Tool use in capuchin monkeys: Distinguishing between performing and understanding

A horizontal plexiglas tube containing a food-reward was presented to four naive tufted capuchins and suitable sticks were provided to push the reward out. Three monkeys out of four spontaneously used the tools and showed very different styles of solving the task. In more complex conditions, in which the sticks needed to be combined or actively modified in order to become effective, the monkeys were always successful; however, their performance was loaded with errors which did not disappear throughout the trials. Evidence of a difference between success in solving the problem and its understanding was found. This suggests that although capuchins can discover new means through active experimentation, they do not mentally represent the characteristics necessary for a tool to be effective, nor do they modify the tool appropriately beforehand. At this level, a major difference with chimpanzees emerges.     

Science in the age of mechanical reproduction: moral and epistemic relations between diagrams and photographs

Sociologists, philosophers and historians of science are gradually recognizing the importance of visual representation. This is part of a more general movement away from a theory-centric view of science and towards an interest in practical aspects of observation and experimentation. Rather than treating science as a matter of demonstrating the logical connection between theoretical and empirical statements, an increasing number of investigations are examining how scientists compose and use diagrams, graphs, photographs, micrographs, maps, charts, and related visual displays. This paper focuses on diagrams in biology, and tries to demonstrate how diagrams are an integral part of the production of scientific knowledge. In order to disclose some of the distinctive practical and analytical uses of diagrams, the paper contrasts the way diagrams and photographs are used in biological texts. Both diagrams and photographs are shown to be “constructions” that separately and together mediate the investigation of scientific phenoman.     

A method for determining overall protein fold from NMR distance restraints

Summary We describe a simple method for determining the overall fold of a polypeptide chain from NOE-derived distance restraints. The method uses a reduced representation consisting of two particles per residue, and a force field containing pseudo-bond and pseudo-angle terms, an electrostatic term, but no van der Waals or hard shell repulsive terms. The method is fast and robust, requiring relatively few distance restraints to approximate the correct fold, and the correct mirror image is readily determined. The method is easily implemented using commercially available molecular modeling software.     

Climate–ecosystem modelling made easy: The Land Sites Platform

Dynamic Global Vegetation Models (DGVMs) provide a state-of-the-art process-based approach to study the complex interplay between vegetation and its physical environment. For example, they help to predict how terrestrial plants interact with climate, soils, disturbance and competition for resources. We argue that there is untapped potential for the use of DGVMs in ecological and ecophysiological research. One fundamental barrier to realize this potential is that many researchers with relevant expertize (ecology, plant physiology, soil science, etc.) lack access to the technical resources or awareness of the research potential of DGVMs. Here we present the Land Sites Platform (LSP): new software that facilitates single-site simulations with the Functionally Assembled Terrestrial Ecosystem Simulator, an advanced DGVM coupled with the Community Land Model. The LSP includes a Graphical User Interface and an Application Programming Interface, which improve the user experience and lower the technical thresholds for installing these model architectures and setting up model experiments. The software is distributed via version-controlled containers; researchers and students can run simulations directly on their personal computers or servers, with relatively low hardware requirements, and on different operating systems. Version 1.0 of the LSP supports site-level simulations. We provide input data for 20 established geo-ecological observation sites in Norway and workflows to add generic sites from public global datasets. The LSP makes standard model experiments with default data easily achievable (e.g., for educational or introductory purposes) while retaining flexibility for more advanced scientific uses. We further provide tools to visualize the model input and output, including simple examples to relate predictions to local observations. The LSP improves access to land surface and DGVM modelling as a building block of community cyberinfrastructure that may inspire new avenues for mechanistic ecosystem research across disciplines.     

The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine pancreatic trypsin inhibitor dynamics in water as a test case for solvent influences.

In this paper the NMR secondary chemical shifts, that are estimated from a set of 3D-structures, are compared with the observed ones to appraise the behaviour of a known x-ray diffraction structure (of the bovine pancreatic trypsin inhibitor protein) when various molecular dynamics are applied. The results of a 200 ps molecular dynamics under various conditions are analysed and different ways to modify the molecular dynamics are considered. With the purpose of avoiding the time-consuming explicit representation of the solvent (water) molecules, an attempt was made to understand the role of the solvent and to develop an implicit representation, which may be refined. A simulation of hydrophobic effects in an aqueous environment is also proposed which seems to provide a better approximation of the observed solution structure of the protein.     

Effects of NEM on Voltage-activated Chloride Conductance in Toad Skin

The regulation of the voltage-activated chloride current conductance (G _Cl ) in toad skin was investigated by the use of the SH reagents N-ethylmaleimide (NEM) and p-chloro-mercuricbenzenesulfonic acid PCMBS. This anion pathway is controlled by a voltage-sensitive gating regulator. Mucosal application of NEM decreased the voltage-activation in a time and concentration dependent manner, half-maximal inhibition being exerted at a concentration of 30 μm within 20 min. At concentrations higher than 100 μm, the voltage-activated G _Cl was near-completely and irreversibly inhibited in less than 10 min. Resting, deactivated conductance was essentially unaffected. NEM had no effect on active sodium transport (measured as I _sc ) under conditions, which fully dissipated the voltage-activated G _Cl . After complete inhibition of the voltage-activated G _Cl with NEM, chloride conductance could still be stimulated by CPT-cAMP as in control tissues. Under these conditions, NEM at concentrations above 1 mm decreased G _Cl reversibly. Mucosal application of PCMBS at 500 μm inhibited the activated conductance by 35%, which was slightly reversible. Inhibition of voltage-activated G _Cl , which was observed after mucosal addition of the membrane-impermeable NEM analogue, eosin-5-maleimide, was completely reversible after washout. This suggests that the binding site for the maleimide is not accessible from the external face of the apical membrane. Brief application of NEM at lower concentrations (1–3 min, ≤100 μm) led to partial inhibition of G _Cl , followed by occasionally complete recovery upon washout of NEM. Recovery of voltage-activated G _Cl was progressively attenuated and eventually disappeared after subsequent brief applications of NEM. This could reflect recruitment of permeation/control sites from a finite pool. The data are discussed in the frame of a working model for the voltage-activated Cl⁻-pathway, that contains two principle components, i.e., an anion-selective permeation path which is controlled by regulatory protein(s). Received: 18 December 1996/Revised: 28 April 1997     

Graphical comparison of resemblance measures in phytosociology

A simple graphical method, COREM, is described for the comparison of quantitative resemblance measures. The basis of the method is the ordered comparison case series (OCCAS) composed of relevé pairs ranked in decreasing order of similarity. For a given OCCAS, values of given resemblance functions are calculated and plotted in COREM.Delta resemblance (DR) is defined as the rate of change between two neighbouring relevé pairs in the OCCAS. High mean delta resemblance (% MathType!MTEF!2!1!+-% feaafeart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqaqpepeea0xe9qqVa0l% b9peea0lb9sq-JfrVkFHe9peea0dXdarVe0Fb9pgea0xa9pue9Fve9% Ffc8meGabaqaciGacaGaaeqabaWaaeaaeaaakeaadaqdaaqaaGqaai% aa-reacaWFsbaaaaaa!392E!\[\overline DR \]) of a resemblance measure indicates a high power of resolution and small standard deviation (SDDR) is indicative of linearity. A measure of efficiency combines % MathType!MTEF!2!1!+-% feaafeart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqaqpepeea0xe9qqVa0l% b9peea0lb9sq-JfrVkFHe9peea0dXdarVe0Fb9pgea0xa9pue9Fve9% Ffc8meGabaqaciGacaGaaeqabaWaaeaaeaaakeaadaqdaaqaaGqaai% aa-reacaWFsbaaaaaa!392E!\[\overline DR \] and SDDR in the coefficient of variation for delta resemblance (CVDR). An efficient measure shows balanced sensitivity to the common and differential species. With the method COREM locally optimal resemblance measures may be selected for any given set of relevés which produce the sharpest separation of clusters. A reasonable compromise is to use types of measures, such as the similarity ratio (SIM6), Czekanowski coefficient (SIM8), or floristic similarity (SIM9), which have the best chance of being successful in most relevé sets. A study of transformation functions on Braun-Blanquet values with the help of COREM demonstrates that the combined transformation is the most advantageous for clustering. It is shown that standardization by relevés, or conversion to unit sum has undesirable effects.During the preparation of this paper the author was a recipient of a Postgraduate Scholarship, Deutscher Akademischer Austauschdients, Dortmund, KFA Abteilung Algenforschung, Germany. The author would like to thank L. Orlóci, P. Juhász-Nagy and E. van der Maarel for valuable suggestions, and comments.     

Chaos game representation of coding regions of human globin genes and alcohol dehydrogenase genes of phylogenetically divergent species

Summary Chaos game representation (CGR) is a novel holistic approach that provides a visual image of a DNA sequence quite different from the traditional linear arrangement of nucleotides. Although it is known that CGR patterns depict base composition and sequentiality, the biological significance of the specific features of each pattern is not understood. To systematically examine these features, we have examined the coding sequences of 7 human globin genes and 29 relatively conserved alcohol dehydrogenase (Adh) genes from phylogenetically divergent species. The CGRs of human globin cDNAs were similar to one another and to the entire human globin gene complex. Interestingly, human globin CGRs were also strikingly similar to human Adh CGRs. Adh CGRs were similar for genes of the same or closely related species but were different for relatively conserved Adh genes from distantly related species. Dinucleotide frequencies may account for the self-similar pattern that is characteristic of vertebrate CGRs and the genome-specific features of CGR patterns. Mutational frequencies of dinucleotides may vary among genome types. The special features of CG dinucleotides of vertebrates represent such an example. The CGR patterns examined thus far suggest that the evolution of a gene and its coding sequence should not be examined in isolation. Consideration should be given to genome-specific differential mutation rates for different dinucleotides or specific oligonucleotides. Offprint requests to: S. M. Singh