Two new species of Leporinus (Characiformes: Anostomidae) from the Brazilian Amazon,and redescription of Leporinus striatus Kner 1858

Two new species of Leporinus are described from tributaries of the Rio Amazonas in Brazil. One species is known from the Jari and Tapajós River basins, and is identified on the basis of a gas bladder reduced in size, a dark midlateral stripe on the body, dark transverse bars on the dorsum, a subinferior mouth, three teeth on the premaxilla, four teeth on the dentary and 16 scale rows around the caudal peduncle. The second new species is known from the Tocantins, Xingu and Tapajós River basins, and is identified on the basis of three dark longitudinal stripes on the body, a subinferior mouth, three teeth on the premaxilla, four teeth on the dentary and 12 scale rows around the caudal peduncle. In addition, Leporinus striatus is redescribed based on type and additional specimens from the Río de La Plata, Amazonas, Orinoco, Atrato, Magdalena and Sinu River basins. Leporinus striatus is identified on the basis of four dark longitudinal stripes on the body, a subterminal mouth, three teeth on the premaxilla, four teeth on the dentary and 16 scale rows around the caudal peduncle.     

Site selection in a polymorphic mangrove snail

Three species of littorinid snail live on mangroves of the genus Rhizophora on the north coast of Papua New Guinea. They have recently been placed in the genus Littoraria. The species are L. scabra and L. intermedia , which are monomorphic and cryptic and live on bark, and L. pallescens which is polymorphic and lives in foliage. Littoraria intermedia was found mostly on mangroves facing on to partially fresh water, while L. scabra occurred only at sites facing on to the sea; L. pallescens occurs at both types of site. When kept together in plastic containers, L. pallescens shows a greater propensity to climb than the other two species. The morphs of L. pallescens are principally yellow, orange or dark. Orange is present at a frequency of 0–9% and yellow at 10–50%. There is little evidence of geographical variation in frequency over 80 km of coast, although one central locality has a significantly higher frequency of yellow than sites to the north or south of it. Throughout the tropics where the species occurs, orange is the rarest and yellow usually the next rarest morph. Larger individuals are on average higher in the foliage than smaller ones, and there is a higher frequency of yellows among larger shells than smaller ones. As the air temperature increases, a progressively larger fraction of a sample was found to be on the under-surfaces of leaves rather than on the upper epidermis or on flower or leaf buds. When over 30% of a sample is situated on lower surfaces there is a significant excess of yellows and a deficiency of darks on the upper surfaces. This indicates that individuals selectively take up different positions depending on morph colour, resulting in a degree of optimal background matching. Such a choice of location may be of direct relevance to the maintenance of the polymorphism. A difference in morph frequency between the same sites examined in 1979 and 1984 is interpreted as being a result of site selectivity.     

Defence glands in the giant spiny phasmid Extatosoma tiaratum

Adults of Extatosoma tiaratum liberate a strong smell when handled. The smell is associated with a colourless, volatile liquid which is apparently harmless to man. It is ejected on to the thorax of the insect, and on to the hands of the investigator, from a pair of tubercles located on the anterior border of the prothorax. The tubercles have a slit-like aperture through which the secretion is sprayed on attack. The secretion is produced by two glands in the thorax, each comprising a pair of tubes which unite just beneath the tubercle. The tubes consist of a thick, glandular epithelium lined with a thin layer of cuticle; most of the gland is enveloped in a layer of muscle. The defence reaction is discussed in relation to that of other phasmids.     

Risk assessment: the importance of genetic polymorphisms in man

Spontaneous mutation was greatly increased in a localized region of the chromosome of Haemophilus influenzae, but not at other loci, by a nov gene mutation called novC that increased DNA supercoiling. Another nov gene mutation, called novD, decreased spontaneous mutation in the same localized region and depressed DNA supercoiling. Both mutations, which code for the gyrase B subunit, have been cloned, and the cloned versions also altered mutagenesis and supercoiling in a similar fashion as the two mutations on the chromosome, although novC on the plasmid caused somewhat less mutation than on the chromosome. We postulate that the effects of the gyrase B mutations on the chromosome result from their effects on supercoiling because of increased gyrase near its site of production. The fact that the novC on a plasmid does not cause mutagenesis except in the same localized region that is altered by this mutation on the chromosome, is difficult to explain. One possibility is that there is a complex of proteins in this region which is necessary for the effects on supercoiling and thus, also on mutagenesis.     

Receptor regulation, competitive antagonism and pA2.

A growing body of evidence suggests that the number of drug receptors on cell surfaces is not fixed, but is dynamically regulated by circumstances that include exposure to the ligand itself. Because most traditional theories of drug action are based on the assumption of a fixed number of receptors, it is desirable to examine the importance of this regulatory process on the interpretation of dose-effect data. Of special interest is the impact of a variable receptor number on the equation of competitive antagonism and associated pA2 which, in the traditional theory, is a quantitative measure of antagonist-receptor affinity. Using a simple model of drug-induced endocytosis or exocytosis, it is shown that if the rate of either is appreciable, the pA2 is no longer a simple measure of affinity.     

Testing for ordered group effects in binary and continuous outcomes

A likelihood ratio test is proposed for the detection of an ordered group effect on bivariate responses where one response is binary and the other is continuous. The procedure is based on a conditional logistic model for the binary response given the continuous outcome. We also develop a likelihood ratio test for simultaneously determining the goodness of fit of the ordering assumption on both responses. Our approach is motivated by a particular toxicity study application involving laboratory animals that focused on the effect of a food color additive on the development of reticuloendothelial (RE) tumors. A brief discussion on extensions to the methodology introduced here is also given, along with a comparison of the approach with a marginal strategy where the presence of an ordered group effect is assessed independently for each of the two responses.     

Detection and Prediction of Tooth Mobility During the Periodontitis Healing Process

The focus of the article is on a generic approach to prediction of a healing process based on automatic measurement and modelling of mechanical disease indicators. As a specific example the healing process after treatment of advanced periodontitis is characterised and predicted based on measurement of tooth mobility (TM). For the measurement a new mechatronic instrument was developed that includes a pneumatically driven probe with incorporated sensors of tooth displacement and loading force. TM is measured by a computer controlled data acquisition system and predicted by a non-parametric regression. Similarly as in the characterisation of technical processes, a measured sample is described by TM time series detected on a particular patient, while the regression is determined by a set of samples obtained from a group of patients following periodontal therapy. The influence of surgical access therapy and systemic administration of metronidazole as an adjunct to the mechanical treatment is demonstrated. For this purpose the average changes of tooth mobility are determined on variously treated subgroups. A new method of healing process prediction is demonstrated and its performance is described by a prediction quality.     

Detection and prediction of tooth mobility during the periodontitis healing process

The focus of the article is on a generic approach to prediction of a healing process based on automatic measurement and modelling of mechanical disease indicators. As a specific example the healing process after treatment of advanced periodontitis is characterised and predicted based on measurement of tooth mobility (TM). For the measurement a new mechatronic instrument was developed that includes a pneumatically driven probe with incorporated sensors of tooth displacement and loading force. TM is measured by a computer controlled data acquisition system and predicted by a non-parametric regression. Similarly as in the characterisation of technical processes, a measured sample is described by TM time series detected on a particular patient, while the regression is determined by a set of samples obtained from a group of patients following periodontal therapy. The influence of surgical access therapy and systemic administration of metronidazole as an adjunct to the mechanical treatment is demonstrated. For this purpose the average changes of tooth mobility are determined on variously treated subgroups. A new method of healing process prediction is demonstrated and its performance is described by a prediction quality.     

Offspring-parent regression for a binary trait

Summary Offspring-parent regression is often used to estimate the heritability of a quantitative trait. It is shown that for a purely binary trait, the regression of offspring on one parent is always linear, while that on both parents or mid-parent is generally nonlinear. However, the regressions are linear on a logistic scale.     

The use of pH indicators to identify suitable environments for freezing samples in aqueous and mixed aqueous/nonaqueous solutions

The colours of frozen solutions containing pH indicators are shown to provide a test for changes in pH in the solvent environment which occur on freezing. Yeast alcohol dehydrogenase loses activity on freezing in phosphate buffer (a buffer in which pH indicator colour changes shows a marked decrease in pH on freezing) but when frozen in bis-tris, Hepes, or N-glycylglycine buffers (all of which show little change in the colour of universal pH indicator and hence of pH on freezing) is stable on freezing. The effects of freezing in different buffer systems on the rate of decomposition of NADPH, and on the rate hydrolysis of 4-nitrophenyl acetate, are rationalised in terms of the pH shifts in these buffers which were determined using universal pH indicator. It is proposed that a major reason for the instability of samples on freezing is the pH changes which occur when some systems are frozen. From the results a general scheme for selecting the best environment for safely freezing samples is proposed which is based on the use of pH indicators.     

Confidence intervals and sample sizes.

In a recent paper, Beal (1989, Biometrics 45, 969-977) considers the problem of determining the appropriate sample size when inference about a parameter theta is to be made on the basis of a confidence interval (CI). He suggests that the sample size should be chosen so that the probability that the length of the CI is less than a given value, conditional on the interval including the true theta, is greater than a specified level. In this note, in which we concentrate on two-sided intervals, this suggestion is examined, as is the effect of uncertainty in our knowledge of the population variance sigma 2 on estimates of sample size.     

A Review of: “Immobilized Enzymes: Research and Development,I. Chibata,Ed., Kodansha,Ltd., Tokyo; John Wiley and Sons/HaIsted Press,New York, 1978; hardbound, 284 pages, $35.00”

A device of a new dish for the culturing of cells on a biological substrate, the eye lens capsule, is described. With the aid of this dish it is possible to investigate the possible interrelationships between the cell substratum and various biochemical characteristics of the cell. It is shown that the protein biosynthetic pattern differs between lens cells cultured on lens capsule as a substrate and cells cultured on foil. Moreover, the new dish opens the possibility to culture epithelial cells on a lens capsule, which gives an alternative to the culture of these cells on a collagen substrate.     

Camptothecin inhibits both the cleavage and religation reactions of eukaryotic DNA topoisomerase I.

We investigated the mode of action of the antitumor drug, camptothecin, by use of a partly double-stranded suicide DNA substrate which enables uncoupling of the cleavage and religation half-reactions of topoisomerase I. The suicide DNA substrate contains a single topoisomerase I site at which SDS cleavage is strongly enhanced by camptothecin on normal double-stranded DNA. The results show that the religation reaction of topoisomerase I per se is strongly inhibited at this site compared to site that is only marginally affected by camptothecin on double-stranded DNA. This study hereby directly demonstrates that camptothecin-mediated stability of a topoisomerase I-DNA complex is sequence-dependent. The influence of camptothecin on the suicide cleavage reaction of topoisomerase I was also investigated. Surprisingly, the cleavage reaction per se is strongly inhibited by the drug. However, reformation of a cleavable suicide DNA substrate, which is fully double-stranded downstream from the cleavage position except for a nick, completely reverses the inhibitory effect of the drug on the cleavage reaction. The results suggest that the inhibitory effect of camptothecin on cleavage is due to a general decrease in the noncovalent interaction of topoisomerase I with partly double-stranded suicide DNA substrates. Based on the findings, a plausible model for camptothecin action is discussed.     

Choice of coordinates on a toroidal magnetic surface

Construction of global angular coordinates on an arbitrarily shaped toroidal surface is considered. It is shown that global orthogonal, isothermal, and semigeodesic geometric coordinates can always be introduced on a toroidal surface. Such coordinates can be rather efficient in solving problems of plasma equilibrium and stability in a magnetic field. At the same time, it is impossible to introduce global geodesic coordinates and coordinates based on curvature lines. It is proposed to use a magnetic analogy to search for transformations of global angular geometric coordinates that simplify the expression for the length element on an arbitrary toroidal surface. An algorithm for the computation of such coordinates is offered. With this approach, a “virtual” magnetic field such that its force lines, as well as the lines orthogonal to them, are closed is searched for on the toroidal surface. These lines comprise a geometric coordinate grid on an actual magnetic surface formed by the actual magnetic field.     

Target Specificity of the E3 Ligase LUBAC for Ubiquitin and NEMO Relies on Different Minimal Requirements

The ubiquitination of NEMO with linear ubiquitin chains by the E3-ligase LUBAC is important for the activation of the canonical NF-κB pathway. NEMO ubiquitination requires a dual target specificity of LUBAC, priming on a lysine on NEMO and chain elongation on the N terminus of the priming ubiquitin. Here we explore the minimal requirements for these specificities. Effective linear chain formation requires a precise positioning of the ubiquitin N-terminal amine in a negatively charged environment on the top of ubiquitin. Whereas the RBR-LDD region on HOIP is sufficient for targeting the ubiquitin N terminus, the priming lysine modification on NEMO requires catalysis by the RBR domain of HOIL-1L as well as the catalytic machinery of the RBR-LDD domains of HOIP. Consequently, target specificity toward NEMO is determined by multiple LUBAC components, whereas linear ubiquitin chain elongation is realized by a specific interplay between HOIP and ubiquitin.     

Multiple DNA and protein sequence alignment on a workstation and a supercomputer

This paper describes a multiple alignment method using a workstationand supercomputer. The method is based on the alignment of aset of aligned sequences with the new sequence, and uses a recursiveprocedure of such alignment. The alignment is executed in areasonable computation time on diverse levels from a workstationto a supercomputer, from the viewpoint of alignment resultsand computational speed by parallel processing. The applicationof the algorithm is illustrated by several examples of multiplealignment of 12 amino acid and DNA sequences of HIV (human immunodeficiencyvirus) env genes. Colour graphic programs on a workstation andparallel processing on a supercomputer are discussed. Received on April 26, 1988; accepted on July 7, 1988     

SOCIAL SELECTION AND THE EVOLUTION OF ANIMAL SIGNALS

Social selection is presented here as a parallel theory to sexual selection and is defined as a selective force that occurs when individuals change their own social behaviors, responding to signals sent by conspecifics in a way to influence the other individuals' fitness. I analyze the joint evolution of a social signal and behavioral responsiveness to the signal by a quantitative-genetic model. The equilibria of average phenotypes maintained by a balance of social selection and natural selection and their stability are examined for two alternative assumptions on behavioral responsiveness, neutral and adaptive. When behavioral responsiveness is neutral on fitness, a rapid evolution by runaway selection occurs only with enough genetic covariance between the signal and responsiveness. The condition for rapid evolution also depends on natural selection and the number of interacting individuals. When signals convey some information on signalers (e.g., fighting ability), behavioral responsiveness is adaptive such that a receiver's fitness is also influenced by the signal. Here there is a single point of equilibrium. The equilibrium point and its stability do not depend on the genetic correlation. The condition needed for evolution is that the signal is beneficial for receivers, which results from reliability of the signal. Frequency-dependent selection on responsiveness has almost no influence on the equilibrium and the rate of evolution.     

A Note on Probabilistic Models over Strings: The Linear Algebra Approach

Probabilistic models over strings have played a key role in developing methods that take into consideration indels as phylogenetically informative events. There is an extensive literature on using automata and transducers on phylogenies to do inference on these probabilistic models, in which an important theoretical question is the complexity of computing the normalization of a class of string-valued graphical models. This question has been investigated using tools from combinatorics, dynamic programming, and graph theory, and has practical applications in Bayesian phylogenetics. In this work, we revisit this theoretical question from a different point of view, based on linear algebra. The main contribution is a set of results based on this linear algebra view that facilitate the analysis and design of inference algorithms on string-valued graphical models. As an illustration, we use this method to give a new elementary proof of a known result on the complexity of inference on the “TKF91” model, a well-known probabilistic model over strings. Compared to previous work, our proving method is easier to extend to other models, since it relies on a novel weak condition, triangular transducers, which is easy to establish in practice. The linear algebra view provides a concise way of describing transducer algorithms and their compositions, opens the possibility of transferring fast linear algebra libraries (for example, based on GPUs), as well as low rank matrix approximation methods, to string-valued inference problems.     

Monoclonal antibody to murine embryos defines a stage-specific embryonic antigen expressed on mouse embryos and human teratocarcinoma cells

A murine stage-specific embryonic antigen (SSEA3) is defined by reactivity with a monoclonal antibody prepared by immunization of a rat with 4- to 8-cell-stage mouse embryos. This antigenic determinant, present on oocytes, becomes restricted first to the inner cell mass at the blastocyst stage, and later to the primitive endoderm. Murine teratocarcinoma stem cells do not react with this antibody, whereas human teratocarcinoma stem cells are SSEA3-positive. This antigenic determinant is not expressed on a variety of other human and murine cell lines, but is found on the surface of human erythrocytes. It is a carbohydrate and is present on both cell-surface glycolipids and glycopeptides. These results demonstrate the feasibility of identifying stage-specific antigenic determinants with monoclonal antibody prepared against embryos. The need for thorough screening on a variety of cell types to establish developmentally important cross-reactivities is also emphasized.