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  • 1990-1994  (252)
  • 1985-1989
  • 1890-1899
  • 1880-1889
  • 1993  (252)
  • Biochemistry  (180)
  • Life Sciences
  • 1
    ISSN: 1432-0533
    Keywords: Canine galactosialidosis ; Morphology ; Biochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary An adult-onset lysosomal storage disorder was diagnosed in a 5-year-old Schipperke dog with progressive cerebellar and central vestibular signs. It was characterized by cerebellar atrophy with extensive loss of Purkinje and granular cells, and hydrocephalus. Enlarged and vacuolated neurons were observed in spinal cord and brain; pancreatic centrolobular and islet cells were also vacuolated. Ultrastructurally, enlarged secondary lysosomes laden with lamellated membrane structures were present in neurons and empty enlarged vacuoles were found in pancreatic centroacinar, ductal, and islet cells. On frozen sections neurons stained with Ricinus communis agglutinin-I and wheat germ agglutinin. On paraffin sections neurons stained with luxol fast blue, periodic acid-Schiff, Concanavalia ensiformis agglutinin, and were autofluorescent. These findings indicate an accumulation of glycolipids containing terminal β-galactosyl and α-sialyl residues, and N-linked oligosaccharides. Tissue activity of lysosomal β-galactosidase was 50% of normal and the activity of β-hexosaminidase was elevated. Brain lipid-bound sialic acid was twice normal, with a small increase of GM1-ganglioside, but there was a significant elevation of GM2 (GD2) and GM3 (GD3). In addition, significant elevations of sialylated and non-sialylated oligosaccharides were noted. These clinical, biochemical and pathological findings are similar to those observed in human patients with adult-onset galactosialidosis.
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  • 2
    ISSN: 1432-0878
    Keywords: Gap junction ; Cell junction ; Immunocytochemistry ; Biochemistry ; Heliothis virescens (Insecta)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Subcellular fractions enriched in gap junctions with an ultrastructure similar to those in intact insect tissue have been obtained by extracting crude membranes from the tobacco budworm Heliothis virescens (Lepidoptera: Noctuidae) with 2.5 mM NaOH. n-Octyl-β-d-glucopyranoside (OG) was used to further purify integral membrane proteins in the NaOH-extracted fractions. A polyclonal antibody (R16) is described that specifically labels nonextracted and NaOH-extracted gap junctions in cell fractions by electron microscope immunocytochemistry. R16 immunostaining of sectioned Heliothis testis at the light-microscope level yields a pattern of immunoreactivity consistent with the distribution of gap junctions in the tissue. R16 identifies a 40-kDa protein as a candidate gap junction protein on immunoblots of crude membrane, NaOH-extracted and NaOH/OG-extracted fractions.
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    The @Anatomical Record 235 (1993), S. 611-621 
    ISSN: 0003-276X
    Keywords: Peroxidase ; Parotid gland ; Salivary gland ; Rat ; Growth and development ; Biochemistry ; Cytochemistry ; Ultrastructure ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The course of development of salivary peroxidase, an enzyme that has an important role in oral defense mechanisms, has been well documented in rat submandibular glands. However, the only report on salivary peroxidase activity in the other major salivary glands of the rat has been a cytochemical study of the adult parotid gland. In the present investigation, the accumulation of salivary peroxidase activity in developing parotid glands of rats was followed both biochemically and cytochemically. Specific activity (units per mg protein) attributable to salivary peroxidase began at 1 day after birth, then rose rapidly but unevenly, with peaks at 21 and 70 days, and no difference between the sexes at any age. Activity per gland increased progressively to 42 days in both sexes and was significantly higher in males at 70 days. The cytochemical observations on peroxidase activity localized to the rough endoplasmic reticulum and secretory granules of the developing acini were well correlated with the biochemical findings. Peroxidase-negative cells occurred in immature acini at 1 and 7 days, but only in the intercalated ducts thereafter. This observation suggests that the acini are a source of some of the ductal cells, at least during early postnatal development. The developmental pattern of specific activity differed from those of other rat parotid secretory enzymes, indicating that control of their synthesis during development is noncoordinate. The patterns of specific activity of the parotid and submandibular glands were complementary, suggesting that their combined secretions may supply biologically significant peroxidase activity to the oral cavities of rats throughout postnatal development. © 1993 Wiley-Liss, Inc.
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  • 4
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 237-245 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The affinity of a ligand for a receptor is usually expressed in terms of the dissociation constant (Ki) of the drug-receptor complex, conveniently measured by the inhibition of radioligand binding. However, a ligand can be an antagonist, a partial agonist, or a full agonist, a property largely independent of its receptor affinity. This property can be quantitated as intrinsic activity (1A), which can range from 0 for a full antagonist to 1 for a full agonist. Although quantitative structure-activity relationship (QSAR) methods have been applied to the prediction of receptor affinity with considerable success, the prediction of IA, even qualitatively, has rarely been attempted. Because most traditional QSAR methods are limited to congeneric series, and there are often major structural differences between agonists and antagonists, this lack of success in predicting IA is understandable. To overcome this limitation, we used the method of comparative molecular field analysis (CoMFA), which, unlike traditional Hansch analysis, permits the inclusion of structurally dissimilar compounds in a single QSAR model. A structurally diverse set of 5-hydroxytryptamine1A (5-HT1A) receptor ligands, with literature IA data (determined by the inhibition of 5-HT sensitive forskolin-stimulated adenylate cyclase), was used to develop a 3-D QSAR model correlating intrinsic activity with molecular structure properties of 5HT1A receptor ligands. This CoMFA model had a crossvalidated r2 of 0.481, five components and final conventional r2 of 0.943. The receptor model suggests that agonist and antagonist ligands can share parts of a common binding site on the receptor, with a primary agonist binding region that is also occupied by antagonists and a secondary binding site accommodating the excess bulk present in the sidechains of many antagonists and partial agonists. The CoMFA steric field graph clearly shows that agonists tend to be “flatter” (more coplanar) than antagonists, consistent with the difference between the 5-HT1A agonist and antagonist pharmacophores proposed by Hibert and coworkers. The CoMFA electrostatic field graph suggests that, in the region surrounding the essential protonated aliphatic amino group, the positive molecular electrostatic potential may be weaker in antagonists as compared to agonists. Together, the steric and electrostatic maps suggest that in the secondary binding site region increased hydrophobic binding may enhance antagonist activity. These results demonstrate that CoMFA is capable of generating a statistically crossvalidated 3-D QSAR model that can successfully distinguish between agonist and antagonist 5-HT1A ligands. To the best of our knowledge, this is the first time this or any other QSAR method has been successfully applied to the correlation of structure with IA rather than potency or affinity. The analysis has suggested various structural features associated with agonist and antagonist behaviors of 5-HT1A ligands and thus should assist in the future design of drugs that act via 5-HT1A receptors. © 1993 John Wiley & Sons, Inc.
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  • 6
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 30-36 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We consider the tree search problem for the recurrence relation that appears in the evaluation of molecular integrals over Cartesian Gaussian basis functions. A systematic way of performing tree search is shown. By applying the result of tree searching to the LRL2 method of Lindh, Ryu, and Liu (LRL) (J. Chem. Phys., 95, 5889 1991), which is an auxiliary function-based method, we obtain significant reductions of the floating point operations (FLOPS) counts in the K4 region. The resulting FLOPS counts in the K4 region are comparable up to [dd|dd] angular momentum cases to the LRL1 method of LRL, currently the method requiring least FLOPS for [dd|dd] and higher angular momentum basis functions. For [ff|ff], [gg|gg], [hh|hh], and [ii|ii] cases, the required FLOPS are 24, 40, 51, and 59%, respectively, less than the LRL1 method in the K4 region. These are the best FLOPS counts available in the literature for high angular momentum cases. Also, there will be no overhead in either the K2 or K0 region in implementing the present scheme. This should lead to more efficient codes of integral evaluations for higher angular momentum cases than any other existing codes. © 1993 John Wiley & Sons, Inc.
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  • 7
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 19-29 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is proposed to perform computer simulations of protein dynamics in the long-time regime. The method is based upon a Monte Carlo technique. The only molecular degrees of freedom considered are bond rotations. All other degrees of freedom including the amide plane torsions are kept rigid. These constraints approximately account for all interactions related to chemical bonding. An individual Monte Carlo step adopts the Go and Scheraga algorithm where local conformational changes in a small window of the protein backbone are performed. By using correlated rotations, the conformation of residues outside the window remains invariant. To test the reliability of the method, the nonbonded interactions are turned off in the present application. Exact statistical averages are compared with values obtained from data of computer simulation involving 2 × 106 scans of the window along the protein backbone. Time is related to the number of scans of the window along the protein backbone. End-to-end distance autocorrelation functions decay to 1/e of its initial value in about 103-104 scans of the window algorithm. Time decay follows a stretched exponential Kohlrausch decay law. © 1993 John Wiley & Sons, Inc.
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  • 8
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 45-53 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The antitumor drug cis-diamminedichloroplatinum(II) (cisplatin) binds preferentially to GpG and ApG sequences of DNA, forming N7,N7 intrastrand chelates. Molecular modeling of the intrastrand adducts have been handicapped, so far, by the lack of force-field data describing the Pt-guanine and Pt-adenine binding. We used ab initio calculations with relativistic pseudopotentials to evaluate three important parameters for the platinum-adenine model complex [Pt(NH3)3(Ade)]2+: (1) the force constant for the Pt—N7 bond bending out of the adenine plane; (2) the energy profile for the torsion about Pt—N7; (3) a set of fractional atomic charges that reproduce the ab initio potential for a number of space points placed around the adduct. A population analysis and comparative study on the tetrammine complex [Pt(NH3)4]2+ have shown that for platinum adenine is a better σ-donor than NH3, but its capacity as a π-acceptor is weak. © 1993 John Wiley & Sons, Inc.
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  • 9
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 422-437 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure is reported for the prediction of dense crystal structures of C-, H-, N-, O-, and F-containing organic compounds in the primitive triclinic, monoclinic, and orthorhombic space groups with Z ≤ 4. The crystal environments of molecules in 242 crystal structures have been analyzed to determine the common coordination sphere pattens. This led to the development of the MOLPAK (MOLecular PAcKing) program, which uses a rigid-body molecular structure probe to build packing arrangements (possible crystal structures) in the various space groups. A MOLPAK search, which involves the investigation of all unique orientations of a central molecule and the construction of the appropriate coordination patterns about the central molecule, provides a 3-D map of minimum unit cell volume as a function of the orientation of the central molecule. MOLPAK uses a repulsion-only potential and a preset threshold to place molecules in contact with each other. The 5-10 smallest volume packing arrangements from a search are subjected to a lattice energy minimization refinement with the WMIN program to yield possible crystal structures. The results are described from the analyses of several known compounds starting with the crystal molecular structures as the MOLPAK search probes in the P1, P21, P21/c, and P212121 space groups. In addition, several examples are given in which the search probes were created by AM1 geometry optimization of preliminary molecular models. More extensive data are given in supplementary tables. © 1993 John Wiley & Sons, Inc.
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  • 10
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 312-329 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long-range nonbonded Coulomb and Lennard-Jones interactions, generation of the pairlist, intramolecular bond, angle, dihedral, 1-4 nonbonded interaction terms, coordinate restraints, and the SHAKE bond constraint algorithm. As far as we can determine, this is the first published description where a distributed-memory MIMD parallel implementation of the SHAKE algorithm has been designed to treat not only hydrogen-containing bonds but also all heavy-atom bonds, and where “shaken” crosslinks are supported as well. We discuss the subtasking and partitioning of an MD time-step, load balancing the nonbonded evaluations, describe in algorithmic detail how parallelization of SHAKE was accomplished, and present speedup, efficiency, and benchmarking results achieved when this hypercube adaptation of the MD module AMBER was applied to several variant molecular systems. Results are presented for speedup and efficiency obtained on the nCUBE machine, using up to 128 processors, as well as benchmarks for performance comparisons with the CRAY YMP and FPS522 vector machines. © 1993 John Wiley & Sons, Inc.
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  • 11
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    Journal of Computational Chemistry 14 (1993), S. 349-352 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report the development of a new approximate method of calculating molecular surface areas. Our technique is based upon the method of Sharake and Rupley but incorporates several major advances. First, we represent the state of surface points as bits in a bit string so we can utilize Boolean operations to simultaneously turn off multiple test points in one Boolean AND operation. Second, we use a series of Boolean mask look-up tables to reduce the time complexity of the calculation of molecular surface area down to the same magnitude as doing a potential energy evaluation. When we use a 256 surface point sphere for all of the atoms in BPTI, a 454 nonhydrogen atom protein, and a 1.4-Å solvent probe, we in general underestimate the total solvent-accessible surface area (SASA) by approximately 1.25% with a correlation coefficient of 0.9990 over a wide range of conformations. The average CPU time required to calculate the SASA of a BPTI conformer is 0.58 s on an SGI 4D/220 workstation. We also describe a method by which we can calculate an approximate finite difference SASA gradient for BPTI in 0.79 of CPU time. © 1993 John Wiley & Sons, Inc.
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  • 12
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 378-378 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 13
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 728-735 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is proposed for calculating the forces in path integral theory and tested on semiclassic systems. It takes the range of the classic and quantum interactions into account and uses a second table within the neighbors table for the nearest neighbors. This method is found to be much more efficient than either the standard direct method or the traditional neighbors table, the efficiency increasing with the size of the system. The method can also be applied to clusters whose interaction centers are much farther apart than the distances between two consecutive members of the cluster. © 1993 John Wiley & Sons, Inc.
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  • 14
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 15
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 445-451 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parallelization of the SCF method for closed-shell molecules on the highly parallel transputer-based system PARAM is described. The parallelization has been implemented on three different hardware and software environments: (1) a network of bare 64 transputers; (2) configuration 1 plus a back-end file system (BFS); and (3) configuration 2 with one INTEL i860 processor. The evaluation of electron repulsion integrals (ERIs) and setting up of the Fock matrix is carried out in parallel on 64 nodes using minimal communication strategies. A good load balance is achieved for ERI evaluation with the help of bounds, local symmetry features, and the shell concept, as well as a data randomization technique, resulting into almost linear speedup (for ERI evaluation). In configurations 2 and 3, BFS is used for parallel storage and retrieval of ERIs. Further, in 3 matrix operations are implemented as remote procedure calls on the i860 processor. Routine techniques of level shifting and extrapolation are used for accelerating SCF convergence. The resulting package, INDMOL, has been tested for some randomly selected molecules having up to 255 contractions. Using configuration 3, a factor of 2 to 5 in computation time is obtained over 1, for the systems for which the ERIs cannot be stored in the distributed core memory. In summary, a heterogeneous system, as in configuration 3, can indeed be optimally exploited for programming peculiar diverse requirements of the SCF procedure. © 1993 John Wiley & Sons, Inc.
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  • 16
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 471-477 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: One of the features of the polypeptide backbone is that it represents a flexible chain that contains almost rigid CO—NH peptide bonds. One may try to substitute one or more such bonds by another relatively rigid unit to maintain the overall conformational properties of the backbone and at the same time modify some other properties of the molecule (“pseudopeptide”), such as the ability to form hydrogen bonds. By a detailed conformational analysis, it is shown that the carbon—carbon double bond is quite isosteric with the peptide bond and for this reason suitable for such a substitution. This is accomplished by applying molecular mechanics in calculation of the φ, ψ maps for pseudopeptide analogs of the N-acetyl-Ala-NHMe molecule. © 1993 John Wiley & Sons, Inc.
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  • 17
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 510-521 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present analytical expressions to calculate the gradient of the water-accessible surface area of proteins with respect to Cartesian coordinates and dihedral angles. A detailed mathematical analysis leads to corrected equations for the gradient calculation used previously in the ANAREA program. To study the hydrophobic effect of solvent-protein interactions, our expressions have been implemented to further improve the program package FANTOM. We used this version of FANTOM to minimize the ECEPP/2 and the hydrophobic energy of tendamistat. © 1993 John Wiley & Sons, Inc.
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  • 18
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    Journal of Computational Chemistry 14 (1993), S. 530-540 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electrostatic potentials of 21 molecules containing different functional groups has been computed at the ab initio RHF/6-31G* level on a series of solvent accessible surfaces and compared with MNDO, AM1, and PM3-derived pontentials. We analyzed in detail the distribution of electrostatic potentials on the surfaces around their maximum and minimum values and found out that consistently MNDO gives results similar to ab initio potentials. The actual values of the MNDO electrostatic potentials show a systematic deviation from the “correct” results, but the pattern of the MEP distribution on the surface is similar to that of the ab initio results. In contrast, PM3 fails in some cases to give even the correct number or distribution of “hot spots” of potential (low MEP) on the surface. AM1 behaves somewhere between these two semiempirical methods. As a conclusion, MNDO would be suggested as the best approach to analyses requiring a fast and efficient mapping of electrostatic potentials on simplified models of molecular surfaces. © 1993 John Wiley & Sons, Inc.
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  • 19
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    Journal of Computational Chemistry 14 (1993), S. 556-565 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe, test, and apply a new computational algorithm for generating protein loop conformations subject to distance and secondary structure constraints. The algorithm is based upon initial scaling and subsequent relaxation of covalent bond lengths. The scaling-relaxation procedure needs no additional energy terms and can be readily incorporated into existing molecular modeling packages. The algorithm uses an all-atom energy function from the outset in a straightforward way so that about 60% of the generated loop conformations are free of severe distortions of covalent bond lengths and angles. An extensive application to the major loop conformations of TFIIIA-type zinc fingers (Zif268 and ADR1) is presented, as well as preliminary calculations on hypervariable loops of two immunoglobulins (MCPC603 and Bence-Jones). © 1993 John Wiley & Sons, Inc.
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  • 20
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 928-933 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new index suitable for computing molecular similarity based upon the similarity of molecular properties such as electrostatic potentials or electrostatic fields is presented in two forms. For one form of the present index, general conditions are established for which a linear measure of similarity is obtained. An illustrative example is provided in which the electrostatic field and electrostatic potential of guanine obtained from different wave functions are compared. © 1993 John Wiley & Sons, Inc.
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  • 21
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    Journal of Computational Chemistry 14 (1993), S. 934-943 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using the MM2-87 program and parameter set, conformational analyses have been performed on cocaine (1), the potent analog 2β-carbomethoxy-3β-(4-fluorophenyl)tropane (CFT, 2), and a group of dopamine reuptake blockers that contain two phenyl rings. The latter includes LU 19-005 (3), a 1-amino-4-phenyltetralin (4), a hexahydropyrrolo[2,1-a]isoquinoline (5), diclofensine (6), and a hexahydro[1,2-b]pyridine (7). Using different values for the dielectric constant, the global minimum of 1 and 2 is a conformer in which there is a favorable electrostatic interaction between the ammonium hydrogen and the carbonyl of the carbomethoxy group. The N-methyl groups in 1 and 2 are found to strongly prefer the equatorial position of the piperidine ring. These results were also related to four crystal structures of 1 and its close derivatives. Compounds 3-7 are found to have a common conformation that was used to define the pharmacophore for dopamine reuptake blockers including the required orientation of the ammonium hydrogen. The pharmacophore provides an explanation for why the tertiary amine analogs of 3 and 4 are less potent than the secondary amines because the added N-methyl group occupies the position required for the ammonium hydrogen. This explanation, however, does not work for 7, in which the tertiary amine is again less active than the secondary amine. However, this last series appears to have a number of anomalous features. Superposition of 2 with the pharmacophore suggests that its carbomethoxy may occupy the same region of the receptor as the second phenyl ring in compounds 3-7. © 1993 John Wiley & Sons, Inc.
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  • 22
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 970-976 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N′-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed. © 1993 John Wiley & Sons, Inc.
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  • 23
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 24
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    Journal of Computational Chemistry 14 (1993), S. 1007-1018 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The program AQUARIUS2 calculates probable positions for water molecules within the first hydration shell of any protein for which atomic coordinates are known. Like its predecessor, AQUARIUS, it uses a knowledge of water molecules sites from crystallographically determined protein structures. Energy calculations are not employed. It differs substantially from the original program in that a 3-D probability map (for solvent sites) is generated around the surface of the protein instead of the previously used discrete points. The accuracy of the program has been gauged by comparison with experimentally derived water molecule positions for proteins not used in the knowledge base of the program. It has also been tested by combining the probability density maps with crystallographically determined electron density maps for the protein porphobilinogen deaminase. This procedure filters the most likely solvent electron density peaks from the background noise and has been used in the determination of the solvent structure around the protein nerve growth factor. © John Wiley & Sons, Inc.
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  • 25
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    Journal of Computational Chemistry 14 (1993), S. 1036-1041 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Net atomic charges are derived from a least-squares fitting to electrostatic potentials at atomic sites. The method treats atoms in the molecule as having spherically averaged Hartree-Fock densities, the atomic densities overlapping with one another. The method has the advantage of best reproducing the electrostatic potentials at the atomic nuclei and avoiding the arbitrariness in choosing the points used in the fitting. We have written a FORTRAN program, CHELPN92 (Z. Su, Chemistry Department, SUNY at Buffalo, Buffalo, NY, 1992), based on the method and applied it to deuterated benzene, l-alanine, d,l-histidine, 2-methyl-4-nitroaniline, and deuterated pyridinium-1-dicyanomethylide using the molecular geometry and electrostatic potentials from analysis of accurate X-ray diffraction data. The derived charges are used to calculate the molecular dipole moments. While the charges from this method are in general significantly different from those from the kappa refinement [P. Coppens, T.N. Guru Row, P. Leung, E.D. Stevens, P.J. Becker, and Y.W. Yang, Acta Cryst. A, 35, 63 (1979)], the dipole moments obtained with the new method agree well with those from the kappa refinement. © John Wiley & Sons, Inc.
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  • 26
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    Journal of Computational Chemistry 14 (1993), S. 1050-1065 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several methods are available in the literature for the conformational analysis of small molecules. Each of these methods has some advantages and some disadvantages. Also, each of these methods may be expected to perform better or worse on different types of molecules. There is no clear calibration of each of these methods against a “standardized” set of molecules available in the literature. Such a reference work would be useful to the community because it would allow the choice of methods to be based on some facts. We attempted to provide a start to such a calibration in this article with an examination of the SYBYL SEARCH method. Methods for evaluating the performance of this method are described in detail and will be applied to all other available conformational analysis methods in future papers. © John Wiley & Sons, Inc.
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  • 27
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    Journal of Computational Chemistry 14 (1993), S. 1123-1123 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 28
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    Journal of Computational Chemistry 14 (1993), S. 1125-1135 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The problem of quantifying similarity between crystal structures is transformed into the problem of comparing the associated X-ray powder diagrams. A smooth similarity measure between two powder diagrams, termed a “fold,” is defined. In contrast to conventional comparison methods, the introduced method is still applicable when the peaks of the spectra to be compared have no overlap. The main areas of application of the method are the construction of a molecular crystal structure when only the experimental powder diagram is available and the analysis of possible crystal packings predicted on the basis of molecular information only. A suitable empirical parameterization of the fold has been derived from a large set of experimental and force-field-generated crystals. The analysis of the outcome of an ab initio packing of a flexible molecule is given as an example. The algorithmic details of the method are given as a FORTRAN 77 code. © John Wiley & Sons, Inc.
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  • 29
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    Journal of Computational Chemistry 14 (1993), S. 1184-1193 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe a new method for de novo design of molecules that bind to protein active sites. The method, CONCEPTS (Creation of Novel Compounds by Evaluation of Particles at Target Sites), places a group of atom-like particles in the site. The particles are free to move within the site to improve binding to the protein. A key innovation of this technique is that covalent connections are made among the particles in a stochastic and dynamically reversible manner. These changes in the topology are either accepted or rejected depending on their ability to improve the total energy of the enzyme-inhibitor complex. The method is applied to two test systems: The FK506 binding protein (FKBP-12) and HIV-1 aspartyl protease. In both cases, we are able to predict, de novo, drugs that have striking similarities to known potent inhibitors and that can successfully be used to generate “hits” of the known inhibitors from a data base. © John Wiley & Sons, Inc.
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  • 30
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    Journal of Computational Chemistry 14 (1993), S. 1203-1211 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The separation of the short- and long-range terms in the potentials generated by pairs of Slater functions is reformulated in the context of the Gauss transform method. Analytic expressions of the long-range potentials (in closed form) are derived for equal exponents and generalized (as expansion series) for different exponents. Additionally, the representation of these potentials from small sets of charges or lowest-order multipoles is examined, paying special attention to their values and optimal positions. Finally, numerical tests of the formal developments are presented. It is concluded that the long-range three- and four-center integrals can be calculated with high accuracy in a simple and relatively inexpensive manner. © John Wiley & Sons, Inc.
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  • 31
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    Journal of Computational Chemistry 14 (1993) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 32
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    Journal of Computational Chemistry 14 (1993), S. 1281-1289 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To compare the GROMOS force field with one designed by Ha et al., molecular dynamics simulations of α-D-glucose anhydrate and monohydrate crystals were performed. Also, the long-range interactions were calculated both with a cutoff approximation and with Ewald summations. The results are compared with results obtained experimentally by neutron and X-ray diffraction. The force-field parameters had been optimized with the cutoff approximation; this apparently led to worse results when the Ewald summations were used. However, in all simulations the symmetry was roughly preserved and the mean atomic coordinates and thermal parameters, bond angles, and dihedrals without hydrogen atoms were rather well reproduced. The dihedrals with hydrogen atoms exhibited conformational transitions, which resulted in a disordered hydrogen bonding scheme. In general, the GROMOS force field performed better than the Ha force field. © John Wiley & Sons, Inc.
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  • 33
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    Journal of Computational Chemistry 14 (1993), S. 1301-1312 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Lithium parameters have been optimized for Stewart's standard PM3 method. The average deviation of the heats of formation calculated for 18 reference compounds is 6.2 kcal/mol from the experimental or high-level ab initio data; the average deviation with Li/MNDO is 18.9 kcal/mol. The average error in bond lengths is also reduced by a factor of two to three. Ionization potentials and dipole moments are reproduced with comparable accuracy than Li/MNDO. However, the mean deviation for the heats of formation of both methods increases when being applied to other systems, especially to small inorgnic molecules. The applicability of the new parameter set is demonstrated further for various compounds not included in the reference set, for the calculation of the activation barriers of several lithiation reactions, as well as for the estimation of oligomerization energies of methyl lithium (including the tetramer). Li/PM3 gives reliable results even for large dimeric complexes, like [{4-(CH3CR)C5H4N}Li]2, containing TMEDA or THF as coligands and reproduces the haptotropic interaction between Li+ and π-systems (e.g., in benzyl lithium) as well as the relative energies and structural features of compounds with “hypervalent” atoms (e.g., in lithiated sulfones). © John Wiley & Sons, Inc.
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  • 34
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    Journal of Computational Chemistry 14 (1993), S. 1333-1338 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We apply a recently developed method, the multicanonical algorithm, to the problem of tertiary structure prediction of peptides and proteins. As a simple example to test the effectiveness of the algorithm, metenkephalin is studied and the ergodicity problem, or multiple-minima problem, is shown to be overcome by this algorithm. The lowest-energy conformation obtained agrees with that determined by other efficient methods such as Monte Carlo simulated annealing. The superiority of the present method to simulated annealing lies in the fact that the relationship to the canonical ensemble remains exactly controlled. Once the multicanonical parameters are determined, only one simulation run is necessary to obtain the lowest-energy conformation and further the results of this one run can be used to calculate various thermodynamic quantities at any temperature. The latter point is demonstrated by the calculation of the average potential energy and specific heat as functions of temperature. © John Wiley & Sons, Inc.
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  • 35
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    Journal of Computational Chemistry 14 (1993), S. 1376-1384 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Optimized geometries and total energies for the conformers of 3,6-dihydro-1,2-dithiin (2) and 3,6-dihydro-1,2-dioxin (3) were calculated at several ab initio MO levels: RHF/3-21G(*), RHF/6-31G*, MP2/6-31G*, and MP2/6-31G*/ /RHF/3-21G(*). For the dioxin, in addition to the above levels the corresponding nonextended basis sets ab initio methods were also carried out. The dithiin results are compared with those of simple disulfanes, HSSH and (CH3)2S2, whose optimized geometries agree closely with the observed structures, which is the gauche (C2 symmetry). For the disulfanes, the gauche geometries from RHF/3-21G(*) are in good agreement with the observed structure while the RHF/3-21G results best fit the dioxin. Pertinent structural data at the RHF/3-21G(*) for the half-chair (C2) dithiin are: bond lengths, —SS—, —CS—, —CC=, and —C=C—, 2.050, 1.817, 1.515, and 1.317 Å, respectively; bond angles, CSS, =CCS, and C=CS, 98.0, 114.2, and 127.8°, respectively; CSSC dihedral angle of 63.2°; and twist angle of 36.5°. The total energy for half-chair dithiin at MP2/6-31G*//RHF/3-21G(*) is less than the planar (C2v) and the half-boat (Cs) structures by 69.67 and 29.05 kJ/mol, respectively. The calculated structural data (vs. observed) at RHF/3-21G for the half-chair dioxin are: bond lengths, —OO—, —CO—, —CC=, and C=C, 1.464 (1.463), 1.454, 1.509, and 1.313 Å (1.338 Å), respectively; bond angles, COO, =CCO, and C=CO, 105.0, 109.8 (110.3), and 120.7° (119.9°), respectively; COOC dihedral angle of 79.7° (80 ± 2°); and twist angle of 39.0 (38.3°). The total energy for half-chair dioxin at MP2/6-31G//RHF/3-21G is less than the planar and the half-boat structures by 70.35 and 42.85 kJ/mol, respectively. The total energies calculated at the extended basis sets (*) ab initio levels for the C2 symmetry dioxin are much lower than those of the nonextended basis sets. © John Wiley & Sons, Inc.
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  • 36
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    Journal of Computational Chemistry 14 (1993), S. 1417-1422 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A common problem in the solution of the Poisson-Boltzmann equation using finite difference methods is the self-energy of the system, also known as the grid energy. Because atoms are typically modeled as a point charge, the infinite self-energy of a point charge is likewise modeled. In this article, a simple, alternate treatment of atomic charge is described where each atom is represented as a sphere of uniform charge. Unlike the point charge model, this method converges as the grid spacing is reduced. The uniform charge model generates the same electrostatic field outside the atoms. In addition, the use of fine grids reduces the variations in the potential due to variations in the position of atoms relative to the grid. Calculations of Born ion solvation energies, small-molecule solvation energies, and the electrostatic field of superoxide dismutase are used to demonstrate that this method yields the same results as the point charge model. © John Wiley & Sons, Inc.
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  • 37
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    Journal of Computational Chemistry 14 (1993), S. 1454-1459 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is introduced that tests whether a proposed elementary reaction can be realized within a specified number of cleavages and formations of covalent bonds. This is related to the problem of computing the minimum chemical distance of a given stoichiometry, but differs from it in important ways that are exploited in the algorithm design. One application of the algorithm is as a filter in MECHEM - a computer aid for the elucidation of reaction pathways. In that application, reaction steps implying more changes to covalent bonds than a given threshold are ruled implausible, and in practice such tests need to be carried out many thousands of times. Future applications of the algorithm can be expected because the question addressed is a fundamental one: What elementary reactions can occur? © 1993 by John Wiley & Sons, Inc.
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  • 38
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    Journal of Computational Chemistry 14 (1993), S. 1272-1280 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Computer methods for analytic surface calculations of molecular systems suffer from numerical instabilities and are CPU time consuming. In this article, we present proposals toward the solution of both problems. Singularities arise when nearly collinear triples of neighboring atoms or multiple vertices are encountered during the calculation. Topological decisions in analytic surface calculation algorithms (accessibility of vertices and arcs) are based upon the comparison of distances or angles. If two such numbers are nearly equal, then currently used computer programs may not resolve this ambiguity correctly and can subsequently fail. In this article, modifications in the analytic surface calculation algorithm are described that recognize singularities automatically and treat them appropriately without restarting parts of the computation. The computing time required to execute these alterations is minimal. The basic modification consists in defining an accuracy limit within which two values may be assumed as equal. The search algorithm has been reformulated to reduce the computational effort. A new set of formulas makes it possible to avoid mostly the extraction of square roots. Tests for small-and medium-sized intersection circles and for pairs of vertices with small vertex height help recognize fully buried circles and vertex pairs at an early stage. The new program can compute the complete topology of the surface and accessible surface area of the protein crambin in 1.50-4.29 s (on a single R3000 processor of an SGI 4D/480) depending on the compactness of the conformation where the limits correspond to the fully extended or fully folded chain, respectively. The algorithm, implemented in a computer program, will be made available on request. © John Wiley & Sons, Inc.
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  • 39
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    Journal of Computational Chemistry 14 (1993), S. 1320-1325 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The problem of the representation of the RKR (or IPA) diatomic potential by a simple analytic function is considered. This old problem has for a fairly good solution the Coxon-Hajigeorgiou function U(x) = D[1 - exp-fn(x)]2 with fn(x) = Σm = 1n amxm. The problem of the determination of the disposable parameters a1 … an [in order that U(r) fits the given RKR potential] is reduced to that of a set of linear equations in am where a standard least-squares technique is used. The application to several states (ground or excited) of several molecules shows that a fairly “good” fit is obtained for n ∼ 10, even for the state XOg - I2 bounded by 109 vibrational levels, for which the RKR potential is defined by the coordinates of 219 points. It is shown that the percentage deviation |U(r)RKR - U(r)| throughout the range of r values is about 0.04% for XΣ—Li2, 0.0005% for XΣ—HCl, 0.06% for XOg—I2, and 0.05% for BOu—I2 (as examples). This approach shows the same success for deep and shallow potentials. The comparison of the computed Ev (vibrational energy) and Bv (rotational constant) with their corresponding experimental values shows that a good agreement is reached even for high vibrational levels close to the dissociation. © John Wiley & Sons, Inc.
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  • 40
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.
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  • 41
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    Journal of Computational Chemistry 14 (1993), S. 1066-1076 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The nonbonded portion of a force field for lecithins was characterized by application to the study of the crystal packing geometry and energetics of eight different molecules. The molecules were either lecithin fragments or chosen to isolate particular intermolecular features to test the accuracy of the force field specifically for those interactions. In particular, the hydrocarbon interactions, hydrogen bonding, electrostatics, and phosphate interactions were critiqued. The results support previous findings that indicated that this force field is reasonably accurate for lecithins. For all molecules, a minimum was found near the experimentally determined crystal structure. Using D-glucitol as an example, it is shown that the structural effect of hydrogen bonding is better represented by a nonelectrostatic force-field model than by a purely electrostatic model. Results obtained with glycerylphosphocholine and four smaller organic phosphate molecules suggest that further study of nonbonded interactions of phosphate groups is needed. © John Wiley & Sons, Inc.
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  • 42
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    Journal of Computational Chemistry 14 (1993) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 43
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    Journal of Computational Chemistry 14 (1993), S. 1396-1406 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is presented within the context of the calculation of the time-relaxation behavior of the hydration shells around atomic sites in biomolecules. We report a calculation of the time-relaxation behavior of the first and second hydration shells of polar, hydrophobic, and charged groups in a protein, crambin. The water mean residence times around protein groups are obtained from averages over configurations sampled during a 325-ps molecular dynamics simulation of crambin in solution. A convolution arising in the calculation of the mean relaxation time is implemented using a parallel prefix operator. A new characterization is given of the parallel prefix operator as a linear transformation, and this formulation enables us to derive efficient factorization of the convolution as a product of two parallel prefix operations. The parallel prefix operations are implemented in logarithmic time. © John Wiley & Sons, Inc.
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  • 44
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    Journal of Computational Chemistry 14 (1993), S. 1429-1439 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The recently developed parallel coupled-cluster algorithm of Rendell, Lee, and Lindh [Chem. Phys. Lett., 194, 84 (1992)] is extended to allow four-indexed quantities containing one or two indices in the virtual orbital space to be stored across the global memory of distributed-memory parallel processors. Quantities such as the double-excitation amplitudes can now be distributed over multiple nodes, with blocks of data retrieved from remote nodes by the use of interrupt handlers. As an application of the new code, we have investigated the potential energy surface of the 2-hydroxypyridine/2-pyridone tautomers. Using large basis sets, the structure of each tautomer and the transition state connecting the two minima has been determined at the SCF level. The relative energy difference and the activation energy were then redetermined using the MP2, CCSD, and CCSD(T) methods. All calculations have been performed on Intel distributed-memory supercomputers. The largest coupled-cluster calculations contained over 2 million double-excitation amplitudes. © John Wiley & Sons, Inc.
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  • 45
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    Journal of Computational Chemistry 14 (1993), S. 1460-1467 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for the estimation of pKa from empirically calculated atomic charges has been developed and tested on a diverse set of organic oxyacids. The approach involves a comparison of the atomic charges calculated for both the acid and the negative ion that is formed after loss of the acidic proton. These charges have been used in conjunction with the familiar concepts of induction and resonance to develop an accurate formula to predict pKa. Results for a set of 135 compounds, including alcohols, phenols, and carboxylic acids, yielded a fit of pKa with r = 0.993 and an rms error of 0.455. © John Wiley & Sons, Inc.
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  • 46
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 47
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
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  • 48
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The ligninolytic fungus Phlebia radiata growing in a low-nitrogen medium with wheat bran as the sole carbon source was induced by some lignin monomers, e.g. vanillic, veratric and ferulic acids. In the medium these substances showed a mainly stimulating influence on the hemicellulolytic enzymes activity except for arabinofuranosidase and ferulic acid esterase.
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  • 49
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    Acta Biotechnologica 13 (1993), S. 59-70 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: This paper approaches the problem of oxygen mass transfer. This transfer is in antibiotic biosynthesis liquids produced by microorganisms belonging to the actinomycete and fungi classes, which exhibit a shear thinning non-Newtonian rheological behaviour.The volumetric oxygen mass transfer coefficients in these liquids (kL ab) change during biosynthesis processes. The change is mainly due to rheological parameter modifications, such as increasing the consistency index (K) and decreasing the flow behaviour index (n). The values of kL ab were 3.0-6.5 times lower than those recorded in water, and their decreasing depended on the kL a values obtained without biological liquid and on the nature of fermentation broths, as well.Starting from experimental data, two correlations were established between kL ab and P/V,υSG and P/V,υSG, N, respectively. These correlations contain a dimensionless factor (ηam/ηg)a6, which takes into account the rheological properties of the liquid phase and offers the possibility for a fast and sufficiently accurate estimation of kL ab. The empirical correlations developed in the paper correspond reasonably well with the relatively wide variety of experimental data, as in the model proposed by PEREZ and SANDALL, and allow for the comparison of the fermentation batches of the same or different microorganisms; also, they may be applied to the workings of design, scale-up, control and monitoring of bioreactors.
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  • 50
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 79-82 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: A covalent binding to cellulose granules of two yeast strains Candida tropicalis and Trichosporon cutaneum was achieved. The maximum activity for destroying furfural by the immobilized cells was obtained when the procedure conditions were: reaction medium at pH 5.0, 20°C and cell suspension concentration of 80 mg/ml. The continuous furfural transformation was studied using a growth medium in a fermenter with immobilized Trichosporon cutaneum in which a 84% bioconversion was achieved. The reduced values of furfural remained constant even after 10-fold transformation.
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  • 51
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 83-87 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: A thermophilic bacterial mixed culture was isolated from spent liquor of pulp mills, using a chemostat under aerobic conditions. It consists of two components belonging to genus Bacillus. The thermophilic Bacilli were cultivated aerobically and continuously at 67-70°C and pH 6.8-7, rising the percentage of spent liquor in stages. The dilution rate ranged from 0.2 to 0.33 h-1 during the experiments. The composition of the cell mass produced was analyzed.
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  • 52
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 71-78 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The growth of different strains of Pleurotus spp. on sugar cane agrowastes was evaluated. Three hybrid strains with good production outcomes and yields exceeding 17% were selected. Strain 184 (P. ostreatus x P. pulmonarius) showed the best results.Three spawn materials (wheat grain, millet grain and milled corn cob) at different spawning levels were tested and a significant influence was found. The obtained results were best explained in terms of total nitrogen content of the initial mixture (spawn + substrate), suggesting a probable nitrogen limited growth of the mushroom on sugar cane residues. A 10% millet grain spawn was found to be a reasonable compromise.Productive responses decreased with an increase in bag's capacity (8-10-12 kg), even though the same diameter was maintained in order to avoid pronounced temperature profiles. Smaller bag's capacities (8-10 kg) were recommended.It was also shown that the utilization of water hyacinth (Eichhornia crassipes) mixed 50/50 with sugar cane residues as substrate caused a twofold increase of crop responses, confirming the advantages of this substrate supplementation.The obtained results identified sugar cane agrowastes as a feasible substrate for Pleurotus spp. production with yields and biological efficiencies comparable and to some extent better than others reported with conventional lignocellulosic residues such as cereal straw.
    Additional Material: 2 Ill.
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  • 53
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    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Optimization studies have been carried out for the production of L-lactic acid from the fermentation of beet molasses by Lactobacillus delbrueckii. A PLACKETT-BURMAN Design and a Central Composite Design have been used to determine the most suitable nutrient medium for obtaining a maximum cell concentration. A second-order polynomial empirical model relating both the cell and nutrient concentrations was formulated. The variables selected for the study were Yeast Extract, Peptone, Tween 80 (antifoam), MgSO4 · 7H2O, MnSO4·4H2O, FeSO4 · 7H2O and K2HPO4/KH2PO4. Among them, only Yeast Extract and Peptone were found to significantly affect the cell concentration. A maximum cell yield was found when the concentrations of Yeast Extract and Peptone were, respectively, 5.31 g/l and 5.08 g/l. All conclusions are restricted to the experimental range studied.
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  • 54
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 131-139 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The biodegradation of leguminous and non-leguminous organic materials by Pleurotus sajor-caju and P. ostreatus was studied. Comparisons were made between mushroom yield on both types of substrates. The conversion percentage from dry substrate to fresh mushroom (biological efficiency) was determined. Mushrooms were analyzed for their protein content, carbohydrates, percentages of ash, fat content and crude fibre. The energy value of fruit bodies was computed. The yield obtained from leguminous substrates was significantly high as compared to that yield which was obtained from non-leguminous substrates. The lowest yield of P. sajor caju (10 g ± 0.3 g) and P. ostreatus (6.5 g ± 1.2 g) was obtained using the Bougainuillea substrate and the highest one (519 g ± 16 g, P. sajor-caju and 488 g ± 18 g, P. ostreatus) using nitrogen-fixing leguminous Leucaena leucocepholea. The nitrogen content in fruit bodies was found to be higher with leguminous substrate than with non-leguminous ones.
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  • 55
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  • 56
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  • 57
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    Acta Biotechnologica 13 (1993), S. 161-175 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Results of pilot plant studies using an external-loop airlift bioreactor (170 l fermentation volume, liquid height-to-riser diameter: 27, loop-to-tower cross-section-area: 0.1225) have proven the relative merits of such a system in the bacitracin biosynthesis produced by the Bacillus licheniformis submerged aerobic cultivation.The results were compared to those obtained in a pilot-scale stirred-tank bioreactor with the same values of kLa. Excepting the aeration rate of 0.2 vvm, the fermentation process performed at 0.5 vvm and 1/0 vvm, respectively, unfolded similarly in the two fermentation devices with respect to the cell mass production, substrate utilization and bacitracin production during the fermentation process.In the riser section of the airlift bioreactor, the dissolved oxygen levels were higher, while in the downcomer section they were lower than those realized in the stirred tank bioreactor.Power requirements of the airlift fermenter were by 17-64% lower than those for a mechanically agitated system, depending on the aeration rates, which led to an important energy saving.Moreover, the lack of mechanical devices in the airlift system provides safety and a more gentle environment for the cultivation of microorganisms.
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  • 58
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    Acta Biotechnologica 13 (1993), S. 177-183 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The enzymatic esterification of octanoic acid with racemic butanol-2 was investigated. Esterifications of the acid were performed in a forced flow enzyme membrane reactor. The used membrane was prepared by a phase inversion process in polyamide-6 solution followed by the chemical immobilization of a lipase-catalyst.Influences of water content and pH were estimated. Their optimum values are equal to 0.5% w/w and pH 8. The reaction rate (at 303 K) of 5.1 × 10-5 mol/h·cm2 of the membrane area, and at least 85% enantiomeric excess in the produced ester mixture were obtained.The activity of immobilized lipase in the membrane process is about two times higher than that of the native lipase in the esterification performed in a tank reactor.
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  • 59
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    Acta Biotechnologica 13 (1993), S. 185-191 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Carbon and nitrogen influence the lipid accumulation and arachidonic acid production by Mortierella alpina CCF 185 cultivated at 28°C for 7 days on a rotary shaker. The fungus grown with glucose, starch or dextrin as the carbon source produced satisfactory amounts of lipid and arachidonic acid. The maximum arachidonic acid values were obtained on media with yeast extract or NaNO3 as the nitrogen source. The C/N ratio of 40:1 resulted in the highest yields of lipid and arachidonic acid with different amounts of NaNO3 concentration.
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  • 60
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    Acta Biotechnologica 13 (1993), S. 193-196 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The lipid accumulation, fatty acid composition and γ-linolenic acid (GLA) production by 28 strains belonging to Mucorales were investigated. The lipid content varied from 5 to 30% on dry biomass and the percentage of γ-linolenic acid in total intracellular lipid was in a range from 2.5 to 15.4% (w/w). The best yield of γ-linolenic acid (expressed as mg GLA per 1 g biomass) was found for Mucor mucedo CCF - 1384 (28.4) and Cunninghamella echinulata CCF - 103 (25.1).
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  • 61
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    Acta Biotechnologica 13 (1993), S. 243-249 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Acetobacter methanolicuswas grown on glucose in the presence of dinitrophenol (DNP) under carbon/energy-limited conditions. DNP affected both the growth yield and the growth rate (Dsh) at which the energy generation was shifted from a complete to an incomplete substrate oxidation by using the PQQ-linked glucose dehydrogenase. The more the growth yield was decreased, the higher both the DNP concentration and the growth rate became. At about 0.53 mM DNP, growth was completely stopped. Dsh decreased from 0.21h-1in the absence of DNP to 0.175 h-1and 0.075 h-1in the presence of 0.2 mM and 0.4 mM DNP, respectively. The experimental data are discussed in terms of the limitations in the generation of energy and some stress situations which are exerted by the presence of the uncoupler.
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  • 62
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  • 63
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    Acta Biotechnologica 13 (1993), S. 251-256 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The presence of dinitrophenol (DNP) during the chemostatic growth of Acetobacter methanolicuson glucose led to i) no significant increase in glucose dehydrogenase, ii) a decrease in the capacity to oxidize glucose by about 30%, not depending on the DNP concentration, and iii) a gradual decrease in the capacity to form gluconic acid, depending on the concentration of the uncoupler. Similar effects of DNP on Acetobacter methanolicuswere observed during the gluconic acid formation process. The loss in the capacity to form gluconic acid is indicated by a drop in the ATP concentration of the cells which cannot be counteracted by the ATP syntheses originating from the oxidation of gluconic acid and of glucose. ATP could be necessary for pumping protons out of the cells that were taken up together with gluconic acid and by the effect of DNP.
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  • 64
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  • 65
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    Acta Biotechnologica 13 (1993) 
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    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 66
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  • 67
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    Acta Biotechnologica 13 (1993), S. 89-91 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The mechanism of catabolic repression is not yet fully understood. Oxygen seems to control the level of cytochrome in the in situ state. The level of glucose seems to control other enzymes; glucose by itself does not repress the cataboism. An unidentified product of glucose metabolism is believed to be involved. In bacterial cultures, there is convincing evidence that cyclic AMP is involved and this operates at the levels of gene trancription. In yeast, it is not clear. The level of CAMP is found to be reduced with catabolic repressed cells, but there is little evidence to conclude that CAMP acts at the transcription level [1]. There are results to indicate that it acts at the translational level or enzyme activation phase in yeast. In order to understand this mechanism, the bioenegetics of yeasts grown under catabolic repression is analyzed with the data available [2] and appended.
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  • 68
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    Acta Biotechnologica 13 (1993), S. 117-122 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Cell disruption studies for the extraction of HBsAg from a recombinant P. pastoris strain (r-HBsAg) were done using a bead mill disintegrator. Three sequential passages (4 min retention time each) were enough to disrupt the cells and extract most of the r-HBsAg and soluble proteins. An acid precipitation step was performed just after cell disruption to precipitate proteins together with the cell debris. Different precipitation pH values (2.5 to 6.0) were investigated. A pH value of 4.2 was selected as a compromise between recovery and improvement of specific activity. A 6 to 8-fold enhancement of the specific activity was obtained, having a r-HBsAg overall yield of about 80%. The influencing presence of a chaotropic salt (potassium thiocyanate) during the acid precipitation step was also studied.
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  • 69
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    Acta Biotechnologica 13 (1993), S. 130-130 
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    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 70
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    Acta Biotechnologica 13 (1993), S. 123-129 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: For the immobilization of spores of Penicillium raistrickii i 477 the formation of polyelectrolyte complexes using the sodium salt of cellulose sulphate as polyanion and poly-dimethyl-diallylammoniumchloride as polycation was used. Light and scanning electron microscopy have shown that during germination of spores the capsule walls do not cause effective limitations on hyphal growth and that there are no significant morphological changes of the mycelium detectable by an outgrowth of immobilized spores. By comparing the 15α-hydroxylation of 13-ethyl-gon-4-en-3,17-dione with free and encapsulated cells it was found that an increase of total dry biomass per immobilized system led to a higher product formation in relation to free cells.
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  • 71
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    Acta Biotechnologica 13 (1993), S. 306-306 
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    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 72
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    Acta Biotechnologica 13 (1993) 
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    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 73
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  • 74
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    Acta Biotechnologica 13 (1993), S. 311-322 
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    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The kinetics of batch fermentation during the growth of S. cerevisiae ATCC 36859 was studied in various glucose/fructose mixtures. It was found that the growth is inhibited equally by glucose and fructose even though fructose is not consumed to any large extent by the yeast under the conditions tested here. The inhibition of growth by the substrate and ethanol is represented by linear equations. These equations were combined with the MONOD expression in order to formulate equations for the biomass growth, glucose and fructose consumption and ethanol production. Parameter estimates were obtained by fitting these equations to batch fermentation data and so developing models which indicate that the growth is completely inhibited when 62 g/l ethanol is produced by the yeast, while glucose consumption and ethanol production continue up to an ethanol concentration of 152 g/l. Products containing a high concentration of fructose are best produced by using a high initial biomass concentration.
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  • 75
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    Acta Biotechnologica 13 (1993), S. 323-331 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Optimization studies have been carried out for the production of L-lactic acid from the fermentation of whey by Lactobacillus casei. Two Statistical Designs, a full 24 Factorial Design and a full 32 Factorial Design, have been used to determine the most suitable values of the operational variables for obtaining the maximum lactic acid production rate. The variables selected for study were temperature, pH, lactose concentration, and inoculum concentration. Among them only temperature and pH were found to affect the response significantly. A second-order polynomial empirical model relating both the response (lactic acid production rate) and the variables was formulated. The maximum acid production rate was found when the values of pH and temperature were 5.4 and 38°C, respectively. All conclusions are restricted to the experimental range studied.
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  • 76
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    Acta Biotechnologica 13 (1993), S. 333-340 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The influence of different process kinetics on the course of phenol degradation has been studied as well as the influence of axial dispersion in the liquid phase on the reactor height with relatively large biofilm thickness in a conventional fluidized bed and air-lift bioreactor. The object of this was to achieve a high conversion of substrate in a device of real size in real process time. For calculating the mathematical model, the method of orthogonal collocation with the STIFF integration routine has been used.
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  • 77
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    Acta Biotechnologica 13 (1993), S. 341-350 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The killing/immunity interactions among killer strains of the genera Kluyveromyces, Hansenula and Saccharomyces from the Czechoslovak Collection of Yeasts were studied with the aim to find the strains with broad specificity and killer activity targeted against a range of undesirable wild yeasts causing stuck fermentations. Among 49 tested Kluyveromyces strains, five strains were found, and among 55 Hansenula strains, ten yeast strains were found with activity against a sensitive strain of Saccharomyces. Hansenula mrakii CCY 38-7-1 and Hansenula saturnus var. subsufficiens CCY 38-4-2 showed exceptional activity against the wine contaminants, Zygosaccharomyces bailii, as well as against pathogenic Candida species within a broad range of pH 2.9-5.1. Their potential biotechnological application is discussed.
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  • 78
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  • 79
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    Acta Biotechnologica 13 (1993), S. 351-359 
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    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: α-Galactosidase (E.C.3.2.1.22) from Penicillium janthinellum was purified by precipitation and fractionation with ammonium sulphate, cold acetone or ethanol, calcium phosphate gel, and column chromatographies on Sephadex G-100 and G-200. The enzyme was purified about 110.39-fold when Sephadex G-100 was used. α-Galactosidase exhibited the optimum pH and temperature at 4.5 and 60°C, respectively. The optimum enzyme stability was obtained at pH 3.5 for 24 h (at room temperature). The enzyme was found to be thermostable below 65°C up to 40 minutes and was gradually inactivated by increasing the temperature above this degree. The MICHAELIS constant was 0.55 mM for p-nitrophenyl-α-D-galactoside. The α-galactosidase activity was strongly inhibited by Hg++ and slightly activated by Mn++. The results show the possibility of producing a thermostable enzyme from a low-priced agricultural product, for instance, lupine.
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  • 80
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    Acta Biotechnologica 13 (1993), S. 3-11 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The cultivation of Acetobacter methanolicus on various substrates revealed that the respective maximum growth rates are obtained at an almost identical oxidative capacity of about 16 mmoles of oxygen g (biomass)-1·h-1 under conditions of energy generations by complete substrate oxidation. This is considered to be an indication that the energy production rate determined by the capacity of the respiratory chain limits the growth rate in this strain. However, with glucose and glycerol, for example, a further increase in the growth rate is observed accompanied by the generation of products (gluconic acid or dihydroxyacetone, respectively). The incomplete oxidation should play the role of an additional energy generation. The potential for this rate increase is looked for in a higher energy gain derived from reduction equivalents (PQQH2) in this periplasmic oxidation step in relation to the cytoplasmic reduction equivalents.
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    Acta Biotechnologica 13 (1993), S. 30-30 
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    Source: Wiley InterScience Backfile Collection 1832-2000
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    Acta Biotechnologica 13 (1993), S. 13-20 
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: In this paper, we consider a model for a chemostat in which two microbial species compete for a single rate-limiting nutrient, while one of the species feeds on another. Under certain simplifying hypotheses, such a chemostat can be described by a system of three nonlinear ordinary differential equations. A theoretical study is conducted to characterize the possible types of solutions. A limit cycle solution was obtained for some parametric values of the system indicating that coexistence of the two species is possible in a significant range of the operating parameters.
    Additional Material: 2 Ill.
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  • 83
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 21-30 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Pretreated wheat straw was enzymatically hydrolyzed in 250-ml flasks using the culture filtrate of Trichoderma reesei QM-9414. The influence of the initial enzymatic activity in the liquid phase was studied. The unreacted core model was used to analyze the experimental data obtained at 40, 46 and 50°C. The model adequately describes the data for hydrolysis times lower than 10 h.
    Additional Material: 8 Ill.
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  • 84
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 31-40 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: This paper intends to focus the attention to characteristic features of microbial lignin degradation from the phenomenological point of view. Six fundamental principles are discussed under special consideration of white-rot fungi. The necessity of mycelial growth and the formation, secretion, and extracellular action of peroxidases are main requirements for a successful microbial attack on polymeric lignin.
    Additional Material: 5 Ill.
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  • 85
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 41-45 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The ligninolytic fungus Phlebia radiata growing in a low-nitrogen medium with Avicel cellulose as the sole carbon source produced a full spectrum of celluloytic enzymes. Some properties of these enzymes were investigated during the growth of the fungal culture.
    Additional Material: 3 Ill.
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  • 86
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 87
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 47-51 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The ligninolytic fungus Phlebia radiata growing in a low-nitrogen medium, with wheat bran as the sole carbon source, produces a wide spectrum of hemicellulolytic enzymes. During the growth of the fungal culture, some properties of these enzymes were investigated.
    Additional Material: 3 Ill.
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  • 88
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993) 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 89
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 90
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 91
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 95-101 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The synthesis of extracellular serine proteinase of Lactococcus lactis was studied during the growth in a batch and a continuous culture on chemically defined media. In a batch culture the proteinase synthesis started during the exponential phase of growth and the highest proteinase concentrations were found at the end of the exponential and beginning of the stationary phase of growth. During the growth in a lactose-limited chemostat with amino acids as the sole source of nitrogen, the specific rate of proteinase synthesis was maximal at a μof 0.23 h-1. At higher growth rates the proteinase productin declined. The proteinase synthesis was dependent on the amino acid sources in the medium. In batch cultures of L. lactis grown on a chemically defined medium with amino acids, the proteinase production was increased four-fold compared to media containing casein or a tryptic digest of casein as the sole source of nitrogen. The inhibition of the rate of proteinase synthesis by casein and peptides was also observed during the growth in a chemostat. The addition of the dipeptide leucylproline (final concentration of 100 μM) to a lactose-limited continuous culture during the steady state (D = 0.23 h-1) resulted in a transient inhibition of the rate of proteinase synthesis. This suggested that exogenously supplied peptides control the regulation of proteinase synthesis of L. lactis.
    Additional Material: 3 Ill.
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  • 92
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 197-201 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: 515 microorganisms of the genus Bacillus which produce starch-degrading enzymes were isolated from natural environments in the course of a screening programme. Treating the Bacillus strains on agar plates with iodine reagent for 30 seconds led to the selection of clones with increased amylolytic activity. This methods is very convenient for the screening of large numbers of amylolytic strains.
    Additional Material: 2 Ill.
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  • 93
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 203-207 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Presently, an urgent problem is the application of artificial intellect (AI) methods as a complex way of controlling and optimizing technological processes. The paper presents major principles of a bystage application of AI in biotechnology as knowledge extraction from data obtained by decomposing the sign space to clusters.
    Additional Material: 3 Ill.
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  • 94
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993) 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 95
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 211-242 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: In biotechnological processes, fundamental performances of microorganisms are used. The economy of these processes is essentially determined by the efficiency, velocity (productivity) and quality of the products. Therefore it is a permanent task and challenge for basic and biotechnological research to seek out measures for improving the actually attained parameters. The auxiliary substrate concept supplics an approach. It is based on the fact that chemo-organo-heterotrophic substrates differ in the carbon: energy ratio, thus, growth yield is limited in energy and/or reducing power. It says that, by simultaneous utilization of physiologically similar substrates (mixed substrates), the growth yield increases. The substrates are to combine in such a way that with their simultaneous utilization a minimum of carbon is dissimilated merely for the purpose of the generation of biologically useful energy and/or reducing power. Since all chemo-organo-heterotrophic substrates are more or less energy-deficient, an increase in growth efficiency can be expected if the individual substrates of the mixture are assimilated more efficiently than the respective substrates alone. This may result, for instance, from an immediate assimilation of a substrate (according to the “manner of finished part construction”).An increased growth rate is rather the rule than the exception in mixed substrate utilization.In product syntheses the substrates are, depending on the concrete product and metabolic pathway, either energy-excess or energy-excess or energy-deficient. or, in other words, the processes are energy-generating or energy-consuming, respectively. If this is responsible for discrepancies between the possible yields determined by the carbon metabolism and the experimentally obtained yields, the discrepancies should be able to be decreased and the yields increased by mixing substrates. The substrates are to choose and combine so that, due to simultaneous utilization, the product formation process becomes energy neutral.As a rule, the enhanced efficiency is accompanied by an increased velocity. This does not only apply to syntheses, but also to degradation (and detoxification) reactions. Even supposedly inert compounds or persistent substances can be activated by simultaneous (co-)metabolization of another (an auxiliary substrate, victim substrate or co-substrate) and converted at a considerable rate. It is of interest for syntheses of products but in particular for degradation and decontamination of harmful and waste products in the environment that the residual concentrations of the substrates are smaller than those achieved if the compounds of a mixture are metabolized separately.The auxiliary substrate concept has proven to be fruitful, both for theoretical and practical questions. It was practically already being used before it was formulated (mixed substrate utilization, cometabolism). However, an abundance of regulatory and energetic aspects are waiting to be investigated in more detail.
    Additional Material: 9 Ill.
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  • 96
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 269-274 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The basic parameters were studied influencing the conversion of orbitol to sorbose by Gluconobacter oxydans(industrial strain from FARMAKON Co., Czechoslovakia). The most effective conversion in the stationary phase was reached at pH 5.0, no inhibitory effect of sorbitol in a concentration ranging from 20 to 200 g/l and a minimum inhibitory effect of the sorbose concentration up to 200 g/l were observed. According to the optimum conditions mentioned above the optimized course of the fed-batch cultivation was proposed. The final concentration of sorbose of 410 g/l was reached after 36 hours.
    Additional Material: 6 Ill.
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  • 97
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    Acta Biotechnologica 13 (1993), S. 257-268 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: The optimization task was performed using the gluconic acid synthesis by the Acetobacter methanolicusMB 58 strain. The microorganisms were grown continuously on methanol as the growth substrate. After finishing the growth process by the deficiency of N and P, the gluconic acid synthesis was started by adding glucose. The synthesis process was performed continuously. The oxygen transfer rate depended on the gluconic acid concentration. During the growth process, the oxygen transfer rate reached a value of about 13 g O2 · kg-1 · h-1using a 30-l glass fermenter equipped with a 6 blade stirrer and fully baffled. This rate declined to a value of between 2 and 5 g O2 · kg-1 · h-1 in the presence of gluconic acid concentrations above 150 g gluconic acid · kg-1medium. The yield (g gluconic acid · g-1glucose) depended on the gluconic acid concentration and amounted to y = 0.7 in relation to 150 g gluconic acid · kg-1medium and y = 0.8 in relation to 200 g · kg-1medium, respectively. The fermenters were coupled with ultrafiltration moduls (Fa. ROMICON and Fa. SARTORIUS). The biomass concentrations amounted from 5 to 40 g dry mass kg-1medium. The ultrafiltration modules retained the biomass within the fermentation system. A glucose solution (30 to 50 weight percent glucose) was continuously dosed into the fermenter. The retention time was chosen between 2 and 30 h. The gluconic acid synthesis rate reached values of up to 32 g gluconic acid · kg-1 · h-1. Within a range of up to 250 g gluconic acid · kg-1medium, the acid concentration had no influence on the enzyme activity.
    Additional Material: 8 Ill.
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  • 98
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Cylinder-shaped sintered glass carriers were successfully used for immobilizing and cultivating cells of murine line L929. The process has been performed in a fixed-bed bioreactor (working volume of 150 ml) with perfusion and aeration of the medium (total volume of 3.5 l). The maximum cell density of 1.23 × 107cells/ml was achieved when the basal medium (MEM + 10% bovine serum) was enriched with glucose (up to 2 g/l) and L-glutamine (up to 4 mM). The carriers have proved to be nontoxic, mechanically stable and reusable.
    Additional Material: 5 Ill.
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  • 99
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
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  • 100
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    Berlin : Wiley-Blackwell
    Acta Biotechnologica 13 (1993), S. 283-288 
    ISSN: 0138-4988
    Keywords: Life Sciences ; Life Sciences (general)
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: In order to optimize the thermophilic lactic acid fermentation on saccharose as the sole carbon source and improve the effectiveness of the process, alternative nitrogen sources were tested and a minimal broth composition was found. Of the alternative nitrogen sources, whey protein hydrolyzate (WPH) was the best; the broth composition was reduced from seven down to three items. Application of ammonium as a neutralizing agent instead of sodium hydroxide brought an important positive change.
    Additional Material: 3 Ill.
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