Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin.
The influence of hydration on the internal dynamics of a typical EF-hand calciprotein, parvalbumin, was investigated by incoherent quasi-elastic neutron scattering (IQNS) and solid-state 13C-NMR spectroscopy using the powdered protein at different hydration levels. Both approaches establish an increase in protein dynamics upon progressive hydration above a threshold that only corresponds to partial coverage of the protein surface by the water molecules. Selective motions are apparent by NMR in the 10-ns time scale at the level of the polar lysyl side chains (externally located), as well as of more internally located side chains (from Ala and Ile), whereas IQNS monitors diffusive motions of hydrogen atoms in the protein at time scales up to 20 ps. Hydration-induced dynamics at the level of the abundant lysyl residues mainly involve the ammonium extremity of the side chain, as shown by NMR. The combined results suggest that peripheral water-protein interactions influence the protein dynamics in a global manner. There is a progressive induction of mobility at increasing hydration from the periphery toward the protein interior. This study gives a microscopic view of the structural and dynamic events following the hydration of a globular protein. (+info)
Using maximum likelihood to estimate population size from temporal changes in allele frequencies.
We develop a maximum-likelihood framework for using temporal changes in allele frequencies to estimate the number of breeding individuals in a population. We use simulations to compare the performance of this estimator to an F-statistic estimator of variance effective population size. The maximum-likelihood estimator had a lower variance and smaller bias. Taking advantage of the likelihood framework, we extend the model to include exponential growth and show that temporal allele frequency data from three or more sampling events can be used to test for population growth. (+info)
Hemolytic activity and siderophore production in different Aeromonas species isolated from fish.
The hemolytic activity and siderophore production of several strains of motile aeromonads were determined. The hemolytic activity of Aeromonas caviae and Aeromonas eucrenophila was enhanced after trypsinization of the samples. The enhancement of hemolysis was observed in strains that carried an aerolysin-like gene, detected by a PCR procedure. Siderophore production was demonstrated in all but one strain of Aeromonas jandaei. No apparent relationship was observed between the presence of plasmid DNA and hemolysis or siderophore production. (+info)
Squamous epithelial proliferation induced by walleye dermal sarcoma retrovirus cyclin in transgenic mice.
Walleye dermal sarcoma (WDS) is a common disease of walleye fish in the United States and Canada. These proliferative lesions are present autumn through winter and regress in the spring. Walleye dermal sarcoma virus (WDSV), a retrovirus distantly related to other members of the family Retroviridae, has been etiologically linked to the development of WDS. We have reported that the D-cyclin homologue [retroviral (rv) cyclin] encoded by WDSV rescues yeast conditionally deficient for cyclin synthesis from growth arrest and that WDSV-cyclin mRNA is present in developing tumors. These data strongly suggest that the rv-cyclin plays a central role in the development of WDS. To test the ability of the WDSV rv-cyclin to induce cell proliferation, we have generated transgenic mice expressing the rv-cyclin in squamous epithelia from the bovine keratin-5 promoter. The transgenic animals were smaller than littermates, had reduced numbers of hair follicles, and transgenic females did not lactate properly. Following injury the transgenic animals developed severe squamous epithelial hyperplasia and dysplasia with ultrastructural characteristics of neoplastic squamous epithelium. Immunocytochemistry studies demonstrated that the hyperplastic epithelium stained positive for cytokeratin and were abnormally differentiated. Furthermore, the rv-cyclin protein was detected in the thickened basal cell layers of the proliferating lesions. These data are the first to indicate that the highly divergent WDSV rv-cyclin is a very potent stimulator of eukaryotic cell proliferation and to demonstrate the potential of a cyclin homologue encoded by a retrovirus to induce hyperplastic skin lesions. (+info)
Multimodal sensory integration in the strike-feeding behaviour of predatory fishes.
The search for useful model systems for the study of sensory processing in vertebrate nervous systems has resulted in many neuroethological studies investigating the roles played by a single sensory modality in a given behaviour. However, behaviours relying solely upon information from one sensory modality are relatively rare. Animals behaving in a complex, three-dimensional environment receive a large amount of information from external and internal receptor arrays. Clearly, the integration of sensory afference arising from different modalities into a coherent 'gestalt' of the world is essential to the behaviours of most animals. In the last several years our laboratory team has examined the roles played by the visual and lateral line sensory systems in organizing the feeding behaviour of two species of predatory teleost fishes, the largemouth bass, Micropterus salmoides, and the muskellunge, Esox masquinongy. The free-field feeding behaviours of these fishes were studied quantitatively in intact animals and compared to animals in which the lateral line and visual systems had been selectively suppressed. All groups of animals continued to feed successfully, but significant differences were observed between each experimental group, providing strong clues as to the relative role played by each sensory system in the organization of the behaviour. Furthermore, significant differences exist between the two species. The differences in behaviour resulting when an animal is deprived of a given sensory modality reflect the nature of central integrative sensory processes, and these behavioural studies provide a foundation for further neuroanatomical and physiological studies of sensory integration in the vertebrate central nervous system. (+info)
Empirical Bayes procedure for estimating genetic distance between populations and effective population size.
We developed an empirical Bayes procedure to estimate genetic distances between populations using allele frequencies. This procedure makes it possible to describe the skewness of the genetic distance while taking full account of the uncertainty of the sample allele frequencies. Dirichlet priors of the allele frequencies are specified, and the posterior distributions of the various composite parameters are obtained by Monte Carlo simulation. To avoid overdependence on subjective priors, we adopt a hierarchical model and estimate hyperparameters by maximizing the joint marginal-likelihood function. Taking advantage of the empirical Bayesian procedure, we extend the method to estimate the effective population size using temporal changes in allele frequencies. The method is applied to data sets on red sea bream, herring, northern pike, and ayu broodstock. It is shown that overdispersion overestimates the genetic distance and underestimates the effective population size, if it is not taken into account during the analysis. The joint marginal-likelihood function also estimates the rate of gene flow into island populations. (+info)
Abortive secretion of an enamel matrix in the inner enamel epithelial cells during an enameloid formation in the gar-pike, Lepisosteus oculatus (Holostei, Actinopterygii).
The tooth in the gar-pike, Lepisosteus oculatus, an actinopterygian fish, is characterized by the occurrence of both enamel and enameloid, the former covering the tooth shaft and the latter, the tooth cap. Our previous research demonstrated that the enamel in this species was, as in the lungfish, immunoreactive for amelogenin, indicating its homologous nature with the mammalian tooth enamel, whereas the enameloid was completely immunonegative. The present study demonstrates that, during the early maturation stage of the enameloid formation, the inner enamel epithelial cells (IEECs) synthesize through a well-developed Golgi apparatus a fine-granular substance which is intensely immunoreactive for amelogenin. This substance was accumulated in a large saccule extended in a suprabasal zone of the cell; we were unable to find any morphological sign indicating a connection of the substance with the enameloid matrix. The abortive secretion of the enamel matrix-like substance in the IEEC during an enameloid formation was considered to be an instance of rudimental enamel formation. In the gar-pike, the synthesis of amelogenin in the IEEC has been demonstrated to occur independently from that of the enameloid matrix. The present findings demonstrate a prominent difference between the tooth enamel and enameloid. (+info)
Molecular mechanisms of calcium and magnesium binding to parvalbumin.
Molecular dynamics simulations have been used to investigate the relationship between the coordinating residues of the EF-hand calcium binding loop of parvalbumin and the overall plasticity and flexibility of the protein. The first simulation modeled the transition from Ca(2+) to Mg(2+) coordination by varying the van der Waals parameters for the bound metal ions. The glutamate at position 12 could be accurately and reversibly seen to be a source of selective bidentate ligation of Ca(2+) in the simulations. A second simulation correlated well with the experimental observation that an E101D substitution at EF loop position 12 results in a dramatically less tightly bound monodentate Ca(2+) coordination by aspartate. A final set of simulations investigated Ca(2+) binding in the E101D mutant loop in the presence of applied external forces designed to impose bidentate coordination. The results of these simulations illustrate that the aspartate is capable of attaining a suitable orientation for bidentate coordination, thus implying that it is the inherent rigidity of the loop that prevents bidentate coordination in the parvalbumin E101D mutant. (+info)