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PubMed1995

Neurochemical and functional characterization of the preferentially selective dopamine D3 agonist PD 128907.

The present study determined the biochemical and pharmacological effects of PD 128907 [R-(+)-trans-3,4,4a,10b-tetrahydro-4-propyl-2H,5H- [1]benzopyrano[4,3-b]-1,4-oxazin-9-ol], a dopamine (DA) receptor agonist that shows a preference for the human D3 receptor. In transfected Chinese hamster ovary cells (CHO K1), PD 128907 displaced [3H]spiperone in a biphasic fashion which fit best to a two-site model, generating Ki values of 20 and 6964 nM for the high- and low-affinity sites for the D2L receptors and 1.43 and 413 nM for the corresponding sites for the D3 receptors. Addition of sodium and the GTP analog Gpp(NH)p to both the D2L and D3 caused a modest reduction in the affinity of the compound suggestive of an agonist type action. In agonist binding ([3H]N-0437), PD 128907 exhibited an 18-fold selectivity for D3 versus D2L, a selectivity similar to that found with antagonist binding to the high-affinity sites. PD 128907 exhibited only weak affinity for D4.2 receptors (Ki = 169 nM). No significant affinity for a variety of other receptors was observed. PD 128907 stimulated cell division (measured by [3H]thymidine uptake) in CHO p-5 cells transfected with either D2L or D3 receptors exhibiting about a 6.3-fold greater potency in activating D3 as compared to D2L receptors. In vivo the compound was active in reducing DA synthesis both in normal and gamma-butyrolactone (GBL) treated rats; in the GBL model, the decrease was greater in the higher D3-expressing mesolimbic region as compared with striatum which has a lower expression of D3 receptors. PD 128907 decreased DA release (as measured by brain microdialysis) both in rat striatum, nucleus accumbens and medial frontal cortex, as well as in monkey putamen. Behaviorally PD 128907 decreased spontaneous locomotor activity (LMA) in rats at low doses, whereas at higher doses stimulatory effects were observed. PD 128907 at high doses reversed the reserpine-induced decrease in LMA and induced stereotypy in combination with the D1 agonist SKF 38393 indicating postsynaptic DA agonist actions. It is unclear which of the subtypes of DA receptors might be mediating the pharmacological effects of PD 128907. However, the present findings indicating that PD 128907 shows a preference for DA D3 over D2L and D4.2 receptors indicates that its action at low doses may be due to interaction with D3 receptors and at higher doses, with both D2 and D3 receptors.

Animals↗
PubMed1997

Accuracy of indirect estimates of maternal mortality: a simulation model.

A simulation model was developed to test the accuracy of indirect estimates of maternal mortality (the sisterhood method). The model generated a first generation of grandmothers, a second generation of mothers (with brothers and sisters), and a third generation of children (births). In the second generation, maternal mortality was introduced. Empirical values for the parameters of fertility and mortality were taken from a prospective survey in Senegal (Niakhar). Results based on 100 simulations of the same situation revealed several limitations of the sisterhood method: The indirect estimates could fall as far as 33 percent from the true values on individual cases; the indirect estimates tended to be systematically higher than the direct estimates; their range was wider, as were their confidence intervals; and biases were particularly strong for the younger age groups of respondents. Reasons for these biases are explored.

Adolescent↗
PubMed2006

Rabbits killing birds revisited.

We formulate and study a three-species population model consisting of an endemic prey (bird), an alien prey (rabbit) and an alien predator (cat). Our model overcomes several model construction problems in existing models. Moreover, our model generates richer, more reasonable and realistic dynamics. We explore the possible control strategies to save or restore the bird by controlling or eliminating the rabbit or the cat when the bird is endangered. We confirm the existence of the hyperpredation phenomenon, which is a big potential threat to most endemic prey. Specifically, we show that, in an endemic prey-alien prey-alien predator system, eradication of introduced predators such as the cat alone is not always the best solution to protect endemic insular prey since predator control may fail to protect the indigenous prey when the control of the introduced prey is not carried out simultaneously.

Animals↗
PubMed2004

The use of morphometric characters to discriminate specimens of laboratory-reared and wild populations of Gyrodactylus salaris and G. thymalli (Monogenea).

Gyrodactylus thymalli Zitnan, 1960 and G. salaris Malmberg, 1957 have an indistinguishable ribosomal internal transcribed spacer (ITS) DNA sequence, but exhibit surprisingly high levels of intra- and interspecific sequence variation of the mitochondrial cytochrome oxidase I (CO1) gene. To test whether different populations of these reportedly very similar species could be discriminated using morphometric methods, we examined the morphometry of four different populations representing different mitochondrial clades. Twenty five point-to-point measurements, including five new characters of the attachment hooks, were recorded from three Norwegian laboratory populations (G. salaris from the Rivers Lierelva and Rauma, and G. thymalli from the River Rena), and from one wild population of G. thymalli from the River Test, UK. The Norwegian populations were kept under identical environmental conditions to control for the influence of temperature on the haptoral attachment hooks. Data were subsequently subjected to univariate and linear stepwise discriminant analyses. The model generated by the linear stepwise discriminant analysis used 18 of the 25 original variables, the first two roots accounting for 96.6% of the total variation between specimens. The hamulus shaft length accounts for 66.7% of the overall correct classification efficiency. Based on morphometry, all specimens were assigned to the correct species. Apart from three specimens of G. salaris from the River Lierelva population which were misclassified as belonging to the G. salaris Rauma population, all specimens were assigned to the correct population. Thus, populations of Gyrodactylus identified by mtDNA can also be discriminated using morphometric landmark distances.

Animals↗
PubMed2005

Biomodels of bone: a review.

In this paper, a definition of a biomodel is presented, based on which different specific types of biomodels are identified, viz., virtual biomodels, computational biomodels, and physical biomodels. The paper then focuses on both physical and virtual biomodels of bone, and presents a review of model generation methodologies, giving examples of typical biomodel applications. The use of macroscale biomodels for such issues as the design and preclinical testing of surgical implants and preoperative planning is discussed. At the microscale, biomodels of trabecular bone are examined and the link with scaffolds for tissue engineering is established. Conclusions are drawn on the state of the art, and the major developments necessary for the continued expansion of the field are identified. Finally, arguments are given on the benefits of integrating the use of the different types of biomodels reviewed in this paper, for the benefit of future research in biomechanics and biomaterials.

Animals↗
PubMed1996

Food antigen activates intraepithelial and lamina propria lymphocytes in food-sensitive enteropathy in mice.

Morphologic and immunologic changes in the gut mucosa of food-hypersensitive mice, from a study model generated by feeding ovalbumin (OVA) to female BALB/c mice after intraperitoneal injection of cyclophosphamide (CY), were investigated in an effort to clarify the mechanisms of food-sensitive enteropathy. Villous atrophy, crypt hyperplasia, and increased numbers of intraepithelial lymphocytes (IEL) were confirmed in the antigen-challenged OVA-sensitive mice as seen in food-sensitive enteropathy in humans, whereas no significant morphologic changes were observed in the nontreated control group or groups treated with OVA or CY alone. IEL and lamina propria lymphocytes (LPL) were isolated from the intestinal mucosa before and after the antigen challenge, and surface markers were analyzed by FACScan. After the antigen challenge, the numbers of CD8+ cells increased among the IEL, and the occurrence of both CD4+ and CD8+ cells increased among the LPL. The numbers of Thy-1+ cells and TCR- alpha/beta + cells increased among both the IEL and LPL, and LFA-1 expression was enhanced in both of these lymphocyte populations. The proliferative response of IEL and LPL to OVA increased in a dose-dependent manner after the antigen challenge in the OVA-sensitive mouse model. These results indicate that IEL and LPL, possibly those that have migrated from peripheral blood, are activated by orally administered antigens and cause mucosal damage in the food-sensitive enteropathy.

Animals↗
PubMed2002

Identification of ligand binding sites on proteins using a multi-scale approach.

Identification of a ligand binding site on a protein is pivotal to drug discovery. To date, no reliable and computationally feasible general approach to this problem has been published. Here we present an automated efficient method for determining binding sites on proteins for potential ligands without any a priori knowledge. Our method is based upon the multiscale concept where we deal with a hierarchy of models generated using a k-means clustering algorithm for the potential ligand. This is done in a simple approach whereby a potential ligand is represented by a growing number of feature points. At each increasing level of detail, a pruning of potential binding site is performed. A nonbonding energy function is used to score the interactions between molecules at each step. The technique was successfully employed to seven protein-ligand complexes. In the current paper we show that the algorithm considerably reduces the computational effort required to solve this problem. This approach offers real opportunities for exploiting the large number of structures that will evolve from structural genomics.

Algorithms↗
PubMed2006

Molecular characterization of two superoxide dismutases from Hydra vulgaris.

Apparent full-length cDNA sequences coding for manganese superoxide dismutase (HvMnSOD) and extracellular superoxide dismutase (HvEC-SOD) were isolated from Hydra vulgaris in order to understand their expression and 3D structures; and explore their possibility of being used as for biomarkers for environmental stress and toxicity. The deduced HvMnSOD protein consists of 219 amino acids of which first 21 amino acids constitute a presumed mitochondria-targeting signal peptide whereas HvEC-SOD protein consists of 189 amino acids of which first 19 amino acids constitute a presumed signal peptide. Molecular model generated for HvMnSOD displayed the N-terminal long alpha antiparallel hairpin and the C-terminal mixed alpha/beta fold characteristic of MnSODs and that for HvEC-SOD displayed the characteristic CuZnSOD â-barrel fold. Hydrae subjected to thermal, starvation, metal and oxidative stress responded by regulating MnSOD and EC-SOD mRNA transcription. These results indicated that these genes are involved in the cellular stress response and (anti)oxidative processes triggered by stressor and contaminant exposure. Hence the expression of these SODs in hydra may have potential as molecular biomarkers for assessing stress, toxicity and pro-oxidant quality of chemicals and aquatic environmental quality.

Animals↗
PubMed2005

Structural basis of cellulosome efficiency explored by small angle X-ray scattering.

Cellulose, the main structural component of plant cell walls, is the most abundant carbohydrate polymer in nature. To break down plant cell walls, anaerobic microorganisms have evolved a large extracellular enzyme complex termed cellulosome. This megadalton catalytic machinery organizes an enzymatic assembly, tenaciously bound to a scaffolding protein via specialized intermodular "cohesin-dockerin" interactions that serve to enhance synergistic activity among the different catalytic subunits. Here, we report the solution structure properties of cellulosome-like assemblies analyzed by small angle x-ray scattering and molecular dynamics. The atomic models, generated by our strategy for the free chimeric scaffoldin and for binary and ternary complexes, reveal the existence of various conformations due to intrinsic structural flexibility with no, or only coincidental, inter-cohesin interactions. These results provide primary evidence concerning the mechanisms by which these protein assemblies attain their remarkable synergy. The data suggest that the motional freedom of the scaffoldin allows precise positioning of the complexed enzymes according to the topography of the substrate, whereas short-scale motions permitted by residual flexibility of the enzyme linkers allow "fine-tuning" of individual catalytic domains.

Biophysics↗
PubMed2003

A test of the endogenous and exogenous selection hypotheses for the maintenance of a narrow avian hybrid zone.

The contributions of genetic and environmental factors to differential reproductive success across hybrid zones have rarely been tested. Here, we report a manipulative experiment that simultaneously tested endogenous (genetic-based) and exogenous (environmental-based) selection within a hybrid zone. We transplanted mated pairs of two chickadee species (Poecile atricapilla and P. carolinensis) and their hybrids into isolated woodlots within their hybrid zone and monitored their reproductive success. Although clutch sizes were similar, based on an estimate of the genetic compatibility of a pair, hybrid pairs produced fewer nestlings and fledglings than did pairs of either parental species. According to a linear model generated from the data, a pure pair of either parental species would be expected to produce 1.91-2.48 times more fledglings per nesting attempt, respectively, than the average or least compatible pair in the experiment. Our result of decreased reproduction for hybrid pairs relative to parental species pairs within same environment (the hybrid zone in this experiment) support the endogenous selection hypothesis for maintenance of this hybrid zone. Because the experiment was conducted entirely within the hybrid zone (i.e., the same environment for parental and hybrid pairings), our data do not support the exogenous selection hypothesis as it predicts either all pairings doing poorly or the hybrid pairs more successful than the parental pairs.

Animals↗
PubMed2004

Structure of adeno-associated virus serotype 5.

Adeno-associated virus serotype 5 (AAV5) requires sialic acid on host cells to bind and infect. Other parvoviruses, including Aleutian mink disease parvovirus (ADV), canine parvovirus (CPV), minute virus of mice, and bovine parvovirus, also bind sialic acid. Hence, structural homology may explain this functional homology. The amino acids required for CPV sialic acid binding map to a site at the icosahedral twofold axes of the capsid. In contrast to AAV5, AAV2 does not bind sialic acid, but rather binds heparan sulfate proteoglycans at its threefold axes of symmetry. To explore the structure-function relationships among parvoviruses with respect to cell receptor attachment, we determined the structure of AAV5 by cryo-electron microscopy (cryo-EM) and image reconstruction at a resolution of 16 A. Surface features common to some parvoviruses, namely depressions encircling the fivefold axes and protrusions at or surrounding the threefold axes, are preserved in the AAV5 capsid. However, even though there were some similarities, a comparison of the AAV5 structure with those of ADV and CPV failed to reveal a feature which could account for the sialic acid binding phenotype common to all three viruses. In contrast, the overall surface topologies of AAV5 and AAV2 are similar. A pseudo-atomic model generated for AAV5 based on the crystal structure of AAV2 and constrained by the AAV5 cryo-EM envelope revealed differences only in surface loop regions. Surprisingly, the surface topologies of AAV5 and AAV2 are remarkably similar to that of ADV despite only exhibiting approximately 20% identity in amino acid sequences. Thus, capsid surface features are shared among parvoviruses and may not be unique to their replication phenotypes, i.e., whether they require a helper or are autonomous. Furthermore, specific surface features alone do not explain the variability in carbohydrate requirements for host cell receptor interactions among parvoviruses.

Amino Acid Sequence↗
PubMed2005

A luciferase transgenic mouse model: visualization of prostate development and its androgen responsiveness in live animals.

Numerous mouse models of prostate carcinogenesis have been developed, but hitherto there has been no model in which the prostate gland could be imaged in live animals. The transgenic model generated here targeted mouse prostate gland using a firefly luciferase enzyme under the control of a small but highly active and specific supra prostate-specific antigen (sPSA) promoter. We evaluated postnatal prostate development, involution and androgen-induced restoration of prostate growth in adult transgenic mice using bioluminescence imaging. Results of our study showed that: (i) the prostate gland of male offspring did not yield a significant bioluminescence signal until after sexual maturity. Luciferase was detected in the luminal epithelial cells of the ventral and dorsolateral lobes of the prostate gland and caput epididymis, with little or no activity in 18 other organs evaluated. (ii) While a constant high level of bioluminescence was detected in the mouse prostate from 5 to 35 weeks of age, a slight drop in bioluminescence was detected at 36 to 54 weeks. (iii) Upon castration, the luciferase activity signal associated with mouse prostate detected by a cooled charge-coupled device camera was dramatically reduced. This signal could be rapidly restored to pre-castration levels after androgen administration. Androgen-induced luciferase activity subsided to nearly basal levels 5 days following the last injection. These data demonstrate that a bioluminescent mouse model with luciferase activity restricted to the prostate gland under the control of a (sPSA) promoter can be used on a real-time basis in live animals to investigate the development and responsiveness of the prostate gland to exogenously administered androgen. This model can be extended to detect the responsiveness of the prostate gland to therapy and used as a founder strain to visualize tumors in hosts with different genetic backgrounds.

Androgens↗
PubMedDate not supplied

[Introduction of a process of deterioration in the study of adult mortality: application of a simulation model to Norwegian generations, 1866-1916].

Increases in adult mortality after age 45 are examined using a Monte Carlo-type simulation model based on data for Norwegian generations from 1866 to 1916. "In this model, the observed mortality of a generation depends upon two variables: 1) the risk of dying in the mortality strata for each individual at a certain time; 2) the level of deterioration of each person as given by the distribution of the individuals in the different mortality strata." Results suggest that the increase in the risk of dying after the age of 45 is due to two causes, namely, an increase in the percentage of weaker individuals (natural selection) and a change in life-style patterns, which include alcohol and tobacco consumption, nutrition, and physical exercise (cultural selection). (summary in ENG, ITA)

Adult↗
PubMed1998

Are regional variations in bone growth related to mechanical stress and strain parameters?

A three-dimensional finite element analysis was used to quantify the patterns of mechanical stresses within the rabbit distal femur growth plate, and test the hypothesis that these patterns are correlated to measured patterns of bone growth rates. This investigation of normal development is the first step toward improving our understanding of the role of mechanical factors in bone growth abnormalities. Rabbits from five age groups ranging from 1 to 42 days were evaluated, and four different loading conditions were analyzed, representing specific time points in the normal gait cycle. Finite element models generated directly from micro-computed tomography images of the distal femurs identified regional variations in stress and strain parameters, similar to the variations in bone growth rates measured using fluorochrome labeling. A linear regression analysis supports the hypothesis that high compressive stresses are correlated with lower bone growth rates. However, for the loading conditions considered in this study, the variations in mechanical stress and strain parameters explain no more than 15% of the overall variations in bone growth rates. The greatest variations in both growth rates and mechanical stresses were present in the anterior frontal plane from the 42 day age group, in which correlations between reduced bone growth rates and compressive stresses were much stronger (r2 up to 0.80).

Animals↗
PubMed2006

Dynamic contrast-enhanced magnetic resonance imaging in the assessment of early response to tumor necrosis factor alpha in a colon carcinoma model.

OBJECTIVE: We describe the effects of tumor necrosis factor alpha (TNFalpha) on tumor microvasculature in a murine colon carcinoma model using serial dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI). MATERIAL AND METHODS: Mice with subcutaneous murine colon carcinomas (MC-38) were imaged at 4.7 T after administration of 0.2 mmol/kg gadolinium-DTPA. Both treated and control mice (each group, n = 4), were scanned at baseline and 2, 4, 6, and 96 hours. A 2-compartment pharmacokinetic model generated parameters such as K, kep, and initial area under the gadolinium concentration curve (IAUC). RESULTS: The treatment group revealed significant differences in K at all time points after TNFalpha. kep and IAUC were significantly reduced at 2, 6, and 96 hours. The coefficient of variation in control animals ranged from 0.13 for IAUC to 0.30 for K. Mild histologic changes were observed at 2 to 6 hours, but considerable central necrosis with a vascular tumor rim was seen at 96 hours. CONCLUSION: DCE MRI can be used to detect early effects of TNFalpha. Serial DCE MRI is a promising tool in assessing the early effects of antivascular therapies.

Animals↗
PubMed1999

Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer.

Integral membrane proteins containing at least one transmembrane (TM) alpha-helix are believed to account for between 20% and 30% of most genomes. There are several algorithms that accurately predict the number and position of TM helices within a membrane protein sequence. However, these methods tend to disagree over the beginning and end residues of TM helices, posing problems for subsequent modeling and simulation studies. Molecular dynamics (MD) simulations in an explicit lipid and water environment are used to help define the TM helix of the M2 protein from influenza A virus. Based on a comparison of the results of five different secondary structure prediction algorithms, three different helix lengths (an 18mer, a 26mer, and a 34mer) were simulated. Each simulation system contained 127 POPC molecules plus approximately 3500-4700 waters, giving a total of approximately 18,000-21,000 atoms. Two simulations, each of 2 ns duration, were run for the 18mer and 26mer, and five separate simulations were run for the 34mer, using different starting models generated by restrained in vacuo MD simulations. The total simulation time amounted to 11 ns. Analysis of the time-dependent secondary structure of the TM segments was used to define the regions that adopted a stable alpha-helical conformation throughout the simulation. This analysis indicates a core TM region of approximately 20 residues (from residue 22 to residue 43) that remained in an alpha-helical conformation. Analysis of atomic density profiles suggested that the 18mer helix revealed a local perturbation of the lipid bilayer. Polar side chains on either side of this region form relatively long-lived H-bonds to lipid headgroups and water molecules.

Amino Acid Sequence↗
PubMed2001

Localization of the site of origin of cardiac activation by means of a heart-model-based electrocardiographic imaging approach.

We have developed a new approach to solve the inverse problem of electrocardiography in terms of heart model parameters. The inverse solution of the electrocardiogram (ECG) inverse problem is defined, in the present study, as the parameters of the heart model, which are closely related to the physiological and pathophysiological status of the heart, and is estimated by using an optimization system of heart model parameters, instead of solving the matrix equation relating the body surface ECGs and equivalent cardiac sources. An artificial neural network based preliminary diagnosis system has been developed to limit the searching space of the optimization algorithm and to initialize the model parameters in the computer heart model. The optimal heart model parameters were obtained by minimizing the objective functions, as functions of the observed and model-generated body surface ECGs. We have tested the feasibility of the newly developed technique in localizing the site of origin of cardiac activation using a pace mapping protocol. The present computer simulation results show that, the present approach for localization of the site of origin of ventricular activation achieved an averaged localization error of about 3 mm [for 5-muV Gaussian white noise (GWN)] and 4 mm (for 10-muV GWN), with standard deviation of the localization errors of being about 1.5 mm. The present simulation study suggests that this newly developed approach provides a robust inverse solution, circumventing the difficulties of the ECG inverse problem, and may become an important alternative to other ECG inverse solutions.

Algorithms↗
PubMed1997

The role of synaptic and voltage-gated currents in the control of Purkinje cell spiking: a modeling study.

We have used a realistic computer model to examine interactions between synaptic and intrinsic voltage-gated currents during somatic spiking in cerebellar Purkinje cells. We have shown previously that this model generates realistic in vivo patterns of somatic spiking in the presence of continuous background excitatory and inhibitory input (). In the present study, we analyzed the flow of synaptic and intrinsic currents across the dendritic membrane and the interaction between the soma and dendrite underlying this spiking behavior. This analysis revealed that: (1) dendritic inward current flow was dominated by a noninactivating P-type calcium current, resulting in a continuous level of depolarization; (2) the mean level of this depolarization was controlled by the mean rate of excitatory and inhibitory synaptic input; (3) the synaptic control involved a voltage-clamping mechanism exerted by changes of synaptic driving force at different membrane potentials; (4) the resulting total current through excitatory and inhibitory synapses was near-zero, with a small outward bias opposing the P-type calcium current; (5) overall, the dendrite acted as a variable current sink with respect to the soma, slowing down intrinsic inward currents in the soma; (6) the somato-dendritic current showed important phasic changes during each spike cycle; and (7) the precise timing of somatic spikes was the result of complex interactions between somatic and dendritic currents that did not directly reflect the timing of synaptic input. These modeling results suggest that Purkinje cells act quite differently from simple summation devices, as has been assumed previously in most models of cerebellar function. Specific physiologically testable predictions are discussed.

Action Potentials↗