Development and use of probability models: The industry perspective

Summary In the processed meat industry, food safety and microbiological shelf life issues lend themselves to the use of probability modeling. Our research concentrated on predicting the effectiveness of sodium lactate as an antibotulinal agent in vacuum packaged, uncured and cured turkey breast model systems. In uncured turkey breast containing 1.4% NaCl, 0.3% Na phosphate, and 0–3% Na lactate, the antibotulinal effect of sodium lactate can be predicted using the following model: Days to toxicity = 3.13+0.39(Na lactate)². Using cured turkey breast with 0.3% Na phosphate, 0.2% sucrose, 0–3% Na lactate, the time to toxicity can be predicted from the following model: Days to toxicity = 1.69+4.88(NaCl)–11.16(Na lactate)+7.23(Na lactate)². Probability models have also been developed to predict the refrigerated shelf life of specific processed meat products. The usefulness of the predictive modeling for food safety and quality in the food industry will also be discussed.This paper was presented at The International Conference on the Application of Predictive Microbiology and Computer Modeling Techniques to the Food Industry, April 12–15 1992, Hyatt Regency Hotel, Tampa, FL, USA.     

PocketOptimizer 2.0: A modular framework for computer-aided ligand-binding design

The ability to design customized proteins to perform specific tasks is of great interest. We are particularly interested in the design of sensitive and specific small molecule ligand-binding proteins for biotechnological or biomedical applications. Computational methods can narrow down the immense combinatorial space to find the best solution and thus provide starting points for experimental procedures. However, success rates strongly depend on accurate modeling and energetic evaluation. Not only intra- but also intermolecular interactions have to be considered. To address this problem, we developed PocketOptimizer, a modular computational protein design pipeline, that predicts mutations in the binding pockets of proteins to increase affinity for a specific ligand. Its modularity enables users to compare different combinations of force fields, rotamer libraries, and scoring functions. Here, we present a much-improved version––PocketOptimizer 2.0. We implemented a cleaner user interface, an extended architecture with more supported tools, such as force fields and scoring functions, a backbone-dependent rotamer library, as well as different improvements in the underlying algorithms. Version 2.0 was tested against a benchmark of design cases and assessed in comparison to the first version. Our results show how newly implemented features such as the new rotamer library can lead to improved prediction accuracy. Therefore, we believe that PocketOptimizer 2.0, with its many new and improved functionalities, provides a robust and versatile environment for the design of small molecule-binding pockets in proteins. It is widely applicable and extendible due to its modular framework. PocketOptimizer 2.0 can be downloaded at https://github.com/Hoecker-Lab/pocketoptimizer .     

Entwicklungsgeschichtliche untersuchungen an einer Blattmutante vonHyoscyamus niger L.

Summary The leaf shape of the mutantfiliformis (fil) ofHyoscyamus niger L. is strongly modified by external factors (like nutrition and light) as well as by the height of insertion. The name filiformis refers to thread-like leaves which always occur in the inflorencence; they may also be formed in the vegetative region, especially under short day conditions. Other leaves may have a small rhombic blade or a larger blade with irregular edges and deep incisions. Even pinnate leaves have been found. In contrast to the leaves of normalHyoscyamus, all mutant leaves (hypsophylls included) have a stalk-like basal portion that seems to be homologous to the basal part of the normal blade. This mutant is caused by one recessive factor which is linked neither toann nor topall.the submarginal initials of the normalHyoscyamus blade were always found dividing according to the periclinal-anticlinal type, while in the mutant the activity of the submarginal initials frequently resulted in a primarily biseriate mesophyll (so-called double-edged segmentation).This is apparently the first time that gene control of the mode of submarginal blade growth has been observed. Further differences between mutant and normalHyoscyamus concern the venation, the lengths of palisade cells and of stomata guard cells, the frequency of stomata per mm², and the thickness of the blade.

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Cell Cycle Timing of Replication of the Nuclear Gene Encoding Chloroplastic NADP-Specific Glutamate Dehydrogenase Isoenzymes in Chlorella sorokiniana

In synchronized Chlorella sorokiniana cells, the NH₄⁺ inducibleNADP-specific glutamate dehydrogenase enzyme (NADP-GDH) accumulatedin a linear manner throughout the first cell cycle. Early inthe following second cell cycle, an increase in its rate ofaccumulation occurred that was proportional to the increasein total cellular DNA in the previous cell cycle. In synchronizedbacterial cells, increases in rate of linear accumulation ofinducible enzymes coincide with the time of replication of theirstructural genes. To determine whether the rate change in NADPGDHaccumulation resulted from a delay in replication of its nuclearstructural gene (gdhN) in fully induced C. sorokiniana cells,the cell cycle timing of replication of this gene was comparedto that of another nuclear gene, nitrate reductase (nia), andof a chloroplast gene, ribulose bisphosphate carboxylase large-subunit(rbcL), in synchronized cells cultured in NH₄⁺ or NO₃^–(uninduced) medium. The gdhN and nia genes replicated withinthe period of nDNA synthesis and rbcL within the period of ctDNAsynthesis in cells growing in either nitrogen source. Therefore,the delayed rate change in enzyme accumulation results froma process that regulates expression of the gdhN gene after itsreplication. (Received July 16, 1994; Accepted November 28, 1994)     

Applicability of a continuum solvation model to the octanol water transfer: CFF91 based model for amino acids

A continuum hydration model based upon the atomic charges provided with the CFF91 force field [A. B. Schmidt and R. M. Fine (1994) Molecular Simulation, 13. 347–365] has been extended to the octanol–water transfer. The electrostatic component of the transfer free energy is calculated using the finite-difference solution to the Poisson–Boltzmann equation while the nonpolar contributions are assumed to be proportional to the solute-excluded volume in water. All atomic charges and radii besides the aromatic carbon radius are equal in both solvents. The octanol dielectric constant and the probe radius are the main fitting parameters defining the octanol phase. The model has been tested for 38 organic molecules related to the amino acid residues and generally provides a high accuracy. In particular, the mean unsigned error for N-acetyl amino acid amides is 0.5 kcal/mol. © 1995 John Wiley & Sons, Inc.     

Are the funnel-canal organs the “campaniform sensilla” of the shore crab Carcinus maenas (Crustacea,Decapoda)?

Summary The topography of the funnel-canal organs of Carcinus maenas (Decapoda, Crustacea) and their stimulus-receiving cuticular and sensory apparatus were studied in the light and electron microscopes.About 4000 funnel-canal organs are situated within the exoskeleton of Carcinus. Almost all of them are on the distal segments of the walking legs, in particular on the epicuticular cap at the tip of the dactyl. They were not found to be arranged in groups or sensilla fields, and no sex-specific differences were observed.Characteristic features of the funnel-canal organs are as follows: (a) There is a terminal pore (0.5×0.8 m diameter) in the cuticle, at the tip of a small projection. It is closed by a plug of electron-dense material. (b) The terminal sections of the dendrites are enclosed in a dendritic sheath up to ca. 10 m below the pore. (c) The dendrites, 3–24 in number, end below the plug; none of the dendrites exhibits a tubular body; two of the dendrites are distinguished from the others by the greater number of microtubules in their outer segments.The structural characteristics, in particular the gustatory pore and the number of dendrites, are typical of bimodal receptors in arthropods. In such receptors, as in the contact chemoreceptors of insects and arachnids, mechano-and chemosensitive sensory cells are combined.This interpretation of the function of the funnel-canal organs is supported by electrophysiological data of other authors.The morphological parameters we find for the funnelcanal organs, in comparison with those of insect campaniform sensilla, provide clear evidence against the reclassification of the funnel-canal organs as crustacean campaniform organs proposed by Shelton and Laverack (1968).Supported by the Deutsche Forschungsgemeinschaft (W.G., SFB 45/A1)We thank Professor Dr. F.G. Barth for valuable discussion and Mr. K. Grommet for drawing the Figs. 1 and 6c     

Studies on the (pro) insulin biosynthesis of islets of Langerhans of sand rats (Psammomys obesus).

By feeding a regular laboratory chow, sand rats (Psammomys obesus) from our breeding colony gained different body weights, though they received approximately the same quantity of calories. Sand rats, reaching a body weight above 160 g (group B) showed significantly increased blood glucose values in contrast to the animals with a body weight under 160 g (group A). Isolated pancreatic islets of these two groups of sand rats were incubated with [3H]-leucine to study the incorporation of this amino acid into proinsulin and insulin. The incorporation into proteins of pancreatic islets of sand rats of group B was stimulated by 0.45 mg and 3.0 mg/ml glucose. In group A there was no further stimulation from 0.45 mg to 3.0 mg/ml glucose. Insulin secretion could be stimulated by glucose in both groups, but the stimulation was stronger in group B than in group A.     

Proton magnetic relaxation dispersion in solutions of the cuproprotein diamine oxidase.

Proton nuclear magnetic resonance relaxation measurements were made over the range 4.7--220 MHz for aqueous solutions of hog kidney diamine oxidase. The values of 1/T1 give rise in two distinct dispersions, at 16 and 75 MHz, whereas 1/T2 displays a minimum at 20 MHz. The temperature dependence of relaxation rates in all cases yield apparent activation energies less than 0.6 kcal/mol. These data indicate to us that the two Cu(II) ions of diamine oxidase are intrinsically different in terms of their electronic relaxation characteristics and hence, chemical environments. Low field limits of the two electronic relaxation times are 2 and 10 ns, with one of these correlation times being frequency dependent. The value of the frequency-dependent electronic relaxation time is governed by interactions that are modulated by a process having a correlation time of 5 ps.