Knowledge-based simulation of DNA metabolism: prediction of enzyme action

We have developed a knowledge-based simulation of DNA metabolismthat accurately predicts the actions of enzymes on DNA undera large number of environmental conditions. Previous simulationsof enzyme systems rely predominantly on mathematical models.We use a frame-based representation to model enzymes, substratesand conditions. Interactions between these objects are expressedusing production rules and an underlying truth maintenance system.The system performs rapid inference and can explain its reasoning.A graphical interface provides access to all elements of thesimulation, including object representations and explanationgraphs. Predicting enzyme action is the first step in the developmentof a large knowledge base to envision the metabolic pathwaysof DNA replication and repair. Received on February 1, 1990; accepted on October 2, 1990     

Seismic and auditory tuning curves from bullfrog saccular and amphibian papular axons

We present seismic and auditory frequency tuning curves of individual bullfrog, Rana catesbeiana, saccular and amphibian papilla axons that responded to both seismic and auditory stimuli. In this study we found: 1) most saccular axons respond well to auditory stimuli with moderate signal strength (50-70 dB SPL) as well as to seismic stimuli; 2) most amphibian papilla axons respond well to seismic stimuli as well as to auditory stimuli, and their seismic sensitivities are comparable to those of saccular axons (responding to sinusoidal stimuli with peak accelerations in the range 0.001 to 0.1 cm/S2); 3) the responses to both seismic and auditory stimuli from both saccule and amphibian papilla are tuned, i.e. the strength of the response varies with the frequency of the stimulus; and this tuning is clearly not the result of second order resonance; 4) in individual axons the tuning properties for seismic stimuli often are not the same as those for auditory stimuli, a fact that may provide clues about how the stimulus signal energy is transferred to the hair cells in each case.     

Physiology and taxonomy of scleractinian corals: a case study in the genus Stylophora

The morphology and skeletal characteristics of colonies of the coral genus Stylophora living on the reef edge at 1 m depth on the Jordanian coast of the Gulf of Aqaba (Red Sea) are those of S. mordax (Dana 1846) which has not been reported previously from that area. These colonies were considered earlier as ecomorphs of S. pistillata (Esper 1797) which lives down to at least 67 m on the reef slopes. Growth, organic content and metabolism were compared in colonies living at different depths (1,5,10 and 30 m). The trends of twelve parameters between 1 and 5 m were different from the variation observed between 5 and 30 m. Colonies living at 1 m have a higher chlorophyll content but a lower metabolic activity and growth rate than colonies living at 5 m. Most of these pecularities cannot be explained by the influence of environmental factors. It is therefore suggested that S. mordax is a valid taxon.     

Fossil primate hands: A review and an evolutionary inquiry emphasizing early forms

The paleontological evidence pertaining to the evolution of the modern diversity in structure and function of primate hands is reviewed. A reconstructed digit ofPlesiadapis shows characters and functional capacities typical of an arboreal way of life. In euprimates, we describe the strepsirhine morphotype hand, characterized by a relatively high degree of pollical divergence, features of the ulnocarpal articulation that imply an enhanced capacity for ulnar deviation, and relatively long digits; this hand is specialized for grasping. Hand remains ofSmilodectes, Adapis and a Messel adapiform reveal a remarkable diversity in carpal structure achieved in these Eocene adapiforms, due to differing locomotor evolutionary pathways. The subfossil lemuriformsMegaladapis andPalaeopropithecus both show stereotyped (but different) grasping capabilities. The simiiform morphotype hand combines a relatively low degree of pollical divergence, features of the ulnocarpal articulation that imply a limited capacity for ulnar deviation, and relatively long metacarpals and short digits. This type of hand anatomy is mechanically well-suited to arboreal palmigrade quadrupedalism. The hands ofPliopithecus andMesopithecus are generally monkey-like.Oreopithecus' hand fits with its presumed suspensory habits. The hand ofProconsul suggests palmigrade quadrupedalism and climbing.Australopithecus afarensis' hand remains primarily a branch-grasping organ, with indications of enhanced manipulatory abilities.Homo habilis andParanthropus robustus illustrate two lines of increased tool-use abilities. The euprimate morphotype hand was elongated, had a short carpus and limited mobility, but the corresponding locomotor mode remains speculative. Considerations on hand evolution in some living primate groups are included in the final summary of hand evolution in primates.     

The cyclophilin multigene family of peptidyl-prolyl isomerases. Characterization of three separate human isoforms.

Cyclophilin (CyP), a major cytosolic protein possessing peptidyl-prolyl cis-trans isomerase activity, has been implicated as the specific receptor of the immunosuppressive drug cyclosporin A (CsA). To identify other potential CsA receptors related to CyP, two human cDNA libraries were screened under low stringency conditions using human CyP cDNA (encoding hCyP1) as a probe. Two cDNAs were identified which encode distinct proteins related to human hCyP1. These two novel proteins, designated hCyP2 and hCyP3, share 65 and 76% amino acid sequence homology with hCyP1, respectively. Both hCyP2 and hCyP3 contain NH2-terminal hydrophobic extensions of 32 and 42 amino acids, respectively. Protein-specific antibodies revealed the predominant association of hCyP2 and hCyP3 with membranes and subcellular organelles, which suggests that the amino-terminal leader sequences of the two CyP isoforms may act as signal peptides. In contrast to the results with hCyP1, Southern blot analysis indicated that both hCyP2 and hCyP3 gene sequences are represented infrequently in the human genome. Northern and Western blot analysis showed that the distribution of mRNA and proteins of the three hCyPs in differing tissues and cell types was similar. Each hCyP protein was expressed in Escherichia coli, purified, and shown to be an active peptidyl-prolyl isomerase. Substrate specificity was examined with 11 synthetic peptides (Suc-Xaa-Yaa-Pro-Phe-4-nitroanilide), and inhibition of the peptidyl-prolyl isomerase activities associated with hCyP1, hCyP2, and hCyP3 was studied with CsA, MeAla6-CsA and MeBm2t1-CsA. From both equilibrium considerations and the results of kinetic characterizations it is proposed that of these three CyP proteins, hCyP1 is the most likely intracellular target for CsA.     

Two-dimensional NMR investigation of iron-sulfur cluster electronic and molecular structure of oxidized Clostridium pasteurianum ferredoxin. Interpretability of contact shifts in terms of cysteine orientation.

A two-dimensional NMR study has been carried out on the four-iron clusters of a bacterial oxidized ferredoxin for the purpose of investigating the relationship between contact shift patterns and the orientation of the individual coordinated cysteines. The ferredoxin from Clostridium pasteurianum, CpFdox, was selected because of its extensive sequence homology, and likely close structural similarity, to the crystallographically characterized ferredoxin from Peptococcus aerogenes, Pa Fdox (Adman, E.T., Sieker, L.C., and Jensen, L. H. (1973) J. Biol. Chem. 248, 3987-3996). Rapid data collection rates with minimal but adequate acquisition time allowed the detection of numerous CpFdox cross-peaks from the contact-shifted and strongly relaxed coordinated cysteinyl C beta H protons in the resolved 10-20 ppm window. Relatively strong magnitude COSY cross peaks from the resolved eight cysteinyl C beta H resonance unambiguously locate the geminal C beta H partner for each residue; weaker cross-peaks locate the C alpha Hs from three of the residues. The geminal nature of the magnitude-COSY detected partners to the resolved C beta H peaks is confirmed by strong NOESY cross-peaks. The NOESY spectra, moreover, assign an additional two cysteinyl C alpha H resonances. The present results confirm some previous one-dimensional NOE assignments, revise others, and locate resonances previously undetected (Bertini, I., Briganti, F., Luchinat, C., and Scozzafara, A. (1990) Inorg. Chem. 29, 1874-1880). A striking pairwise pseudo-symmetry in cysteinyl contact shift patterns is observed which is attributed to the previously recognized pseudo-symmetry in the crystal of PaFdox. A detailed analysis of the structural/electronic determinants of the coordinated cysteine C beta H contact shift pattern is made, and the NMR data necessary for unique interpretation are identified. It is shown that analysis of the relaxation properties of cysteine beta-methylene protons provides the stereospecific assignments necessary for comparison of shift ratios with crystallographic structural data. The available structural data on PaFdox (Backes, G., Mino, Y., Loehr, T., Meyer, T., Cusanovich, M., Sweeney, W., Adman, E., and Sanders-Loehr, J. (1991) J. Am. Chem. Soc. 13, 2055-2064) are qualitatively but not quantitatively consistent with the observed cysteinyl contact shift pattern, with the NMR data reflecting more asymmetry than previous studies. A tentative assignment of a single pair of symmetry-related cysteines is proposed.(ABSTRACT TRUNCATED AT 400 WORDS)