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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 28-37 
    ISSN: 0887-3585
    Keywords: protein evolution ; structure prediction ; information theory ; amino acid substitution ; multiple sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using an information theoretic formalism, we optimize classes of amino acid substitution to be maximally indicative of local protein structure. Our statistically-derived classes are loosely identifiable with the heuristic constructions found in previously published work. However, while these other methods provide a more rigid idealization of physicochemically constrained residue substitution, our classes provide substantially more structural information with many fewer parameters. Moreover, these substitution classes are consistent with the paradigmatic view of the sequence-to-structure relationship in globular proteins which holds that the three-dimensional architecture is predominantly determined by the arrangement of hydrophobic and polar side chains with weak constraints on the actual amino acid identities. More specific constraints are imposed on the placement of prolines, glycines, and the charged residues. These substitution classes have been used in highly accurate predictions of residue solvent accessibility. They could also be used in the identification of homologous proteins, the construction and refinement of multiple sequence alignments, and as a means of condensing and codifying the information in multiple sequence alignments for secondary structure prediction and tertiary fold recognition. © 1996 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 63-67 
    ISSN: 0887-3585
    Keywords: entropy ; thermodynamics ; binding energetics ; translational entropy ; macromolecular interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The loss of translational degrees of freedom makes an important, unfavorable contribution to the free energy of binding. Examination of experimental values suggest that calculation of this entropy using the Sackur-Tetrode equation produces largely overestimated values. Better agreement is obtained using the cratic entropy. Theoretical considerations suggest that the volumes available for the movement of a ligand in solution and in a complex are rather similar, suggesting also that the cratic entropy provides the best estimate of the loss of translational entropy. © 1994 John Wiley & Sons, Inc.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 38-47 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; Bayesian statistics ; amino acid substitution ; information theory ; solvent accessibility ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We introduce a novel Bayesian probabilistic method for predicting the solvent accessibilities of amino acid residues in globular proteins. Using single sequence data, this method achieves prediction accuracies higher than previously published methods. Substantially improved predictions - comparable to the highest accuracies reported in the literature to date - are obtained by representing alignments of the example proteins and their homologs as strings of residue substitution classes, depending on the side chain types observed at each alignment position. These results demonstrate the applicability of this relatively simple Bayesian approach to structure prediction and illustrate the utility of the classification methodology previously developed to extract information from aligned sets of structurally related proteins. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 11 (1969), S. 417-426 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Utilization of n-heptane by a Pseudomonad was studied in pilot-size butch cultures. Optimal pH and temperature were determined by a factorial design and a medium based upon mineral uptake rates was formulated. High cell yields were obtained by volatilizing heptane in the incoming air and thereby achieving good hydrocarbon dispersion. Hydrocarbon carried by effluent gases was recovered and recycled. In cultures where pH is not controlled, decrease in the electrolytic conductivity of the medium was found to be indicative of viable cells and was used in monitoring bacterial propagation. If not checked, increase in salinity in pH controlled cultures was found to affect cell production negatively. Viscosity changes were not very significant. Heptane to aqueous medium ratio was found to affect oxygen supply to the system due to higher dissolved oxygen concentrations associated with hydrocarbons.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 17 (1975), S. 241-251 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A simple mechanism of hydrocarbon uptake by microorganisms is examined. This model considers the presence of micelles of surface active agents as essential for growth of microbial cells on hydrocarbon substrates. Larger hydrocarbon droplets serving as reservoirs may also be present. Experimental results to support the model are presented. The results of others are explained on the basis of this model.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 27 (1985), S. 1512-1515 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 36 (1990), S. 92-96 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Fluctuations in pH and head-space pressure in a fermentor introduce temporary changes in off-gas CO2 concentrations. These changes are quantified using a simple model based on kinetics of CO2 hydration and gas-liquid mass transfer. The model is verified experimentally. An eigenvalue analysis of the model indicates that mass transfer is the parameter which controls the dynamics of CO2 equilibration.
    Additional Material: 4 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 40 (1992), S. 235-246 
    ISSN: 0006-3592
    Keywords: Fed-batch fermentation ; concentration fluctuations ; mixing effects ; Saccharomyces cerevisiae ; circulation time distribution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In production-scale, fed-batch fermentations, feed is often added to a single point at the top of the fermentor, which, combined with poor mixing, results in formation of a “feed zone” rich in nutrients. Frequent exposure of the culture to high concentrations of nutrients in the feed zone for sufficient duration can produce unexpected effects on its performance. The effect of the feed zone was evaluated by conducting aerobic fed-batch fermentations of Saccharomyces cerevisiae with both complex and defined media. The broth was recirculated between a recycle loop and a bench-scale fermentor, and feed was intermittently added into the recycle loop to simulate the circulation of cells through the feed zone. Experiments were carried out for a range of residence times in the recycle loop from 0.5 to 12 min. Biomass yields from the complex-media fermentations were not affected by exposure to high nutrient levels in the recycle loop for residence times up to 12 min. Ethanol consumption was reduced by as much as 50% for residence time in the loop up to 3 min. Very long exposure of yeast cells to excess nutrient levels (12 min) gave acetic acid formation. In a defined medium, the simulated feed zone effect increased biomass yield by up to 10%, but had no effect on ethanol levels. This study indicates that the feed zone effect on biomass yield in yeast fermentation, using complex substrates, will be negligible under fully aerobic conditions.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 26 (1984), S. 1475-1484 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Enzymatic corn starch liquefaction with α-amylase was carried out. Molecular weight distributions of the resulting hydrolysates are presented using aqueous size exclusion chromatographic techniques. It is demonstrated that despite the fact that the enzyme employed reacts in a random endoacting manner, the product distributions are nonrandom. The results are explained in part by a multimerization process whereby the polymeric substrate molecules preferentially associate, forming intermolecular aggregates. These aggregates are either a consequence of the manner in which the material is deposited into the native granular structure of starch or due to intrinsic physical chemical properties of the polysaccharide. In the latter case, the results are shown to correspond to known multimerized amylose, although complete characterization of the polysaccharide is currently not available. The results presented are used to develop a simplified kinetic model of starch liquefaction and shown to simulate the product distributions accurately.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 38 (1991), S. 1203-1209 
    ISSN: 0006-3592
    Keywords: oxygen fluctuations ; cephamycin C ; antibiotics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: An experimental Monte Carlo method was used to study the effect of fluctuations in oxygen concentration on the synthesis of antibiotics by Streptomyces clavuligerus. Air was supplied to the culture in a 2-L fermentor in random cycles following the lognormal distribution in order to model the circulation within large production-scale vessels. Each cycle consisted of air supply for 5 s followed by no aeration for the balance of the cycle time which ranged from 8 to 44 s, with a mean time of 20 s. Comparable experiments were also conducted with constant period cycling of air and with continuous supply of air. The yields of cephamycin C and its precursor, penicillin N, were suppressed by the Monte Carlo simulation of circulation in a large tank, as compared to constant period cycling. The concentration of dissolved oxygen remained at a low, ca. 5% of saturation, for 5-10 h longer during the Monte Carlo experiment than during the periodic aeration experiment. The biosynthetic enzymes, which are sensitive to oxygen levels, were likely affected not only by the mean time of cycling but also by the distribution of the cycles.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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