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PubMed2006

Nature of the chemical bond in protonated methane.

Protonated methane, CH(5)(+), is a key reactive intermediate in hydrocarbon chemistry and a borderline case for chemical structure theory, being the simplest example of hypercoordinated carbon. Early quantum mechanical calculations predicted that the properties of this species could not be associated with only one structure, because it presents serious limitations of the Born-Oppenheimer approximation. However, ab initio molecular dynamics and diffusion Monte Carlo calculations showed that the most populated structure could be pictured as a CH(3) tripod linked to a H(2) moiety. Despite this controversy, a model for the chemical bonds involved in this ion still lacks. Here we present a modern valence bond model for the electronic structure of CH(5)(+). The chemical bond scheme derived directly from our calculations pictures this ion as H(3)C...H(2)(+). The fluxionality can be seen as the result of a proton transfer between C-H bonds. A new insight on the vibrational bands at approximately 2400 and approximately 2700 cm(-1) is suggested. Our results show that the chemical bond model can be profitably applied to such intriguing systems.

Journal Article↗
PubMed2003

Dynamic transitions through scattors in dissipative systems.

Scattering of particle-like patterns in dissipative systems is studied, especially we focus on the issue how the input-output relation is controlled at a head-on collision where traveling pulses or spots interact strongly. It remains an open problem due to the large deformation of patterns at a colliding point. We found that a special type of unstable steady or time-periodic solutions called scattors and their stable and unstable manifolds direct the traffic flow of orbits. Such scattors are in general highly unstable even in the one-dimensional case which causes a variety of input-output relations through the scattering process. We illustrate the ubiquity of scattors by using the complex Ginzburg-Landau equation, the Gray-Scott model, and a three-component reaction diffusion model arising in gas-discharge phenomena.

Journal Article↗
PubMed1989

In-plane phase transition of an integral membrane protein: nucleation of the OmpF matrix porin rectangular polymorph.

A hexagonal polymorph (a = 79 A) of OmpF matrix porin from Escherichia coli spontaneously transforms to a rectangular form (a = 79 A, b = 137 A) after several months' storage in the refrigerator. Nucleation of this second polymorph is first disclosed by diffuse streaks in electron diffraction patterns or in computer-generated Fourier transforms of electron microscope images. With time, this streaking is resolved as an apparent superlattice, and eventually domains of orthorhombic polymorph are detected in the parent hexagonal lattice that can be oriented in either of three directions, depending on the polarity of the orthorhombic crystal growth. Models for this phenomenon based on protein trimer rotation successfully explain the progress of the phase transition and, if protein-protein interactions are the most important interactions between adjacent trimers in the lipid matrix, the transition is quite similar to what occurs with molecular crystals.

Bacterial Outer Membrane Proteins↗
PubMed2005

Light source position and reflectance estimation from a single view without the distant illumination assumption.

Several techniques have been developed for recovering reflectance properties of real surfaces under unknown illumination. However, in most cases, those techniques assume that the light sources are located at inifinity, which cannot be applied safely to, for example, reflectance modeling of indoor environments. In this paper, we propose two types of methods to estimate the surface reflectance property of an object, as well as the position of a light source from a single view without the distant illumination assumption, thus relaxing the conditions in the previous methods. Given a real image and a 3D geometric model of an object with specular reflection as inputs, the first method estimates the light source position by fitting to the Lambertian diffuse component, while separating the specular and diffuse components by using an iterative relaxation scheme. Our second method extends that first method by using as input a specular component image, which is acquired by analyzing multiple polarization images taken from a single view, thus removing its constraints on the diffuse reflectance property. This method simultaneously recovers the reflectance properties and the light source positions by optimizing the linearity of a log-transformed Torrance-Sparrow model. By estimating the object's reflectance property and the light source position, we can freely generate synthetic images of the target object under arbitrary lighting conditions with not only source direction modification but also source-surface distance modification. Experimental results show the accuracy of our estimation framework.

Algorithms↗
PubMed1990

Time-domain analysis of auditory-nerve-fiber firing rates.

Time-domain analysis of firing-rate data from over 200 fibers from the auditory nerve of cat has been used to estimate the formants of the synthetic-syllable stimuli. Distinct groups of fibers are identified based on intervals between peaks in the fiber firing rates. The large extent of some of these groups--over an octave in terms of characteristic frequency--and the lack of short intervals in the longer-interval groups suggest that the behavior of the nonlinear cochlear filters for these signals is effectively wideband with steep high-frequency cutoffs. The measured intervals within each group are very similar, and correspond to the period of the formant that dominates the group's response. These intervals are used to estimate the dynamic speech formants. The overall formant estimates are better than those of the previous spectral analyses of the neural data, and the details of lower-formant dynamics are tracked more precisely. The direct temporal representation of the formant in contrasted with the diffuse spectral representation, the dependence of spectral peaks on nonformant parameters, and the distortion of the spectrum by rectification. It is concluded that a time-domain analysis of the responses to complex stimuli can be an important addition to frequency-domain analysis for neural data, cochlear models, and machine processing of speech.

Animals↗
PubMed2007

AAV1 mediated co-expression of formylglycine-generating enzyme and arylsulfatase a efficiently corrects sulfatide storage in a mouse model of metachromatic leukodystrophy.

Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder caused by a deficiency of arylsulfatase A (ASA) and is characterized by deposition of sulfatide in all organs, particularly the nervous system. Recently, formylglycine-generating enzyme (FGE) was found to be essential for activation of sulfatases. This study examined the utility of FGE co-expression in AAV type 1 vector (AAV1)-mediated gene therapy of ASA knockout (MLD) mice. AAV1-ASA alone or AAV1-ASA and AAV1-FGE were co-injected into a single site of the hippocampus. Enzyme assay and immunohistochemical analysis showed that ASA was detected not only in the injected hemisphere but also in the non-injected hemisphere by 7 months after injection. Level of ASA activity and extent of ASA distribution were significantly enhanced by co-introduction of AAV1-FGE. Marked reductions in sulfatide levels were observed throughout the entire brain. The unexpectedly widespread distribution of ASA may be due to a combination of diffusion in extracellular spaces, transport through axons, and circulation in cerebrospinal fluid. The rotarod test revealed improvement of neurological functions. These results demonstrate that direct injection of AAV1 vectors expressing ASA and FGE represents a highly promising approach with significant implications for the development of clinical protocols for MLD gene therapy.

Animals↗
PubMed1994

Dynamic properties of water at phosphatidylcholine lipid-bilayer surfaces as seen by deuterium and pulsed field gradient proton NMR.

The dynamic properties of water in phosphatidylcholine lipid/water dispersions have been studied, applying a combination of 2H-NMR techniques (quadrupole splitting and spin-lattice relaxation time) and self-diffusion measurements using pulsed filed gradient (PFG) 1H-NMR. The hydration properties of POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine) were compared with those of DOPC (1,2-dioleoyl-sn-glycero-3-phosphatidylcholine) and EYL (egg yolk phosphatidylcholine (lecithin)). A model is presented that assumes an exponentially decaying influence of the bilayer surface on water dynamics as well as on water orientation with increasing hydration. This assumption is based on an exponentially decaying hydration potential which results from direct lipid-water and water-water interactions. The model describes successfully the experimental data for a large water concentration range, especially at low hydration, where other models failed. With the exception of a small fraction of water which is significantly influenced by the surface in slowing down the mobility, the interbilayer water has isotropic, free water characteristics in terms of correlation times and molecular order. Hydration properties of POPC are comparable with those of EYL but differ from DOPC. At very low water content the correlation times of headgroup segmental reorientation and water are similar, indicating a strong coupling of this water to the lipid lattice. The hydration properties of the three lipids studied are explained in terms of slightly different headgroup conformations due to different lateral packing of the molecules by their fatty acid chain composition.

Chemical Phenomena↗
PubMed1996

Transmitter concentration profiles in the synaptic cleft: an analytical model of release and diffusion.

A three-dimensional model for release and diffusion of glutamate in the synaptic cleft was developed and solved analytically. The model consists of a source function describing transmitter release from the vesicle and a diffusion function describing the spread of transmitter in the cleft. Concentration profiles of transmitter at the postsynaptic side were calculated for different transmitter concentrations in a vesicle, release scenarios, and diffusion coefficients. From the concentration profiles the receptor occupancy could be determined using alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor kinetics. It turned out that saturation of receptors and sufficiently fast currents could only be obtained if the diffusion coefficient was one order of magnitude lower than generally assumed, and if the postsynaptic receptors formed clusters with a diameter of roughly 100 nm directly opposite the release sites. Under these circumstances the gradient of the transmitter concentration at the postsynaptic membrane outside the receptor clusters was steep, with minimal cross-talk among neighboring receptor clusters. These findings suggest that for each release site a corresponding receptor aggregate exists, subdividing an individual synapse into independent functional subunits without the need for specific lateral diffusion barriers.

Animals↗
PubMed1983

Expiratory and arterial partial pressure relations under different ventilation-perfusion conditions.

Inert tracer gas exchange across the human respiratory system is simulated in an asymmetric lung model for different oscillatory breathing patterns. The momentary volume-averaged alveolar partial pressure (PA), the expiratory partial pressure (PE), the mixed expiratory partial pressure (PE), the end-tidal partial pressure (PET), and the mean arterial partial pressure (Pa), are calculated as functions of the blood-gas partition coefficient (lambda) and the diffusion coefficient (D) of the tracer gas. The lambda values vary from 0.01 to 330.0 inclusive, and four values of D are used (0.5, 0.22, 0.1, and 0.01). Three ventilation-perfusion conditions corresponding to rest and mild and moderate exercise are simulated. Under simulated exercise conditions, we compute a reversed difference between PET and Pa compared with the rest condition. This reversal is directly reflected in the relation between the physiological dead space fraction (1--PE/Pa) and the Bohr dead space fraction (1--PE/PET). It is argued that the difference (PET--Pa) depends on the lambda of the tracer gas, the buffering capacity of lung tissue, and the stratification caused by diffusion-limited gas transport in the gas phase. Finally some determinants for the reversed difference (PET--Pa) and the significance for conventional gas analysis are discussed.

Humans↗
PubMed1995

Endotoxin-induced hydrogen peroxide production in intact pulmonary circulation of rat.

Although the importance of free oxygen radical has been reported in acute lung injury, the direct evidence in vivo model was lacking. We report a new method, which for the first time allows direct detection of hydrogen peroxide in the intact rat pulmonary microcirculation. We used the computer image-analyzing system and 2',7'-dichlorofluorescin diacetate for the marker of hydrogen peroxide production in vivo. A rat sepsis model was produced by continuous infusion of endotoxin for 30, 60, and 120 min. Hydrogen peroxide production in the pulmonary microcirculation of the sepsis rat was higher than in the control rat at each time point (p < 0.01) and increased time-dependently (p < 0.01). Catalase (5,000 U/kg) almost completely inhibited the hydrogen peroxide production in the sepsis rat (p < 0.01). In high-power view, hydrogen peroxide was detected in granulocytes that adhered to the capillaries and endothelial cells that were adjoining adherent granulocytes. These observations suggest that hydrogen peroxide in the endothelium was diffused from granulocytes. In this study, we demonstrated direct evidence of hydrogen peroxide production from adherent granulocytes in intact rat lung treated with endotoxin. We conclude that endotoxin causes the granulocyte adhesion and oxidative stress to the endothelium due to adherent granulocytes within 30 min in the pulmonary microcirculation.

Animals↗
PubMed1993

Architecture of the Xenopus nuclear pore complex revealed by three-dimensional cryo-electron microscopy.

The nuclear pore complex spans the nuclear envelope and functions as a macromolecular transporter in the ATP-dependent process of nucleocytoplasmic transport. In this report, we present three dimensional (3D) structures for both membrane-associated and detergent-extracted Xenopus NPCs, imaged in frozen buffers by cryo-electron microscopy. A comparison of the differing configurations present in the 3D maps suggests that the spokes may possess an intrinsic conformational flexibility. When combined with recent data from a 3D map of negatively stained NPCs (Hinshaw, J. E., B. O. Carragher, and R. A. Milligan. 1992. Cell. 69:1133-1141), these observations suggest a minimal domain model for the spoke-ring complex which may account for the observed plasticity of this assembly. Moreover, lumenal domains in adjacent spokes are interconnected by radial arm dimers, forming a lumenal ring that may be responsible for anchoring the NPC within the nuclear envelope pore. Importantly, the NPC transporter is visualized as a centrally tapered cylinder that spans the entire width of the NPC, in a direction normal to the nuclear envelope. The central positioning, tripartite structure, and hollow nature of the transporter suggests that it may form a macromolecular transport channel, with a globular gating domain at each end. Finally, the packing of the transporter within the spokes creates a set of eight internal channels that may be responsible, in part, for the diffusion of ions and small molecules across the nuclear envelope.

Animals↗
PubMed1976

Acute hypersensitivity pneumonitis in the rabbit. I. An animal model with horseradish peroxidase as antigen.

An experimental model of acute hypersensitivity pneumonitis was developed in rabbits using horseradish peroxidase as antigen. The lesion, produced by aerosol challenge with horseradish peroxidase 21 days after a single parenteral immunization with horseradish peroxidase and complete Freund adjuvant, was characterized by diffuse infiltration of respiratory bronchioles and of alveolar ducts and walls with approxomately equal numbers of mononuclear cells (lymphocytes and macrophages) and polymorphonuclear cells. This lesion, which was specific for the antigen, was distinct from the variable granulomatous component that was directly attributable to the use of complete Freund adjubant. Development of the lesion did not correlate with the humoral immune response, as indicated by antigen-binding, precipitin, and homologous passive cutaneous anaphylaxis assays, by negative serum transfer studies, by lack of correlation with immediate and intermediate Arthuslike) skin reactivity, by absence of electron microscopic and immunofluorescent evidence for immune complex processes, and by lack of evidence for complement activation. Development of the lesion did correlate with delayed (12- to 48-hour) skin reactivity, although rigid identification of cell-mediated immunity was not possible on histologic examination.

Acute Disease↗
PubMedDate not supplied

[Novel biophysical and biological aspects of mechanisms of effects of low doses of ionizing radiation (low LET) on eukaryotic cells].

Novel biophysical and biological aspects of eukaryotic cell response to low doses of low-LET radiation are considered in the present paper. The model of universal nuclear target in eukaryotic cells is proposed. The target is considered as a spherical volume homogeneously filled of DNA with adjacent water layer. Thickness of water layer equals to diffusion length of hydroxil radicals hitting DNA. Two subregions are proposed of the cellular membrane with different ability to respond to low doses of ionizing radiation. An original mechanism of repair of DNA double strand breaks (dsb) is described. This mechanism suggests directional conformational movement of separate locuses of homological chromosomes through narrow tube ("throat") between specialised nuclear regions. The fluxes of nuclear liquid induce a force which is responsible for highly elastic chromosome deformation and chromosome movement resulting in proximity of homological chromosomes in the throat. Close proximity is required for DNA dsb repair. All of DNA dsbs have to be repaired in low doses range owing to high genomic stability of eukaryotic cells. However, it has been hypothesized an existence of a small subpopulation of cells with unstable genome named as cells of evolutionary or/and ontogenetical reserve (ER or/and OR). Genomic instability is induced in these cells by epigenetic program. This program results in DNA damage mainly in chromosomal "hot spots". As a result new genetic variants are originated. The ability of cell population in vivo to eliminate or not eliminate Er/OR cells determinates individual sensitivity of organism and hence health consequences to low dose radiation exposure.

Animals↗
PubMed1993

Renal angiotensin receptor mapping in obese spontaneously hypertensive rats.

Obese spontaneously hypertensive rats (SHR) develop nephropathy with severe proteinuria, but lean littermates do not develop renal disease. Intrarenal angiotensin has been suggested to contribute to nephropathy in other experimental models. We examined the regulation of angiotensin receptors as a reflection of target tissue response to possible changes in the renin-angiotensin system. We visualized angiotensin receptors in kidneys of 6-8-month-old obese SHR and their lean littermates. Both obese and lean rats were hypertensive as determined by tail-cuff or by direct measurement. Histologic studies showed early glomerular sclerosis in obese but not lean rats. Autoradiographic visualization of angiotensin receptor binding sites in both obese and lean SHR showed glomeruli and medullary rays having the highest levels of binding with additional diffuse labeling in cortex and outer medulla. In obese rats, binding was reduced relative to lean littermates, particularly in the medulla, while intense binding in glomeruli was preserved. Loss of receptors did not reflect tissue damage, since the medulla showed no pathological changes. Biochemical assays of the binding of subtype-selective antagonists to 125I-angiotensin sites in intact sections showed that both losartan-sensitive and PD 123319-sensitive sites were decreased in nephrotic obese rats. We conclude that specific binding sites for angiotensin are decreased in obese SHR with early glomerular sclerosis, suggesting that angiotensin receptors may be regulated by pathogenic processes in this model of renal disease.

Angiotensin II↗
PubMed1994

Externally driven countercurrent multiplication in a mathematical model of the urinary concentrating mechanism of the renal inner medulla.

Substitution of measured permeabilities into mathematical models of the concentrating mechanism of the renal inner medulla yields less than the known urine osmolalities. To gain a better understanding of the mechanism we analyse a model in which a force of unspecified origin [expressed as fraction, epsilon, of entering descending thin limb (DTL) concentration] drives fluid from DTL to interstitial vascular space (CORE), thus concentrating the solution in DTL. When flow in the DTL reverses at the hairpin bend of the loop of Henle, the high solute permeability of ascending thin limb (ATL) permits solute to diffuse into the CORE thus permitting epsilon to be multiplied many-fold. Behavior of the model is described by two non-linear differential equations. In the limit for infinite salt permeability of ATL the two equations reduce to a single equation that is formally identical with that for the Hargitay and Kuhn multiplier, which assumes fluid transport directly from DTL to ATL (Z. Electrochem. Angew. Phys. Chem. 55, 539, 1951). Solutions of the equations describing the model with parameters taken from perfused thin limbs show that urine osmolalities of the order of 5000 mosm L-1 can be generated by forces of the order of 20 mosm L-1. It seems probable that mammals including desert rodents use some variant of this basic mechanism for inner medullary concentration.

Animals↗
PubMed2002

Microdialysis: an in vivo approach for measuring drug delivery in oncology.

Microdialysis (MD) is a catheter-based sampling method that provides the opportunity to directly study tumor drug exposure and metabolism in a minimally invasive way. Tumor drug exposure, which is directly linked to clinical outcome, may be substantially reduced due to diffusion barriers in solid tumors. Therefore plasma drug profiles are frequently inappropriate for predicting outcome in oncology. This contribution focuses on the application of MD in preclinical and clinical oncological research and presents an overview of the current literature. It is concluded that MD, in combination with pharmacokinetic/pharmacodynamic modeling, has the potential to contribute to the design of optimal treatment schedules and to select appropriate drug candidates, doses, and dosing intervals for established and new anticancer drugs.

Animals↗
PubMed2004

A functional analysis of the crown architecture of tropical forest Psychotria species: do species vary in light capture efficiency and consequently in carbon gain and growth?

The crown architectures of 11 Psychotria species native to Barro Colorado Island, Panama were reconstructed from field measurements of leaf and branch geometry with the three-dimensional simulation model Y-plant. The objective was to assess the role of species differences in architecture in light capture and carbon gain in their natural understory environment. When species were grouped according to their putative light environment preference, the shade tolerant species were found to have a small but significantly higher efficiency of light capture for both diffuse and direct light as compared to the light demanding species. Within each grouping, however, there were few significant differences in light capture efficiency among species. The lower efficiencies of light demanding species was due to slightly higher self-shading and slightly lower angular efficiencies. Simulations of whole plant assimilation showed that light demanding species had greater daily assimilation in both direct and diffuse light due to the significantly greater light availability in the sites where light demanding species were found, as compared to those where shade tolerant species occurred. Among light demanding species, the above ground relative growth rate measured over a 1-year period by applying allometric equations for mass versus linear dimensions, was positively correlated with diffuse PFD and with mean daily assimilation estimated from Y-plant. For the shade tolerant plants, there was no significant correlation between RGR and mean daily assimilation or with any measure of light availability, probably because they occurred over a much narrower range of light environments. Overall, the results reveal a strong convergence in light capture efficiencies among the Psychotria species at lower values than previously observed in understory plants using similar approaches. Constraints imposed by other crown functions such as hydraulics and biomechanical support may place upper limits on light capture efficiency.

Biometry↗
PubMed2001

Evidence from the Pacific troposphere for large global sources of oxygenated organic compounds.

The presence of oxygenated organic compounds in the troposphere strongly influences key atmospheric processes. Such oxygenated species are, for example, carriers of reactive nitrogen and are easily photolysed, producing free radicals-and so influence the oxidizing capacity and the ozone-forming potential of the atmosphere-and may also contribute significantly to the organic component of aerosols. But knowledge of the distribution and sources of oxygenated organic compounds, especially in the Southern Hemisphere, is limited. Here we characterize the tropospheric composition of oxygenated organic species, using data from a recent airborne survey conducted over the tropical Pacific Ocean (30 degrees N to 30 degrees S). Measurements of a dozen oxygenated chemicals (carbonyls, alcohols, organic nitrates, organic pernitrates and peroxides), along with several C2-C8 hydrocarbons, reveal that abundances of oxygenated species are extremely high, and collectively, oxygenated species are nearly five times more abundant than non-methane hydrocarbons in the Southern Hemisphere. Current atmospheric models are unable to correctly simulate these findings, suggesting that large, diffuse, and hitherto-unknown sources of oxygenated organic compounds must therefore exist. Although the origin of these sources is still unclear, we suggest that oxygenated species could be formed via the oxidation of hydrocarbons in the atmosphere, the photochemical degradation of organic matter in the oceans, and direct emissions from terrestrial vegetation.

Journal Article↗