Validation of the first step of the heuristic refinement method for the derivation of solution structures of proteins from NMR data

A new method for the analysis of NMR data in terms of the solution structure of proteins has been developed. The method consists of two steps: first a systematic search of the conformational space to define the region allowed by the initial set of experimental constraints, and second, the narrowing of this region by the introduction of additional constraints and optional refinement procedures. The search of the conformational space is guided by heuristics to make it computationally feasible. The method is therefore called the heuristic refinement method and is coded in an expert system called PROTEAN. The paper describes the validation of the first step of the method using an artificial NMR data set generated from the known crystal structure of sperm whale carbon monoxymyoglobin. It is shown that the initial search procedure yields a low-resolution structure of the myoglobin molecule, accurately reproducing its main topological features, and that the precision of the structure depends on the quality of the initial data set.     

The intracellular concentration of cyclic adenosine 3',5'-monophosphate is constant throughout the cell cycle of Escherichia coli

Abstract Both the intracellular and the extracellular concentration of cyclic AMP increases logarithmically in synchronously growing cultures of Escherichia coli . Thus, cyclic AMP by itself cannot regulate growth and division of the bacterium during the cell cycle.     

PHYLOGENETIC ANALYSIS OF THE EVOLUTION OF ALTERNATIVE SOCIAL BEHAVIOR IN THE MANAKINS (AVES: PIPRIDAE)

Phylogenetic analyses of lekking, lek spatial organization, and cooperative and coordinated lek display in the manakins (Aves: Pipridae) demonstrate that variation in social behavior in the group has a strong, phylogenetic component. Two of the three classes of social behavior examined also show significant phylogenetic constraints. Current adaptive plasticity models are insufficient to explain the phylogenetic variation in these behaviors in the manakins. These findings support the conclusion that vertebrate reproductive social behavior has an evolutionary history, and that it is not determined solely by adaptive individual plasticity to current conditions. The evolution of social behavior, particularly through sexual selection, can have historical consequences that can limit subsequent behavioral adaptation.     

A physiological analogy of the niche for projecting the potential distribution of plants

Aim  To develop a physiologically based model of the plant niche for use in species distribution modelling. Location  Europe. Methods  We link the Thornley transport resistance (TTR) model with functions which describe how the TTR’s model parameters are influenced by abiotic environmental factors. The TTR model considers how carbon and nutrient uptake, and the allocation of these assimilates, influence growth. We use indirect statistical methods to estimate the model parameters from a high resolution data set on tree distribution for 22 European tree species. Results  We infer, from distribution data and abiotic forcing data, the physiological niche dimensions of 22 European tree species. We found that the model fits were reasonable (AUC: 0.79–0.964). The projected distributions were characterized by a false positive rate of 0.19 and a false negative rate 0.12. The fitted models are used to generate projections of the environmental factors that limit the range boundaries of the study species. Main conclusions  We show that physiological models can be used to derive physiological niche dimensions from species distribution data. Future work should focus on including prior information on physiological rates into the parameter estimation process. Application of the TTR model to species distribution modelling suggests new avenues for establishing explicit links between distribution and physiology, and for generating hypotheses about how ecophysiological processes influence the distribution of plants.     

Cell degeneration during early development of hymenopteran olfactory sensilla

The imaginal pore plates of Hymenoptera apocrita so far examined embody five or six envelope cells respectively. In early developmental stages, however, supernumerary envelope cells have been found. The results are discussed in the context of cell death as a developmental phenomenon.     

On the mechanism of speed and altitude control in Drosophila melanogaster

ABSTRACT The total power output of tethered flying Drosophila melanogaster in still air depends on translational velocity components of image flow on the eye, whereas the orientation of the average flight force in the midsagittal plane of the fly is widely independent of visual input (Götz, 1968). The fly does not seem to control the vertical and the horizontal force component independently. Freely flying flies nevertheless generate different ratios between lift and thrust, simply by changing the inclination of their body. By the combined adjustment of the body angle and the total power output a fly appears to be able to stabilize height and speed (David, 1985). Here a possible mechanism is proposed by which the appropriate torque about the transverse body axis could be generated. Translational pattern motion influences the posture of the abdomen and the plane of wing oscillation. Thus the position of the centre of gravity relative to the flight force vector is changed. When abdomen and stroke plane deviate from an equilibrium state, a lever is generated by which the force vector will rotate the fly about its transverse axis.     

Partitioning of gonococcal LPS into phenol and water: Different LPS composition of in vivo and in vitro selected variants

Abstract Depending on the culture conditions, Pyrodictium occultum cells revealed two different types of fibers with significant differences in their width in the electron microscope. During growth on elemental sulfur preferentially fibres with a diameter of about 23 nm (type I) were produced. When elemental sulfur was substituted by thiosulfate fibers with a diameter of around 15 nm (type II), were the main appendages. Both types form hollow cylinders consisting of helically arranged sub-units with a wall thickness of 2–3 nm. A triple- layered unit membrane could not be found.     

Cell age-related differences in the interaction of a potential-sensitive fluorescent dye with nuclear envelopes of Acetabularia mediterranea

Abstract. To study whether an electrical potential difference exists across the nuclear envelope or inner nuclear membrane of plant cells, the authors have used an optical probe of membrane potential, the cationic fluorescent dye, DiOC₆(3) (MW = 572.5). This dye was microinjected into the nucleoplasm of isolated Acetabularia nuclei (which are still surrounded by a thin layer of cytoplasm) and its subnuclear localization visualized by fluorescence microscopy. Striking differences, which seemed to be correlated with the developmental stage of the isolated nucleus, were observed. In nuclei isolated from cells at the stage of early cap stage formation, the dye was restricted to the nuclear envelope. In nuclei isolated from cells with intermediate or fully developed caps, there was increased nucleoplasmic staining, and the staining of the envelope was frequently diminished or abolished. In all nuclei, the dye remained within the nucleus after injection. Cytoplasmic staining was only observed when nuclei isolated from cells at the stage of early cap formation were incubated in a hyper- or hypo-tonic medium. Various ionophores, injected before the dye into the nucleoplasm, had no effect on the subsequent nuclear localization of DiOC₆(3), although they did rapidly induce nucleolar condensation in nuclei isolated from cells at the stage of early cap formation. The results suggested that the electrical properties of Acetabularia nuclear envelopes or inner nuclear membranes change during cell maturation. Furthermore, the retention of the dye in the nucleoplasm under isotonic conditions indicated that the nuclear pores were not open channels for molecules of this size.     

Characterization of the calcium sensitivity of differentiation in SCC-13 human squamous carcinoma cells

Summary The sensitivity to calcium of the human squamous carcinoma cell line, SCC-13, was demonstrated and characterized. Cultures grown to confluence in the presence of 0.2 to 2 mM calcium had approximately 10-fold higher levels of particulate transglutaminase activity and envelope competence than those grown in low calcium (0.025 to 0.05 mM) medium. Raising the calcium from 0.025 to 1.8 mM induced expression of this enzyme and of competence over the course of a week. Conversely, for cultures grown to confluence in 1.8 mM calcium, subsequent reduction of calcium to 0.025 mM resulted in a substantial decline in transglutaminase over a similar time period. Immunoprecipitable transglutaminase was clearly identifiable in cultures grown in 1.8 mM calcium-containing medium but not in those grown in low calcium medium or in the presence of retinoic acid, suggestive of regulation at the level of mRNA accumulation or translation rather than posttranslational modification. This research was supported by Public Health Service grant AR 27130 from the National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, and National Research Service postdoctoral fellowship ES 05336 from the National Institute of Environmental Health Sciences, Research Triangle Park, NC.