Identification of the gene and characterization of the activity of the trans-aconitate methyltransferase from Saccharomyces cerevisiae.

We have identified the yeast open reading frame YER175c as the gene encoding the trans-aconitate methyltransferase of Saccharomyces cerevisiae. Extracts of a yeast strain with a disrupted YER175c gene demonstrate a complete loss of activity toward the methyl-accepting substrates trans-aconitate, cis-aconitate, DL-isocitrate, and citrate. Reintroduction of the YER175c gene on a plasmid results in an overexpression of the activity toward each of these methyl-accepting substrates. We now designate this gene TMT1 for trans-aconitate methyltransferase. We examined the methyl-accepting substrate specificity of this enzyme in extracts from overproducing cells. We found that trans-aconitate was the best substrate with a Km of 0.66 mM. Other substrates were recognized much more poorly, including cis-aconitate with a Km of 74 mM and the decarboxylation product itaconate with a Km of 44 mM. The ratio of the maximal velocity to the Km of these substrates was only 0.24% and 0.9% that of trans-aconitate; for other substrates including citrate and other tricarboxylate and dicarboxylate derivatives, this ratio ranged from 0.0003% to 0.062% that of trans-aconitate. We then asked if any of these compounds were present endogenously in yeast extracts. We were able to identify trans-aconitate 5-methyl ester as well as additional unidentified radiolabeled products when S-adenosyl-L-[methyl-3H]methionine was mixed with TMT1+ extracts (but not with tmt1- extracts), suggesting that there may be additional substrates for this enzyme. We showed that the product 5-methyl ester of trans-aconitate is not readily metabolized in yeast extracts. Finally, we demonstrated that the activity of the yeast trans-aconitate methyltransferase is localized in the cytosol and increases markedly as cells undergo the metabolic transition at the diauxic shift.     

Disequilibrium distribution of genotypes in the pairs of isozyme loci in the pine populations of the forest-steppe regions of Siberia

We performed an analysis of linkage disequilibrium of alleles of 15 allozyme loci in 35 populations of Scots pine in the Siberian part of the range between 50° and 56° N and 79° and 107° E. We found a significant deviation in the distribution of genotypes of 1–9 pairs of loci in the investigated samples. We established correlations between frequencies of certain pairs of linked loci with ecological conditions and geographical coordinates of habitats of the pine populations. We present the results of comparative analysis of the differences in certain morphological features of trees with significantly predominant genotypes for pairs of linked loci in three isolated populations: in the south of Krasnoyarsk krai, Khakassia, and Tuva.     

Simulation and study of the behaviour of the transversalis fascia in protecting against the genesis of inguinal hernias

Simulating the muscular system has many applications in biomechanics, biomedicine and the study of movement in general. We are interested in studying the genesis of a very common pathology: human inguinal hernia. We study the effects that some biomechanical parameters have on the dynamic simulation of the region, and their involvement in the genesis of inguinal hernias. We use the finite element method (FEM) and current models for the muscular contraction to determine the deformed fascia transversalis for the estimation of the maximum strain. We analysed the effect of muscular tissue density, Young's modulus, Poisson's coefficient and calcium concentration in the genesis of human inguinal hernia. The results are the estimated maximum strain in our simulations, has a close correlation with experimental data and the accepted commonly models by the medical community. Our model is the first study of the effect of various biological parameters with repercussions on the genesis of the inguinal hernias.     

Effects of the geometry of the immunological synapse on the delivery of effector molecules

Recent experiments focusing on the function of the immunological synapse formed between a T cell and an antigen-presenting cell raise many questions about its purpose. We examine the proposal that the close apposition of the cell membranes in the central region of the synapse acts to focus T-cell secretions on the target cell, thus reducing the effect on nearby cells. We show that the efficiency of targeted T-cell responses to closely apposed cells is only weakly dependent on the distance between the cells. We also calculate effective (diffusion-limited) rates of binding and unbinding for molecules secreted within the synapse. We apply our model to the stimulation of B cells by secreted interleukin-4 (IL-4), and find that very few molecules of IL-4 need be released to essentially saturate the IL-4 receptors on the B-cell surface.     

Experimental value of the biliary excretion of the conjugated form of SBP by the in vivo liver and by the isolated and perfused liver]

We first studied the uptake and excretion of the dye BSP by the isolated and perfused rat liver and by the rat liver in vivo. We then studied BSP-glutathion conjugation with these same methods. We found that benziodarone which induces a marked decrease of conjugation is able to inhibit in vitro the combination BSP-glutathion.     

Modelling the effects of adherence to the HIV fusion inhibitor enfuvirtide

Recently, the first drug in a new class of antiretroviral HIV drugs was approved, the fusion inhibitor enfuvirtide. We develop a mathematical model that describes the binding of the virus to T cells. We model the effect of enfuvirtide upon this process using impulsive differential equations. We find equilibria and determine stability in the case of no therapy and then when therapy is taken with perfect adherence. We determine analytical thresholds for the dosage and dosing intervals to ensure the disease-free equilibrium remains stable. We also explore the effects of partial adherence. Our theoretical results suggest that partial adherence may, at times, be worse than no therapy at all, but at other times may in fact as good as perfect adherence. It follows that patients should be counselled on the importance of adherence to this new antiretroviral drug.     

Certain Problems of the Pathophysiology of Schizophrenia in the Light of Data on the Development of Remissions and Recurrences

We shall give consideration to certain problems in the pathophysiology of schizophrenia on the basis of data on the development of remissions and recurrences of this disease. We have accumulated these data over the last several years in a clinical and pathophysiological study, from many aspects, of 640 schizophrenics.     

On the pleiotropic structure of the genotype-phenotype map and the evolvability of complex organisms

Analyses of effects of mutants on many traits have enabled estimates to be obtained of the magnitude of pleiotropy, and in reviews of such data others have concluded that the degree of pleiotropy is highly restricted, with implications on the evolvability of complex organisms. We show that these conclusions are highly dependent on statistical assumptions, for example significance levels. We analyze models with pleiotropic effects on all traits at all loci but by variable amounts, considering distributions of numbers of traits declared significant, overall pleiotropic effects, and extent of apparent modularity of effects. We demonstrate that these highly pleiotropic models can give results similar to those obtained in analyses of experimental data and that conclusions on limits to evolvability through pleiotropy are not robust.     

Deciphering the distribution of the savanna biome

? We aimed to identify the limits of savanna across Africa, Australia and South America. We based our investigation on the rich history of hypotheses previously examined: that the limits of savanna are variously determined by rainfall, rainfall seasonality, soil fertility and disturbance. ? We categorized vegetation on all continents as 'savanna' (open habitats with a C(4) grass layer) or 'not-savanna' (closed habitats with no C(4) grass layer) and used a combination of statistical approaches to examine how the presence of savanna varied as a function of five environmental correlates. ? The presence of savanna is constrained by effective rainfall and rainfall seasonality. Soil fertility is regionally important, although the direction of its effect changes relative to rainfall. We identified three continental divergences in the limits of savanna that could not be explained by environment. ? Climate and soils do not have a deterministic effect on the distribution of savanna. Over the range of savanna, some proportion of the land is always 'not-savanna'. We reconciled previous contradictory views of savanna limits by developing a new conceptual framework for understanding these limits by categorizing environmental factors into whether they had a positive or negative effect on woody growth and the frequency of disturbance.     

Geometrical models of the renewal of the epidermis

We give a review of the different models developed recently that describe the renewal of the epidermis. These models, based on concepts borrowed from statistical mechanics, geometry and topology, shed new light on the understanding of the organization and the dynamics of the system. We discuss in detail a topological model of the dynamics of the inner-most layer of the epidermis: the basal layer.     

Composition and intra-annual variation of the macroinfauna in the estuarine zone of the Pando Stream (Uruguay).

We studied the temporal patterns of macroinfaunal distribution in the estuarine portion of Pando Stream, Uruguay. We found a very low number of species and a high dominance of the polychaete Heteromastus similis. There were clear seasonal patterns in abundance with almost all species peaking in autumn, coinciding with the periods of higher salinity. Minimal values were found in winter and spring when salinity was at a minimum. We suggest that the seasonal pattern is a consequence of the combined effects of recruitment, and of high osmotic stress and disturbance during the periods of freshwater discharge that are common in winter and spring.     

Environmental drivers of the metacommunity structure of insects on the surface of tropical streams of the Amazon

Understanding how species are distributed according to environmental and spatial variation is still one of the main issues in community ecology. We analysed the responses of semiaquatic bugs (Gerromorpha: Hemiptera) to environmental and spatial processes considered drivers of metacommunity structure in Amazonian streams. We tested the hypotheses that environmental variables determine the metacommunity structure and that the spatial structures, both dendritic and overland, are not representative of the metacommunity structure. Environmental variables and semiaquatic bugs were collected from 39 stream sites. Spatial variables were calculated in two configurations – overland and hydrographic distances between streams. We used partial redundancy analysis to test the relative importance of environment and space on the metacommunity structure, considering the two spatial configurations separately. The environmental variables were the metacommunity drivers in tropical streams, mainly structured by the depth, canopy, embeddedness and slope variables. Our results also indicate little or no dispersion limitation, as no spatial patterns were found. Thus, environmental selection determines the semiaquatic bugs' metacommunity structure due to the achievement of optimal habitats through dispersal. We also believe that dispersion cannot be ruled out as a metacommunity driver, since the peculiarities of the group show seasonal changes in dispersion ability, and spatial patterns may occur under different temporal scales.     

Stability of proteins: temperature, pressure and the role of the solvent

We focus on the various aspects of the physics related to the stability of proteins. We review the pure thermodynamic aspects of the response of a protein to pressure and temperature variations and discuss the respective stability phase diagram. We relate the experimentally observed shape of this diagram to the low degree of correlation between the fluctuations of enthalpy and volume changes associated with the folding-denaturing transition and draw attention to the fact that one order parameter is not enough to characterize the transition. We discuss in detail microscopic aspects of the various contributions to the free energy gap of proteins and put emphasis on how a cosolvent may either enlarge or diminish this gap. We review briefly the various experimental approaches to measure changes in protein stability induced by cosolvents, denaturants, but also by pressure and temperature. Finally, we discuss in detail our own molecular dynamics simulations on cytochrome c and show what happens under high pressure, how glycerol influences structure and volume fluctuations, and how all this compares with experiments.     

Gene genealogies when the sample size exceeds the effective size of the population

We study the properties of gene genealogies for large samples using a continuous approximation introduced by R. A. Fisher. We show that the major effect of large sample size, relative to the effective size of the population, is to increase the proportion of polymorphisms at which the mutant type is found in a single copy in the sample. We derive analytical expressions for the expected number of these singleton polymorphisms and for the total number of polymorphic, or segregating, sites that are valid even when the sample size is much greater than the effective size of the population. We use simulations to assess the accuracy of these predictions and to investigate other aspects of large-sample genealogies. Lastly, we apply our results to some data from Pacific oysters sampled from British Columbia. This illustrates that, when large samples are available, it is possible to estimate the mutation rate and the effective population size separately, in contrast to the case of small samples in which only the product of the mutation rate and the effective population size can be estimated.     

Properties of the on-transient of the intracellular response in the barnacle photoreceptor

We have studied the on-transient of the receptor potential of the barnacle photoreceptor. Its amplitude has previously been shown to depend on light intensity and state of light-dark adaptation. We have examined its dependence on 1) the presence of a prolonged depolarizing afterpotential (PDA), 2) a background light, 3) added alcohol, or 4) decreased K⁺ concentration in the bath. We find that the relative on-transient amplitude tends to increase initially with increasing depolarization arising from 1)–4) and then to decrease again at higher depolarization. This behavior is qualitatively explainable by the cell's currentvoltage characteristics and by the adapting effect of the stimulus on the conductances arising from the PDA, the background light and the alcohol.Based on material presented at the European Neurosciences Meeting, Florence, September 1978     

Effect of the rate of phytoplankton growth on the spaced-time dynamics of plankton communities in an homogeneous environment

We use a conceptual mathematical reaction-diffusion model to investigate the mechanisms of spatial structure formation and complex temporal dynamics of plankton in a heterogeneous environment. We take into account basic trophic interactions, namely, "prey-predator" interactions between phytoplankton, zooplankton, and fish in upper layers of natural waters. We consider plankton as a passive contaminant in turbulent waters. We show that plankton structure formation can result from the difference in phytoplankton growth rate in neighboring habitats. Phytoplankton and zooplankton biomass is shown to undergo both regular and chaotic oscillations. The fish predation rate substantially affects the spatial and temporal dynamics of plankton in a heterogeneous environment.     

Effects of glutamate-induced excitotoxicity on calretinin-expressing neuron populations in the area postrema of the rat

We mapped the distribution of calretinin-immunoreactive neuron populations in a circumventricular organ of the rat, the area postrema, and investigated their sensitivity to excitotoxic stimuli mediated by subcutaneously administered monosodium glutamate. We were specifically interested to ascertain whether the presence of calretinin can, per se, confer an in vivo intrinsic resistance for area postrema neurons to glutamate excitotoxicity. We found that dense populations of calretinin-positive neurons displayed a subregional compartmentation in coronal sections of the area postrema along its rostrocaudal axis. We demonstrated that calretinin-positive neurons differ in their sensitivities to monosodium glutamate depending on their position within the area postrema. Neurons in the caudal area postrema were the most sensitive ones, while those in the rostral area postrema were spared of degeneration. We conclude that calretinin-positive neurons in the area postrema are not uniformly protected against glutamate excitotoxicity. It is possible that differences in the local concentrations of monosodium glutamate due to regional heterogeneities in density and permeability of the capillary bed rather than neuronal expression of calretinin account for the observed effects.