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PubMed2005

Fourier shell correlation threshold criteria.

The resolution value claimed for an electron microscopical three-dimensional reconstruction indicates the overall quality of the experiment. The Fourier shell correlation (FSC) criterion has now become the standard quality measure. However, what has continued to be controversial is the issue of the FSC threshold level at which one defines the reproducible resolution. Here, we discuss the theoretical behaviour of the FSC in conjunction with the various factors which influence it: the number of "voxels" in a given Fourier shell, the symmetry of the structure, and the size of the structure within the reconstruction volume. Both the theoretical considerations and our model experiments show that fixed-valued FSC threshold (like "0.5") may never be used in a reproducible criterion. Fixed threshold values are-as we show here-simply the result of incorrect assumptions in the basic statistics. Two families of FSC threshold curves are discussed: the sigma-factor curves and the new family of bit-based information threshold curves. Whereas sigma-factor curves indicate the resolution level at which one has collected information significantly above the noise level, the information curves indicate the resolution level at which enough information has been collected for interpretation.

Computer Simulation↗
PubMed2005

Mollusk shell formation: mapping the distribution of organic matrix components underlying a single aragonitic tablet in nacre.

Control over mineral formation in mollusk shells is exerted by the macromolecules of the organic matrix. Using histochemical methods, we mapped the carboxylates and sulfates of proteins and polysaccharides on the surfaces of decalcified interlamellar matrices from the nacreous shell layer of the cephalopod Nautilus pompilius, expanding upon an earlier study by Crenshaw and Ristedt [Crenshaw, M.A., Ristedt, H., 1976. The histochemical localization of reactive groups in septal nacre from Nautilus pompilius. In: Watabe, N., Wilbur, K.M. (Ed.), The Mechanisms of Mineralization in the Invertebrates and Plants. University of South Carolina Press, Colombia, pp. 355-367]. We observed four different zones underlying a single crystal: (1) a central spot rich in carboxylates; (2) a central ring-shaped area rich in sulfates; (3) an area between the central nucleation region and the imprint periphery containing carboxylates, and (4) the intertabular matrix, rich in carboxylates and sulfates. We also mapped matrix functional groups on the nacreous matrix surfaces of the bivalve Atrina rigida, but did not identify well-defined zones. Immuno-mapping of the constituents of the aragonite-nucleating protein fraction from Atrina nacre showed that these macromolecules are located both in the intertabular matrix and in the center of the crystal imprints for both Atrina and Nautilus matrix surfaces. Their presence at the latter location is consistent with their purported role in aragonite nucleation. The observed differentiation in the distribution of matrix components and their functional groups shows that the different stages of single crystal growth are highly controlled by the matrix.

Animals↗
PubMed2006

Relationship between shell weight and cadmium content in whole digestive gland of the Japanese scallop Patinopecten yessoensis (Jay).

Seasonal and age-specific variations of cadmium (Cd) concentration in the digestive gland were investigated in the Japanese scallop Patinopecten yessoensis from Peter the Great Bay, Sea of Japan, with different degrees of Cd pollution. The seasonal changes in Cd concentrations of the digestive gland were inversely proportional to the dry weight of the gland. Concentrations of Cd and total Cd content (mug Cd per organ) increased with age (age-specific) to the same extent in contaminated and uncontaminated areas. There was also a strong positive correlation between Cd content in the whole digestive gland and shell weight and it is proposed that this relationship can be used as a new criterion for comparative evaluation of Cd levels in scallops from different areas We hypothesize that Cd is uptaken into scallops in proportion to the amount of calcium that absorbed through ion channels, and in addition, Cd in the digestive gland is in immobile forms (e.g. metal-rich granules) that accumulate with age. Moderate environmental pollution has no effect on the relationship between Cd content and shell size and the observed decrease in growth performance of the scallops from polluted areas may be due to other factors.

Animal Structures↗
PubMed2005

Denitrification by the mix-culturing of fungi and bacteria with shell.

Denitrification by pure and mixed culture of Fusarium oxysporum and Pseudomonas stutzeri in different mineral medium and in synthetic wastewater were examined. The results obtained revealed that a rapid N2 evolution by F. oxysporum and P. stutzeri in mineral medium and synthetic wastewater was observed. In co-cultures of F. oxysporum and P. stutzeri, N2O produced by F. oxysporum was rapidly consumed by P. stutzeri. This indicated that mixed culture of F. oxysporum and P. stutzeri could be used for efficient nitrate and nitrite removal. Using synthetic wastewater, about 87% of nitrate was reduced by co-denitrification of F. oxysporum and P. stutzeri after incubation for 6 days. In the further denitrification tests, the interaction of shell and mixed culture of F. oxysporum and P. stutzeri was investigated. The dinitrogen was rapidly evolved (442.48 micromol N2 produced from 1.0 mmol of NO3(-) in 36 h). These results clearly showed that shell provide a suitable microenvironment for P. stutzeri, which is beneficial to the denitrification.

Biodegradation, Environmental↗
PubMed2006

The correlation between organic matrices and biominerals (myostracal prism and folia) of the adult oyster shell, Crassostrea gigas.

The organic membrane at the interface between the myostracum (aragonite) and folia (calcite) was obtained and identified as a chitin-like macromolecule after chemical treatment. It was confirmed that the organic membrane was faced to the crystal (001) plane of the myostracum and folia. The secondary structures in soluble protein of the myostracum and the folia of oyster shell were identified as a great quantity of beta-structure. The acidic amino acids, Asp and Glu, to play a role as templates on shell formation were confirmed in the myostracum and the folia.

Animals↗
PubMed2003

Dopamine hypofunction possibly results from a defect in glutamate-stimulated release of dopamine in the nucleus accumbens shell of a rat model for attention deficit hyperactivity disorder--the spontaneously hypertensive rat.

RUSSELL, V.A. Dopamine hypofunction possibly results from a defect in glutamate-stimulated release of dopamine in the nucleus accumbens shell of a rat model for attention deficit hyperactivity disorder-the spontaneously hypertensive rat. NEUROSCI. BIOBEHAV. REV.27(2003). Disturbances in glutamate, dopamine and norepinephrine function in the brain of a genetic animal model for attention-deficit hyperactivity disorder (ADHD), the spontaneously hypertensive rat (SHR), and information obtained from patients with ADHD, suggest a defect in neuronal circuits that are required for reward-guided associative learning and memory formation. Evidence derived from (i). the neuropharmacology of drugs that are effective in treating ADHD symptoms, (ii). molecular genetic and neuroimaging studies of ADHD patients, as well as (iii). the behaviour and biochemistry of animal models, suggests dysfunction of dopamine neurons. SHR have decreased stimulation-evoked release of dopamine as well as disturbances in the regulation of norepinephrine release and impaired second messenger systems, cAMP and calcium. In addition, evidence supports a selective deficit in the nucleus accumbens shell of SHR which could contribute to impaired reinforcement of appropriate behaviour.

Animals↗
PubMed2006

Altered extracellular levels of DOPAC and HVA in the rat nucleus accumbens shell in response to sub-chronic nandrolone administration and a subsequent amphetamine challenge.

Associated with acts of violence and polydrug use, abuse of anabolic androgenic steroids (AAS) is an increasing problem in society. The aim of the present study was to elucidate whether sub-chronic treatment with the AAS nandrolone decanoate affects dopamine release and dopamine metabolism in the rat nucleus accumbens shell, before and after an amphetamine challenge. Male Sprague-Dawley rats received daily i.m. injections of nandrolone decanoate (15 mg/kg) or vehicle for 14 days. On day 15, the animals were anaesthetized and a microdialysis probe was implanted into the nucleus accumbens shell. Extracellular fluid was collected 1h before and 3h after a single amphetamine injection (5 mg/kg). The samples were then analyzed regarding the content of dopamine, and its metabolites 3,4-dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA), using HPLC with electrochemical detection. Two weeks of nandrolone decanoate administration caused a significant decrease of the basal DOPAC and HVA levels, which remained low during the first hour following the amphetamine challenge. Dopamine levels did not differ significantly between groups, neither after the nandrolone pre-treatment nor the amphetamine challenge. In conclusion, these novel findings indicate that AAS alter the metabolism of dopamine in a brain region involved in the development of drug dependence.

3,4-Dihydroxyphenylacetic Acid↗
PubMed2006

Cocaine increases 5-HT1B mRNA in rat nucleus accumbens shell neurons.

Serotonin 5-HT(1B) receptors modulate behavioral responses to cocaine, but the effects of cocaine on endogenous 5-HT(1B) receptor expression are not known. Therefore, we examined the effect of binge cocaine administration on 5-HT1B mRNA expression in rat brain. We found that chronic, but not acute, binge cocaine exposure increased 5-HT(1B) mRNA by approximately 80% in nucleus accumbens shell and dorsal striatum. Surprisingly, 5-HT(1B) mRNA was increased in nucleus accumbens shell after chronic vehicle treatment as well, but this effect was driven by animals that were housed with cocaine-treated animals. Thus, 5-HT(1B) mRNA is upregulated by repeated exposure to cocaine and perhaps by social stress as well; both of these factors are relevant to the risk for relapse in cocaine addiction.

Analysis of Variance↗
PubMed2006

Typical and atypical antipsychotic drugs target dopamine and cyclic AMP-regulated phosphoprotein, 32 kDa and neurotensin-containing neurons, but not GABAergic interneurons in the shell of nucleus accumbens of ventral striatum.

Specific neurons in the brain are the primary targets of the action of antipsychotic drugs. Identification and characterization of the nature of these neurons are important for understanding how antipsychotic drugs produce their effects. In previous studies GABAergic/dynorphinergic neurons were identified as a principal cell target of antipsychotic drugs in the shell of nucleus accumbens. In the present study, we further characterized which subpopulations of GABAergic neurons in this area respond after acute administration of antipsychotic drugs. Rats were treated with the typical antipsychotic haloperidol, or the prototype atypical antipsychotic clozapine and killed two hours after treatment. In appropriate sections of brain, double immunofluorescence labeling was performed with antibodies directed against markers specific to candidate cell types and Fos-like proteins (a marker to identify drug-induced cell activation). We reported here that haloperidol- and clozapine-activated neurons showed the following features: 1) approximately 54-57% of them express dopamine and cyclic AMP-regulated phosphoprotein, 32 kDa (a marker for GABAergic medium spiny projection neurons), 2) they appear rarely to be GABAergic interneurons, marked by the calcium binding proteins, parvalbumin, calretinin or calbindin-D28K, 3) about 84-86% of them express the neuropeptide neurotensin (a neurotransmitter most often associated with projection neurons in the site tested). The results suggest that most of the antipsychotic drug-activated neurons in the shell of nucleus accumbens are likely to be neurotensin containing projection neurons.

Animals↗
PubMed2006

Effects of trematode double infection on the shell size and distribution of snail hosts.

Infection with larval trematodes sometimes alters the phenotypes of their snail hosts. While some trematode species have distinct effects on host phenotypes, it is still unclear how snail phenotypes are altered when they are parasitized with multiple trematode species. Here, we report that double infection with trematode species averages the effects of parasitic alteration on host phenotype. We found that snail hosts Batillaria attramentaria (Batillariidae) infected with Cercaria batillariae (Heterophyidae) have abnormally large shells and distribute in lower areas of the intertidal zone. Snails with another dominant trematode species, the renicolid cercaria I (Renicolidae), have slightly larger shells and distribute in upper areas of the intertidal zone. A number of double infections with both trematodes was observed in this study. Snails infected with both trematode species exhibited an intermediate size and inhabited a depth between those of snails solely infected with either trematode species, suggesting that the two trematodes simultaneously affected the snail phenotypes. Because altered host phenotypes are frequently beneficial to parasites, two trematode species may compete for successful transmission through alteration of host phenotypes.

Animals↗
PubMed2005

Laser ablation ICP-MS profiling and semiquantitative determination of trace element concentrations in desert tortoise shells: documenting the uptake of elemental toxicants.

The outer keratin layer (scute) of desert tortoise shells consists of incrementally grown laminae in which various bioaccumulated trace elements are sequestered during scute deposition. Laser ablation ICP-MS examination of laminae in scutes of dead tortoises revealed patterns of trace elemental distribution from which the chronology of elemental uptake can be inferred. These patterns may be of pathologic significance in the case of elemental toxicants such as arsenic, which has been linked to both shell and respiratory diseases. Laser ablation transects, performed along the lateral surfaces of sectioned scutes, offered the most successful means of avoiding exogenous contamination that was present on the scute exterior. Semiquantitative determination of elemental concentrations was achieved using sulfur, a keratin matrix element, as an internal standard. The results presented here highlight the potential of laser ablation ICP-MS as a diagnostic tool for investigating toxic element uptake as it pertains to tortoise morbidity and mortality.

Animals↗
PubMed2004

Dynamic acoustic radiation force acting on cylindrical shells: theory and simulations.

An object placed in an acoustic field is known to experience a force due to the transfer of momentum from the wave to the object itself. This force is known to be steady when the incident field is considered to be continuous with constant amplitude. One may define the dynamic (oscillatory) radiation force for a continuous wave-field whose intensity varies slowly with time. This paper extends the theory of the dynamic acoustic radiation force resulting from an amplitude-modulated progressive plane wave-field incident on solid cylinders to the case of solid cylindrical shells with particular emphasis on their thickness and contents of their hollow regions. A new factor corresponding to the dynamic radiation force is defined as Y(d) and stands for the dynamic radiation force per unit energy density and unit cross sectional surface. The results of numerical calculations are presented, indicating the ways in which the form of the dynamic radiation force function curves are affected by variations in the material mechanical parameters and by changes in the interior fluid inside the shell's hollow region. It was shown that the dynamic radiation force function Y(d) deviates from the static radiation force function for progressive waves Y(p) when the modulation frequency increases. These results indicate that the theory presented here is broader than the existing theory on cylinders.

Algorithms↗
PubMed2005

Acoustic radiation force acting on elastic and viscoelastic spherical shells placed in a plane standing wave field.

The theory of the acoustic radiation force acting on elastic spherical shells suspended in a plane standing wave field is developed in relation to their thickness and the content of their hollow regions. The theory is modified to include the effect of a hysteresis type of absorption of compressional and shear waves in the material. The fluid-loading effect on the acoustic radiation force function Y(st) is analyzed as well. Results of numerical calculations are presented for a number of elastic and viscoelastic materials, with the hollow region filled with water or air. These results show how the damping due to absorption, the change of the interior fluid inside the shells' hollow regions, and the exterior fluid surrounding their structures, affect the acoustic radiation force.

Absorption↗
PubMed2006

DNA prime and protein boost immunization with innovative polymeric cationic core-shell nanoparticles elicits broad immune responses and strongly enhance cellular responses of HIV-1 tat DNA vaccination.

Novel biocompatible core-shell cationic nanoparticles, composed of an inner hard core of poly(methylmethacrylate) (PMMA) and a hydrophilic tentacular shell bearing positively charged groups and poly(ethyleneglycol) chains covalently bound to the core, were prepared by emulsion polymerization and characterized in vitro and in vivo for DNA vaccine applications. The nanoparticles reversibly adsorbed large amounts of DNA, mainly through electrostatic interactions, preserved its functional structure, efficiently delivered it intracellularly, and were not toxic in vitro or in mice. Furthermore, two intramuscular (i.m.) immunizations (4 weeks apart) with a very low dose (1 microg) of the plasmid pCV-tat delivered by these nanoparticles followed by one or two protein boosts induced significant antigen-specific humoral and cellular responses and greatly increased Th1-type T cell responses and CTLs against HIV-1 Tat.

AIDS Vaccines↗
PubMed2004

Role of viral vectors and virion shells in cellular gene expression.

The role of the virion shell in viral pathogenesis is relatively unknown yet the use of viral vectors in human gene transfer experiments requires an understanding of these interactions. In this study, we used DNA microarrays to identify genes modulated during pathogenic adenovirus or nonpathogenic adeno-associated virus infections. Responses to wt viruses, recombinant vectors, or empty virion particles were compared. Adeno-associated virus shells induced nearly the full complement of changes elicited by the intact virus. The cellular genes elicited a nonpathogenic response, with antiproliferative genes being induced as a cluster. In contrast, adenovirus and adenovirus empty capsid infection yielded a broader response and subset, respectively, including induction of immune and stress-response genes associated with pathogenic effects. Our studies show that the impact of the viral capsid on cellular gene expression, and potential host toxicity, must be considered independent of the vector genome for safe gene transfer in the clinic.

Adenoviridae↗
PubMed2000

Application of the primary hydration shell approach to locally enhanced sampling simulated annealing: computer simulation of thyrotropin-releasing hormone in water.

A unified model of simulated annealing with locally enhanced sampling (LES) in a primary hydration shell (PHS) aqueous environment is developed and tested by predicting the structure of the tripeptide thyrotropin-releasing hormone (TRH) in solution. The model extends the formulation of the restraining force in the PHS method as a function of temperature, number of copies in the LES method, and shell thickness. The dependence of the restraining force on temperature can be shown to follow the relationship c(1)T - c(2), which can be derived from the expression for kinetic energy in molecular dynamics simulations. The calibration of the restraining force for different simulation conditions reveals the dependence of c(1) and c(2) on the number of copies in the LES method and the thickness of the PHS. The predicted structure of TRH is in very good agreement with results from NMR experiments and from a 10-ns PHS simulation at 300 K. The method promises to be useful in predicting structure of peptides and proteins in an aqueous environment.

Calibration↗
PubMed1989

Cortical shell-liquid core model for passive flow of liquid-like spherical cells into micropipets.

Many nonadherent cells exist as spheres in suspension and when sucked into pipets, deform continuously like liquids within the fixed surface area limitation of a plasma membrane envelope. After release, these cells eventually recover their spherical form. Consequently, pipet aspiration test provides a useful method to assay the apparent viscosity of such cells. For this purpose, we have analyzed the inertialess flow of a liquid-like model cell into a tube at constant suction pressure. The cell is modeled as a uniform liquid core encapsulated by a distinct cortical shell. The method of analysis employs a variational approach that minimizes errors in boundary conditions defined by the equations of motion for the cortical shell where the trial functions are exact solutions for the flow field inside the liquid core. For the particular case of an anisotropic liquid cortex with persistent tension, we have determined universal predictions for flow rate scaled by the ratio of excess pressure (above the threshold established by the cortical tension) and core viscosity which is the reciprocal of the dynamic resistance to entry. The results depend on pipet to cell size ratio and a parameter that characterizes the ratio of viscous flow resistance in the cortex to that inside the cytoplasmic core. The rate of entry increases markedly as the pipet size approaches the outer segment diameter of the cell. Viscous dissipation in the cortex strongly influences the entry flow resistance for small tube sizes but has little effect for large tubes. This indicates that with sufficient experimental resolution, measurement of cell entry flow with different-size pipets could establish both the cortex to cell dissipation ratio as well as the apparent viscosity of the cytoplasmic core.

Cell Adhesion↗
PubMed1994

Pressure denaturation of the bacteriophage P22 coat protein and its entropic stabilization in icosahedral shells.

The pressure stability of bacteriophage P22 coat protein in both monomeric and polymeric forms under hydrostatic pressure was examined using light scattering, fluorescence emission, polarization, and lifetime methodology. The monomeric protein is very unstable toward pressure and undergoes significant structural changes at pressures as low as 0.5 kbar. These structural changes ultimately lead to denaturation of the subunit. Comparison of the protein denatured by pressure to that in guanidine hydrochloride suggests that pressure results in partial unfolding, perhaps by a domain mechanism. Fluorescence lifetime measurements indicate that at atmospheric pressure the local environments of the tryptophans are remarkably similar, suggesting they may be clustered. In contrast to the monomeric protein subunit, the protein when polymerized into procapsid shells is very stable to applied pressure and does not dissociate with pressure up to 2.5 kbar. However, under applied pressure the procapsid shells are cold-labile, suggesting they are entropically stabilized. The significance of these results in terms of virus assembly are discussed.

Bacteriophage P22↗