Statistics of RNA melting kinetics

We present and study the behavior of a simple kinetic model for the melting of RNA secondary structures, given that those structures are known. The model is then used as a map that. assigns structure dependent overall rate constants of melting (or refolding) to a sequence. This induces a landscape of reaction rates, or activation energies, over the space of sequences with fixed length. We study the distribution and the correlation structure of these activation energies. Correspondence to: P. Schuster     

Strange limits of stability in host-parasitoid systems

The classical Nicholson-Bailey model for a two species host-parasitoid system with discrete generations assumes random distributions of both hosts and parasitoids, randomly searching parasitoids, and random encounters between the individuals of the two species. Although unstable, this model induced many investigations into more complex host-parasitoid systems. Local linearized stability analysis shows that equilibria of host parasitoid systems within the framework of a generalized Nicholson-Bailey model are generally unstable. Stability is only possible if host fertility does not exceede ⁴=54.5982 and if superparasitism is unsuccessful. This special situation has already been discovered by Hassell et al. (1983) in their study of the effects of variable sex ratios on host parasitoid dynamics. We discuss global behaviour of the Hassell-Waage-May model using KAM-theory and illustrate its sensitivity to small perturbations, which can give rise to radically different patterns of the population dynamics of interacting hosts and parasitoids.     

Recognition of errors in three-dimensional structures of proteins

A major problem in the determination of the three-dimensional structure of proteins concerns the quality of the structural models obtained from the interpretation of experimental data. New developments in X-ray crystallography and nuclear magnetic resonance spectroscopy have acceleratedd the process of structure determination and the biological community is confronted with a steadily increasing number of experimentally determined protein folds. However, in the recent past several experimentally determined protein structures have been proven to contain major errors, indicating that in some cases the interpretation of experimental data is difficult and may yield incorrect models. Such problems can be avoided when computational methods are employed which complement experimental structure determinations. A prerequisite of such computational tools is that they are independent of the parameters obtained from a particular experiment. In addition such techniques are able to support and accelerate experimental structure determinations. Here we present techniques based on knowledge based mean fields which can be used to judge the quality of protein folds. The methods can be used to identify misfolded structures as well as faulty parts of structural models. The techniques are even applicable in cases where only the C_α trace of a protein conformation is available. The capabilities of the technique are demonstrated using correct and incorrect protein folds. © 1993 Wiley-Liss, Inc.     

Genome organization in Xiphophorus (Poeciliidae; Telostei)

Summary Xiphophorus represents a valuable model for studying genomic contributions to neoplasia. For analyzing these contributions at the molecular level, basic information about the genome organization is a prerequisite. This study presents data on the organization and complexity of the genomes of three species of Xiphophorus, maculatus, variatus and helleri, representative of the problem. Their diploid nuclei, as measured in the erythrocyte, contain 1.19 pg, 1.23 pg, and 1.27 pg DNA, these values representing approximately 50% of that of birds, 20% of that of mammals. The melting curves of native, high molecular weight DNA are homogeneous, the T_m was determined for maculatus as 85.0° C (corresponding to a mean GC-content of 38.3%) for variatus as 86.0° C (GC=40.7%), for helleri as 85.0° C (GC=39.3%). Reassociation of sheared denatured DNA indicated approximately 90% single copy sequences, the remaining 10% are predominantly multiple copy sequences. The complexity of single copy DNA was determined from reassociation kinetics for maculatus as 3.97×10⁸ base pairs, for variatus as 4.31×10⁸ base pairs, and for helleri as 4.49×10⁸ base pairs. The DNA of the three species upon isopycnic density gradient centrifugation in the presence of the fluorescence dye Hoechst 33258 shows in addition to the main band, two heavy (GC-rich) satellites, denoted in the order of increasing density, components I and II. Analytical centrifugation reveals for the main band DNA a buoyant density of 1.6980 gcm^-3 (GC=38.7%), for component I 1.7080 gcm^-3 (GC=48.9%), for component II 1.7150 gcm^-3 (GC=56.1%). Each of the components comprises approximately 0.38% of the total DNA. Complete digestion of components I and II with restriction enzymes EcoRI and BamHI yields a complex banding pattern upon agarose gel-electrophoresis. A 2.4 kb fragment of component I and a 5.3 kb fragment of component II of helleri, cloned and amplified in the pBR322/E. coli RR1 system, hybridize efficiently to purified nuclei of liver. Furthermore, restriction fragments of component II DNA, transferred to nitrocellulose by Southern-blotting, hybridize with 18S and 28S ribosomal DNA.     

The carbonyl reactivity of 3-bromopyruvate and related compounds

The covalent hydration of β-halopyruvic acids and β-halopyruvamides has been investigated in the uv region by stopped-flow techniques. In aqueous solutions of β-bromopyruvate and related compounds, the geminal diol is the predominant form at all pH values. Kinetic investigations have also been carried out on these hydrations. General bases enhance the rate of approaching the equilibrium. Specific acid catalysis was not detected. In the water-catalyzed reaction of pyruvamides, the relationship between the equilibrium constants K and the rate constants of the forward reaction shows that the transition state is more productlike.     

Immunocytochemical identification of proctolinlike immunoreactivity in the terminal ganglion and hindgut of the cockroach Periplaneta americana (L.)

Summary In the American cockroach, the distribution and connections of neuronal elements of the terminal ganglion-proctodeal nerve-hindgut system were investigated by means of immunohistochemical methods and axonal CoCl₂ iontophoresis. Proctolinlike immunoreactivity was localized within neurons of the terminal ganglion projecting into the proctodeal nerve on the one hand, and in nerve cells without a direct connection to this system on the other. Immunohistochemically, in whole mount preparations fibres of the proctodeal nerve and terminal structures in the hindgut musculature exhibit strong proctolinlike immunoreactivity. At the light- and electron-microscopic levels the pathways of about 30 somata of the proctodeal neural system were characterized by cobalt chloride iontophoresis. The relationships of cobalt filled and immunoreactive neuronal structures are discussed.For the preparation of tritiated proctolin we thank Dr. S. Reißmann, WB Biochemie, Sektion Biologie, FSU JenaThe authors wish to thank G. Schörlitz, Film- und Bildstelle, FSU Jena, for photographs of whole mount preparations and Ms. A. Zinßer and Mrs. B. Cosack for excellent technical assistance.