such materials. In addition to viscoelastic properties of the composites, these techniques sense physicochemical characteristics of the particle–polymer interface. Wang & Hill (Soft Matter, vol. 4, 2008, p.

In this work we develop the Spectral Ewald Accelerated Stokesian Dynamics (SEASD), a novel computational method for dynamic simulations of polydisperse colloidal suspensions with full hydrodynamic interactions. SEASD is based on the framework of Stokesian Dynamics (SD) with extension to compressible solvents, and uses the Spectral Ewald (SE) method [Lindbo & Tornberg, J. Comput. Phys. 229 (2010) 8994] for the wave-space mobility computation. To meet the performance requirement of dynamic simulations, we use Graphic Processing Units (GPU) to evaluate the suspension mobility, and achieve an order of magnitude speedup compared to a CPU implementation. For further speedup, we develop a novel far-field block-diagonal preconditioner to reduce the far-field evaluations in the iterative solver, and SEASD-nf, a polydisperse extension of the mean-field Brownian approximation of Banchio & Brady [J. Chem. Phys. 118 (2003) 10323]. We extensively discuss implementation and parameter selection str...

To address the need for a bright, photostable labeling tool that allows long-term in vivo imaging in whole organisms, we recently introduced second harmonic generating (SHG) nanoprobes. Here we present a protocol for the preparation and use of a particular SHG nanoprobe label, barium titanate (BT), for in vivo imaging in living zebrafish embryos. Chemical treatment of the BT nanoparticles results in surface coating with amine-terminal groups, which act as a platform for a variety of chemical modifications for biological applications. Here we describe cross-linking of BT to a biotin-linked moiety using click chemistry methods and coating of BT with nonreactive poly(ethylene glycol) (PEG). We also provide details for injecting PEG-coated SHG nanoprobes into zygote-stage zebrafish embryos, and in vivo imaging of SHG nanoprobes during gastrulation and segmentation. Implementing the PROCEDURE requires a basic understanding of laser-scanning microscopy, experience with handling zebrafish ...

Two new geldanamycin derivatives produced by genetic engineering of Streptomyces hygroscopicus strain K309-27-1 were isolated and characterized. Removal of the 8-methyl group of geldanamycin was achieved by replacing the AT4 domain of the polyketide synthase with a malonyl AT domain. The resulting strain produced 8-demethyl geldanamycin (2) and 4,5-epoxy-8-demethylgeldanamycin (3). The structures of both molecules were elucidated through interpretation of 1D and 2D NMR data as well as comparison with authentic geldanamycin derivatives. Compounds 2 and 3 displayed moderate cytotoxicity against the human breast cancer cell line SK-BR-3.

A procedure for the analysis of short-chain intracellular coenzyme A (CoA) esters and adenine nucleotide pools in microbial cells is described. The simultaneous isolation of bacterial cells from media, quenching of their metabolism, and extraction of metabolites was accomplished by centrifugation of cells through a layer of silicone oil into a denser solution of trichloroacetic acid. The acid was neutralized by extraction into Freon containing tri-n-octylamine to provide a salt-free solution of cell metabolites. After high-performance liquid chromotography separation, CoA, CoA esters, and adenine-containing nucleotides were derivatized by postcolumn reaction with bromoacetaldehyde to form the Xuorescent 1,N 6 -ethenoadenine adducts which were analyzed by a Xuorescence detector at picomolar levels. 

Precursor-directed biosynthesis was used to produce different triketide lactones (R-TKLs) in a fermentation process. Plasmids expressing engineered versions of the first subunit of 6-deoxyerythronolide B synthase (DEBS1) fused to the terminal DEBS thioesterase (TE) were introduced into three different Streptomyces strains. The DEBS1 protein fused to TE had either an inactivated ketosynthase domain (KS1°) or a partial DEBS1 lacking module 1 but containing module 2 (M2+TE). Different synthetic precursors were examined for their effect on R-TKL production. An overproducing strain of S. coelicolor expressing the M2+TE protein was found to be best for production of R-TKLs. Racemic precursors were as effective as enantiomerically pure precursors in the fermentation process. The R group on the precursor significantly affected titer (propyl ≫ chloromethyl > vinyl). The R-TKLs were unstable in fermentation broth at pH 6–8. A two-phase fermentation with a pH shift was implemented to stabilize the products. The fermentation pH initially was controlled at optimal values for cell growth (pH 6.5) and then shifted to 5.5 during production. This doubled peak titers and stabilized the product. Finally, the concentration of synthetic precursor in the fermentation was optimized to improve production. A maximum titer of 500 mg/L 5-chloromethyl-TKL was obtained using 3.5 g/L precursor.

Inhibition of the protein chaperone Hsp90 is a promising new approach to cancer therapy. We describe the preparation of potent non-benzoquinone ansamycins. One of these analogues, generated by feeding 3-amino-5-chlorobenzoic acid to a genetically engineered strain of Streptomyces hygroscopicus, shows high accumulation and long residence time in tumor tissue, is well-tolerated upon intravenous dosing, and is highly efficacious in the COLO205 mouse tumor xenograft model.

The bioconversion of a 6-deoxyerythronolide B analogue to the corresponding erythromycin A analogue (R-EryA) by a Saccharopolyspora erythraea mutant lacking the ketosynthase in the first polyketide synthase module was significantly improved by changing fluxes at a key branch point affecting the erythromycin congener distribution. This was achieved by integrating an additional copy of the eryK gene into the chromosome under control of the eryAIp promoter. Real-time PCR analysis of RNA confirmed higher expression of eryK in the resulting strain, S. erythraea K301–105B, compared to its parent. In shake flasks, K301–105B produced less of the shunt product 15-fluoro-erythromycin B (15F-EryB), suggesting a shift in congener distribution toward the desired product, 15-fluoro-erythromycin A (15F-EryA). In bioreactor studies, K301–105B produced 1.3 g/L of 15F-EryA with 75–80% molar yield on fed precursor, compared with 0.9 g/L 15F-EryA with 50–55% molar yield on fed precursor by the parent strain. At higher precursor feed rates, K301–105B produced 3.5 g/L of 15F-EryA while maintaining 75–80% molar yield on fed precursor.

Isolation and Characterization of 7-Hydroxy-6-demethyl-6-deoxy-erythromycin D, a New Erythromycin Analogue, from Engineered Saccharopolyspora erythraea. -(STARKS, C. M.; RODRIGUEZ, E.; CARNEY, J. R.; DESAI, R. P.; CARRERAS, C.; MCDANIEL, R.; HUTCHINSON, R.; GALAZZO, J. L.; LICARI*, P. J.; J. Antibiot. 57 (2004) 1, 64-67; Discovery Res., Kosan Biosciences, Inc., Hayward, CA 94545, USA; Eng.) -M. Schroeter 33-225

A robust high cell-density fed-batch bioprocess was developed for the heterologous production of 6-deoxyerythronolide B (6-dEB), the macrocyclic core of the antibiotic erythromycin, with a recombinant Escherichia coli strain expressing the 6-deoxyerythronolide B synthase (DEBS) from Saccharopolyspora erythraea. Initial evaluation of the E. coli strain in a 5-l bioreactor with the addition of exogenous propionate for polyketide biosynthesis resulted in a maximum cell density of 30 g l −1 (OD 600 ∼ 60) and the production of 700 mg l −1 of 6-dEB. Retention of the two plasmids harboring the heterologous genes was maintained between 90 and 100% even in the absence of antibiotic selection. However, the accumulation of excess ammonia in the culture medium was found to significantly decrease the productivity of the cells. Through optimization of the medium composition and fermentation conditions, the maximum cell density was increased by two-fold, and a final titer of 1.1 g l −1 of 6-dEB was achieved. This represents an 11-fold improvement compared to the highest reported titer of 100 mg l −1 with E. coli as the production host.

A process for the production of erythromycin aglycone analogues has been developed by combining classical strain mutagenesis techniques with modern recombinant DNA methods and traditional process improvement strategies. A Streptomyces coelicolor strain expressing the heterologous 6-deoxyerythronolide B (6-dEB) synthase (DEBS) for the production of erythromycin aglycones was subjected to random mutagenesis and selection. Several strains exhibiting 2-fold higher productivities and reaching >3 g/L total macrolide aglycones were developed. These mutagenized strains were cured of the plasmid carrying the DEBS genes and a KS1° mutant DEBS operon was introduced for the production of novel analogues when supplemented with a synthetic diketide precursor. The strains expressing the mutant DEBS were screened for improved 15-methyl-6-dEB production, and the best clone, strain B9, was found to be 50% more productive as compared to the parent host strain used for 15-methyl-6-dEB production. Strain B9 was evaluated in 5-L fermenters to confirm productivity in a scalable process. Although peak titers of 0.85 g/L 15-methyl-6-dEB by strain B9 confirmed improved productivity, it was hypothesized that the low solubility of 15-methyl-6-dEB limited productivity. The solubility of 15-methyl-6-dEB in water was determined to be 0.25–0.40 g/L, although higher titers are possible in fermentation medium. The incorporation of the hydrophobic resin XAD-16HP resulted in both the in situ adsorption of the product and the slow release of the diketide precursor. The resin-containing fermentation achieved 1.3 g/L 15-methyl-6-dEB, 50% higher than the resin-free process. By combining classical mutagenesis, recombinant DNA techniques, and process development, 15-methyl-6-dEB productivity was increased by over 100% in a scalable fermentation process.

The flow of a viscous fluid on the outside of a partially submerged, rotating horizontal cylinder is one of the basic fundamental coating flows. The main features of this flow for a Newtonian fluid were described by Ckzmpanella and Cerro [Chem. Engng Sci. 39,1443 (1984)]. A rapid flow approximation [Cerro and Striven Ind. Engng Chem. Fun&ma. 19,40 (1980)] IS used to develop a tilm profile equation for a powerlaw type non-Newtonian fluid. The film profile equation allows to compute a unique critical flow regime for each kind of power law fluid characterized by two rheological constants, K and n. Theoretical results are shown to be in very good agreement with experimental results for a wide range of fluid properties.

Fermentation rates and intracellular compositions have been determined for alginate-entrapped Saccharomyces cerevisiae and for identical cells in suspension. Glucose uptake and ethanol and glycerol production are approximately two times faster in immobilized cells than in suspended cells. Phosphorus-31 nuclear magnetic resonance (NMR) spectroscopy of fermenting immobilized and suspended cells shows differences in intermediate metabolite levels such as fructose-1,6 diphosphate, glucose-6-phosphate, and 3-phosphoglycerate and in internal pH. Carbon-13 NMR shows an increase in polysaccharide production. These data suggest that immobilization has accelerated the rate of glucose transport or of glucose phosphorylation. These effects of immobilization upon cell metabolism are observed in a very short period of time under conditions in which negligible DNA, RNA, or protein synthesis takes place.

Estimation of intracellular intermediary metabolite levels is of fundamental importance to characterize cell metabolic processes and their regulation. Usually, intracellular intermediates are determined by stopping the cell metabolism, e.g., by immersing the cell sample in liquid nitrogen, and performing percNoric acid extracts of the cells. The metabolite levels are then obtained either by standard analytical methods'-3 or by using nuclear magnetic resonance (NMR) ~pectroscopy.~*~ Using this technique, it is possible to obtain only one point per sample because the method is destructive. Thus, transient studies are not possible on the same cell sample, and a series of aliquots are required with the assumption that all have the same dynamic behavior and are exposed to the same initial conditions. Also, information on compartmentalization within the cell is lost when extracts are prepared. For example, this prevents differentiation of compounds in the cytoplasm from those in the vacuole in yeast.

Nongrowing Saccharomyces cerevisiae cells previously grown in alginate exhibit ethanol production rates 1.5 times greater than cells previously grown in suspension. Analysis of glucose, ethanol, and glycerol formation data using quasi-steady-state pathway stoichiometry shows that alginate-grown cells possess phosphofructokinase (PFK), ATPase, and polysaccharide synthesis maximum activities which are approximately two-, two-, and ninefold larger, respectively, than in suspension-grown cells. The estimated change in PFK maximum velocity is consistent with in vitro assays of PFK activity in extracts of suspension- and alginate-grown yeast. Estimation of ethanol production flux control coefficients using in vivo nuclear magnetic resonance (NMR) spectroscopy measurements of intracellular metabolite concentrations and a previously proposed detailed kinetic model of ethanol fermentation in yeast shows that glucose uptake dominates flux control in alginate-grown cells in suspension while earlier research revealed that PFK and ATPase exert significant flux control in suspension-grown cells. When placed in a calcium alginate matrix, alginate-grown cells produced ethanol 1.8 times more rapidly and accumulated substantially more polyphosphate than suspension-grown cells placed in alginate. Cells growing in alginate elicit responses at the genetic level which substantially alter pathway rates and flux control when these cells are used as either a suspended or an immobilized biocatalyst. These responses in gene expression to growth in alginate serve to reconfigure flux controls in alginate to a pattern which is similar to that obtained for suspended-grown cells in suspension.

Measurements of rates of glucose uptake and of glycerol and ethanol formation combined with knowledge of the metabolic pathways involved in S. cerevisiae were employed to obtain in vivo rates of reaction catalysed by pathway enzymes for suspended and alginate-entrapped cells at pH 4.5 and 5.5. lntracellular concentrations of substrates and effectors for most key pathway enzymes were estimated from in vivo phosphorus-31 nuclear magnetic resonance measurements. These data show the validity in vivo of kinetic models previously proposed for phosphofructokinase and pyruvate kinase based on in vitro studies. Kinetic representations of hexokinase, glycogen synthetase, and glyceraldehyde 3phosphate dehydrogenase, which incorporate major regulatory properties of these enzymes, are all consistent with the in vivo data. This detailed model of pathway kinetics and these data on intracellular metabolite concentrations allow evaluation of flux-control coefficients for all key enzymes involved in glucose catabolism under the four different cell environments examined. This analysis indicates that alginate entrapment increases the glucose uptake rate and shifts the step most influencing ethanol production from glucose uptake to phosphofructokinase. The rate of ATP utilization in these nongrowing cells strongly limits ethanol production at pH 5.5 but is relatively insignificant at pH 4.5.

APE1 is the major nuclease for excising abasic (AP) sites and particular 39-obstructive termini from DNA, and is an integral participant in the base excision repair (BER) pathway. BER capacity plays a prominent role in dictating responsiveness to agents that generate oxidative or alkylation DNA damage, as well as certain chain-terminating nucleoside analogs and 5fluorouracil. We describe within the development of a robust, 1536-well automated screening assay that employs a deoxyoligonucleotide substrate operating in the red-shifted fluorescence spectral region to identify APE1 endonuclease inhibitors. This AP site incision assay was used in a titration-based high-throughput screen of the Library of Pharmacologically Active Compounds (LOPAC 1280 ), a collection of well-characterized, drug-like molecules representing all major target classes. Prioritized hits were authenticated and characterized via two high-throughput screening assays -a Thiazole Orange fluorophore-DNA displacement test and an E. coli endonuclease IV counterscreen -and a conventional, gel-based radiotracer incision assay. The top, validated compounds, i.e. 6-hydroxy-DL-DOPA, Reactive Blue 2 and myricetin, were shown to inhibit AP site cleavage activity of whole cell protein extracts from HEK 293T and HeLa cell lines, and to enhance the cytotoxic and genotoxic potency of the alkylating agent methylmethane sulfonate. The studies herein report on the identification of novel, small molecule APE1-targeted bioactive inhibitor probes, which represent initial chemotypes towards the development of potential pharmaceuticals. Citation: Simeonov A, Kulkarni A, Dorjsuren D, Jadhav A, Shen M, et al. (2009) Identification and Characterization of Inhibitors of Human Apurinic/apyrimidinic Endonuclease APE1. PLoS ONE 4(6): e5740.