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PubMed2003

Global conformations, hydrodynamics, and X-ray scattering properties of Taq and Escherichia coli DNA polymerases in solution.

Escherichia coli polymerase 1 (Pol 1) and Thermus aquaticus Taq polymerase are homologous Type I DNA polymerases, each comprised of a polymerase domain, a proofreading domain (inactive in Taq), and a 5' nuclease domain. "Klenow" and "Klentaq" are the large fragments of Pol 1 and Taq and are functional polymerases lacking the 5' nuclease domain. In the available crystal structures of full-length Taq, the 5' nuclease domain is positioned in two different orientations: in one structure, it is extended out into solution, whereas in the other, it is folded up against the polymerase domain in a more compact structure. Analytical ultracentrifugation experiments report s20,w values of 5.05 for Taq, 4.1 for Klentaq, 5.3 for E. coli Pol 1, and 4.6 for Klenow. Measured partial specific volumes are all quite similar, indicating no significant differences in packing density between the mesophilic and thermophilic proteins. Small angle x-ray scattering studies report radii of gyration of 38.3 A for Taq, 30.7 A for Klentaq, and 30.5 A for Klenow. The hydrodynamic and x-ray scattering properties of the polymerases were also calculated directly from the different crystal structures using the programs HYDROPRO (Garcia De La Torre, J., Huertas, M. L., and Carrasco, B. (2000) Biophys J. 78, 719-730) and CRYSOL (Svergun, D. I., Barberato, C., and Koch, M. H. J. (1995) J. Appl. Crystalogr. 28, 768-773), respectively. The combined experimental and computational characterizations indicate that the full-length polymerases in solution are in a conformation where the 5' nuclease domain is extended into solution. Further, the radius of gyration, and hence the global conformation of Taq polymerase, is not altered by the binding of either matched primer template DNA or ddATP.

Biophysical Phenomena↗
PubMed2004

The hydrodynamic properties of dark- and light-activated states of n-dodecyl beta-D-maltoside-solubilized bovine rhodopsin support the dimeric structure of both conformations.

Rhodopsin (Rho) has been extracted in n-dodecyl beta-D-maltoside (DM) from bovine retinal rod outer segments and purified to homogeneity by affinity chromatography on concanavalin A-Sepharose. Because chemical cross-linking of Rho and photoactivated Rho (Rho*) provided initial evidence for the oligomeric nature of the photoreceptor protein, we carried out a hydrodynamic characterization of the native and activated conformations of detergent-solubilized Rho. The molecular weights of the complexes between dark and photoexcited states of Rho and DM were determined by gel filtration chromatography on Sephacryl S-300, in the presence of 0.1% DM. Subtracting the size of the corresponding detergent micelles resulted in molecular masses of 78 kDa for native Rho and 76 kDa for Rho*. The measured content of 0.97 g of detergent/g of protein resulted in a calculated partial specific volume of 0.765 cm(3)/g for the protein-detergent complex and a molar mass of 64-65 kDa for the protein moiety. The sizes of Rho.DM and Rho*.DM complexes were also evaluated by sedimentation on 10-30% sucrose gradients, in the presence of 0.1% DM, and molecular masses of about 60 kDa were estimated for both the dark- and light-activated states of the photoreceptor protein. The size of Rho was determined to be 65,300 and 69,800 Da, respectively, when the purified Rho.DM complex was either chromatographed on Sephacryl S-300 or ultracentrifuged on sucrose gradients in the absence of DM. All these results were consistent with a dimeric quaternary structure for both conformations of Rho. Additionally, the functional integrity of the purified photoreceptor protein following gel filtration chromatography and ultracentrifugation was demonstrated by three criteria as follows: (i) its characteristic UV-visible absorption spectra, (ii) its capability to photoactivate transducin, and (iii) its ability to serve as a substrate for rhodopsin kinase.

Animals↗
PubMed2001

Central imidazoline (I(1)) receptors modulate aqueous hydrodynamics.

The purpose of this work is to determine the relative contributions of central imidazoline (I(1)) receptors to the ocular hydrodynamic action of moxonidine. Moxonidine (MOX), an alpha(2) and I(1) receptor agonist, and efaroxan (EFA), a relatively selective I(1) antagonist, were utilized to study alterations in intraocular pressure (IOP) and aqueous flow in New Zealand white rabbits subjected to intracerebroventricular (i.c.v.) cannulation and sympathectomy. Intracerebroventricular administration of MOX (0.033, 0.33 and 3.33 microg) to normal rabbits produced dose-dependent, bilateral IOP decreases of 3, 6, and 8 mmHg, respectively. The ocular hypotensive response to MOX was immediate (10 min. post drug), lasted for one hour, and was inhibited by prior administration of efaroxan (3.33 microg i.c.v.). In unilaterally sympathectomized (SX) rabbits, the ocular hypotensive response induced by i.c.v MOX in the denervated eye was attenuated approximately 50%, but the duration of ocular hypotension in the surgically altered eye was longer than that of the normal eye. MOX (0.33 microg i.c.v.), caused a statistically significant decrease (2.24 to 1.59 ml/min.) in aqueous flow in normal eyes. In SX eyes, there was no change in aqueous flow by MOX, suggesting that IOP effect in i.c.v. MOX observed in the SX eye might be mediated by changes in outflow resistance. Sedation was observed in all the rabbits treated with MOX (i.c.v.) and was dose-dependent. These in vivo data support the suggestion that centrally located I(1) receptors modulate the early contralateral response to topically administered MOX and are involved in lowering of IOP and aqueous flow in rabbit. In addition, expression of the full ocular hypotensive effect of centrally applied MOX depends on intact sympathetic innervation. Ocular hypotension induced by MOX in the SX eye may involve an effect on uveoscleral outflow.

Adrenergic alpha-Antagonists↗
PubMed2002

Response properties of diencephalic neurons to visual, acoustic and hydrodynamic stimulation in the goldfish, Carassius auratus.

We studied the responses to sensory stimulation of three diencephalic areas, the central posterior nucleus of the dorsal thalamus, the anterior tuberal nucleus of the hypothalamus, and the preglomerular complex. Units sensitive to acoustic (500 Hz tone burst), hydrodynamic (25 Hz dipole stimulus) and visual (640 nm light flash) stimuli were found in both the central posterior and anterior tuberal nucleus. In contrast, unit responses or large robust evoked potentials confined to the preglomerular complex were not found. In the central posterior nucleus, most units were unimodal. Many units responded exclusively to visual stimulation and exhibited a variety of temporal response patterns to light stimuli. In the anterior tuberal nucleus of the hypothalamus, most units responded to more than one modality and showed a stronger response decrement to stimulus repetitions than units in the central posterior nucleus. Our data suggest that units in the central posterior nucleus are primarily involved in the unimodal processing of sensory information whereas units in the anterior tuberal nucleus of the hypothalamus may be involved in multisensory integration.

Journal Article↗
PubMed1997

Post-cranioplasty cerebrospinal fluid hydrodynamic changes: magnetic resonance imaging quantitative analysis.

The syndrome of the trephined has been described in many patients with cranial defects as an indication for cranioplasty. Cerebral blood flow changes, the effect of the atmospheric pressure on the brain, as well as cerebrospinal fluid hydrodynamic changes have been postulated as the possible reasons for this syndrome. Using dynamic phase-contrast magnetic resonance imaging we measured arterial, venous, and cerebrospinal fluid flow into and out of the skull, before and after cranioplasty in one patient whose bone flap was removed because of osteomyelitis. We report significant changes in the oscillatory CSF flow after cranioplasty. A moderate increase in venous outflow as well as a two-fold increase in craniocaudal cerebrospinal fluid systolic flow velocity was measured after the skull closure. The changes in the cerebrospinal fluid oscillatory flow at the level of the craniovertebral junction could reflect changes in the compliance of the craniospinal system produced by closure of the cranial defect.

Adult↗
PubMed2005

Preoperative spinal hydrodynamics versus clinical change 1 year after shunt treatment in idiopathic normal pressure hydrocephalus patients.

Nineteen consecutive cases treated for idiopathic normal pressure hydrocephalus (iNPH) with ventriculo-peritoneal shunts were clinically followed prospectively. Change in clinical state one year after shunt surgery was assessed as change on a 15-3 score NPH Grade Scale. Preoperative spinal hydrodynamics were assessed using a constant-rate lumbar infusion test. The pressure recordings were stored as raw data files and analysed retrospectively with regard to the mean cerebrospinal fluid pressure (CSFP), as well as mean CSFP wave amplitudes. Changes in NPH score 1 year after shunt surgery correlated significantly with the levels of single CSFP wave amplitudes, but not with the lumbar resistance to CSF outflow (R(out)). Mean CSFP wave amplitude was thus, in this cohort, a better predictor of clinical change one year after shunt treatment than R(out).

Aged↗
PubMed2001

Hydrodynamic and mass transfer characteristics of three-phase gaslift bioreactor systems.

This review focuses on the hydrodynamic and mass transfer characteristics of various three-phase, gaslift fluidized bioreactors. The factors affecting the mixing and volumetric mass transfer coefficient (k(L)a), such as liquid properties, solid particle properties, liquid circulation velocity, superficial gas velocity, bioreactor geometry, are reviewed and discussed. Measurement methods, modeling and empirical correlations are reviewed and compared. To the authors' knowledge, there is no 'generalized' correlation to calculate the volumetric mass transfer coefficient, instead, only 'type-specific' correlations are available in the literature. This is due to the difficulty in modeling the gaslift bioreactor, caused by the variation in geometry, fluid dynamics, and phase interactions. The most important design parameters reported in the literature are: gas hold-up, liquid circulation velocity, 'true' superficial gas velocity, mixing, shear rate, aeration rate and volumetric mass transfer coefficient, k(L)a.

Bioreactors↗
PubMed1992

Dynamic light scattering studies on hydrodynamic properties of fibrinogen-fibronectin complex.

A high molecular weight 'cryogel' was obtained as insoluble complexes by cold incubation at near-freezing temperatures from heparinized plasma of patients with rheumatoid arthritis. After the cryogel was solubilized at 37 degrees C, 1:1 complex of fibrinogen and fibronectin was purified at room temperature by affinity chromatography on a gelatin-Sepharose 4B. Hydrodynamic properties of the complex were investigated as a function of temperature and NaCl concentration using a dynamic light scattering. The diffusion coefficients of the complex at 20 degrees C decreased with increasing of NaCl concentration as free fibronectin. The complex appears to be a more compact form at low ionic concentration, which is associated with conformational changes of fibronectin. The diffusion coefficient of the complex at 20 degrees C in 0.05 M TrisHCl(pII7.4) containing 0.5 M NaCl was estimated as 8.5 x 10(-8) cm2s-1. The complex did not dissociate over the temperature range from 20 to 37 degrees C. The diffusion coefficients of the complex decreased significantly at 12 degrees C and 40 degrees C. The thermal denaturation of fibrinogen molecule in the complex was observed at 40 degrees C. The CONTIN analysis of the light scattering data showed that the complex associated to form higher aggregates at 15 degrees C, but not at near-freezing temperature. The equilibrium between the complex and higher aggregates appeared reversible.

Diffusion↗
PubMed2001

Solution structure, hydrodynamics and thermodynamics of the UvrB C-terminal domain.

The solution structure, thermodynamic stability and hydrodynamic properties of the 55-residue C-terminal domain of UvrB that interacts with UvrC during excision repair in E. coli have been determined using a combination of high resolution NMR, ultracentrifugation, 15N NMR relaxation, gel permeation, NMR diffusion, circular dichroism and differential scanning calorimetry. The subunit molecular weight is 7,438 kDa., compared with 14.5+/-1.0 kDa. determined by equilibrium sedimentation, indicating a dimeric structure. The structure determined from NMR showed a stable dimer of anti-parallel helical hairpins that associate in an unusual manner, with a small and hydrophobic interface. The Stokes radius of the protein decreases from a high plateau value (ca. 22 A) at protein concentrations greater than 4 microM to about 18 A at concentrations less than 0.1 microM. The concentration and temperature-dependence of the far UV circular dichroism show that the protein is thermally stable (Tm ca. 71.5 degrees C at 36 microM). The simplest model consistent with these data was a dimer dissociating into folded monomers that then unfolds co-operatively. The van't Hoff enthalpy and dissociation constant for both transition was derived by fitting, with deltaH1=23 kJ mol(-1). K1(298)=0.4 microM and deltaH2= 184 kJ mol(-1). This is in good agreement with direct calorimetric analysis of the thermal unfolding of the protein, which gave a calorimetric enthalpy change of 181 kJ mol(-1) and a van't Hoff enthalpy change of 354 kJ mol(-1), confirming the dimer to monomer unfolding. The thermodynamic data can be reconciled with the observed mode of dimerisation. 15N NMR relaxation measurements at 14.1 T and 11.75 T confirmed that the protein behaves as an asymmetric dimer at mM concentrations, with a flexible N-terminal linker for attachment to the remainder of the UvrB protein. The role of dimerisation of this domain in the excision repair mechanism is discussed.

Amino Acid Sequence↗
PubMedDate not supplied

A simple and inexpensive method for investigating microbiological, enzymatic, or inorganic catalysis using standard histology and microbiology laboratory equipment: assembly, mass transfer properties, hydrodynamic conditions and evaluation.

We introduce a generic, simple, and inexpensive method for performing microbiological, enzymatic, or inorganic catalysis with solids using standard histology and microbiology laboratory equipment. Histology cassettes were used to standardize hydrodynamic conditions and to protect the catalysts and their solid supports. Histology cassettes have the following advantages: they are readily available, inexpensive, solvent and acid resistant, automatable, and the slots in the cassette walls allow liquid to circulate freely. Standard Erlenmeyer flasks were used as reaction vessels. We developed a new camera to observe the movement and position of the histology cassettes as well as the liquid in the Erlenmeyer flasks. The camera produces a stable image of the rotating liquid in the Erlenmeyer flask. This visualization method revealed that in a 250 ml Erlenmeyer flask, stable operating conditions are achieved at a shaking frequency of 300 rpm and a fill volume of 30 ml. In vessels with vertical walls, such as beakers or laboratory bottles, the movement of the histology cassette is not reproducible. Mass transfer characterization using a biological model system and the chemical sulfite-oxidation method revealed that the histology cassette does not influence gas-liquid mass transfer.

Catalysis↗
PubMed2006

A practical extension of hydrodynamic theory of porous transport for hydrophilic solutes.

OBJECTIVE: The equations for transport of hydrophilic solutes through aqueous pores provide a fundamental basis for examining capillary-tissue exchange and water and solute flux through transmembrane channels, but the theory remains incomplete for ratios, alpha, of sphere diameters to pore diameters greater than 0.4. Values for permeabilities, P, and reflection coefficients, sigma, from Lewellen, working with Lightfoot et al., at alpha = 0.5 and 0.95, were combined with earlier values for alpha < 0.4, and the physically required values at alpha = 1.0, to provide accurate expressions over the whole range of 0 < alpha < 1. METHODS: The "data" were the long-accepted theory for alpha < 0.2 and the computational results from Lewellen and Lightfoot et al. on hard spheres (of 5 different alpha's) moving by convection and diffusion through a tight cylindrical pore, accounting for molecular exclusion, viscous forces, pressure drop, torque and rotation of spheres off the center line (averaging across all accessible radial positions), and the asymptotic values at alpha = 1.0. Coefficients for frictional hindrance to diffusion, F(alpha), and drag, G(alpha), and functions for sigma(alpha) and P(alpha), were represented by power law functions and the parameters optimized to give best fits to the combined "data." RESULTS: The reflection coefficient sigma = {1 - [1 - (1 - phi)2]G'(alpha)} + 2alpha2 phi F'(alpha), and the relative permeability P/Pmax = phi F '(alpha)[1 + 9alpha5.5 x (1.0 - alpha5)0.02], where phi is the partition coefficient or volume fraction of the pore available to solute. The new expression for the diffusive hindrance is F'(alpha) = (1 - alpha2)(3/2) phi/[1 + 0.2 x alpha2 x (1 - alpha2)16], and for the drag factor is G'(alpha) = (1 - 2alpha(2)/3 - 0.20217 alpha5)/(1 - 0.75851 alpha5) - 0.0431[1 - (1 - alpha10)]. All of these converge monotonically to the correct limits at alpha = 1. CONCLUSIONS: These are the first expressions providing hydrodynamically based estimates of sigma(alpha) and P(alpha) over 0 < alpha < 1 They should be accurate to within 1-2%.

Animals↗
PubMed2003

Engineering tools for understanding the hydrodynamics of dissolution tests.

In this article, three well-established engineering tools are used to examine hydrodynamics in dissolution testing apparatuses. The application of these tools would provide detailed information about the flow, shear, and homogeneity in dissolution tests. Particle image velocimetry successfully measures two-dimensional cross-sections of the velocity field in an experimental device under both laminar and turbulent conditions. The velocity field is also calculated with computational fluid dynamics (CFD), which can rapidly provide data that is difficult or impossible to obtain experimentally. The occurrence of segregated regions within a USP Apparatus II under mild agitation conditions is revealed by CFD simulations and confirmed by laser-induced fluorescence experiments. The results clearly demonstrate that under current operation settings, the USP Apparatus II operates in a regime where the flow is in incipient turbulence, which is a highly time-dependent condition that might explain possible inconsistencies in dissolution results. It is further demonstrated that proposed changes advocating lower speeds or smaller vessels displace the system toward laminar flow conditions characterized by segregation, compromising the robustness of the test and making it vulnerable to variability with respect to sample location.

Fluorescence↗
PubMed2004

The macromolecular polymers for the preparation of hydrodynamically balanced systems--methods of evaluation.

Evaluation of macromolecular polymers used as excipients for the preparation of hydrodynamically balanced systems (HBS) was carried out. Hard gelatine capsules were filled with polymeric substances belonging to various chemical groups (chitosan, sodium alginate, hydroxypropylmethycellulose--HPMC). The following properties of the HBS were investigated: density, hydration, erosion and floating force. The solvent penetration process into the HBS was visualized using magnetic resonance imaging (MRI) technique. Densities of the HBS in hydrochloric acid (0.1 M) ranged from 0.37 g/cm3 to 0.71 g/cm3. Each polymer demonstrated different hydration/erosion abilities and floating properties. The maximum floating force (F(float max)) for capsules size 0, ranged from 26.7 mN (sodium alginate) to 64.7 mN (chitosan). HBS formulations also varied in time to reach maximum floating force (T(float max)). HPMC and sodium alginate formulation reached F(float max) within half an hour after immersion, while in the case of chitosan formulations (deacetylation degree (d.d.) 66% and d.d. 93%), the time was 184 minutes and 218 minutes respectively. The floating properties of the dosage forms were reliant on type of the polymer and the medium-fasted state simulated gastric fluid (FaSSGF) or fed state simulated gastric fluid (FeSSGF). The size of the HBS influenced the floating force value. The mechanisms of erosion and swelling of the polymeric matrices play a dominant role in flotation of the dosage forms.

Alginates↗
PubMed1966

The effects of adenosine triphosphate and related compounds on some hydrodynamic properties of glycerinated cilia.

Cilia were isolated from Tetrahymena pyriformis by a glycerol method. The addition of low concentrations of ATP, but not of other nucleoside triphosphates, caused an increase of up to twofold in the amount of cilia pelleted in a low-speed centrifugation assay and decreased the density of the pellets compared to control pellets. Pellet size and density depend on pH, both in the absence and in the presence of low concentrations of ATP. High concentrations (5 mM and above) of ATP and of other nucleoside triphosphates tend to "dissolve" the cilia. Heating the cilia for 11 min at 40 degrees C abolishes the increase in pellet size and the decrease in pellet density caused by low ATP, but slightly increases the ATPase activity of the cilia. Heat treatment, however, does not prevent the dissolving effect of high ATP. There are, thus, two independent effects of ATP on the hydrodynamic properties of cilia suspensions.

Adenosine Triphosphatases↗
PubMed1982

Hydrodynamic models of viscous coupling between motile myosin and endoplasm in characean algae.

Cytoplasmic streaming in characean algae is thought to be driven by interaction between stationary subcortical actin bundles and motile endoplasmic myosin. Implicit in this mechanism is a requirement for some form of coupling to transfer motive force from the moving myosin to the endoplasm. Three models of viscous coupling between myosin and endoplasm are presented here, and the hydrodynamic feasibility of each model is analyzed. The results show that individual myosinlike molecules moving along the actin bundles at reasonable velocities cannot exert enough viscous pull on the endoplasm to account for the observed streaming. Attachment of myosin to small spherical organelles improves viscous coupling to the endoplasm, but results for this model show that streaming can be generated only if the myosin-spheres move along the actin bundles in a virtual solid line at about twice the streaming velocity. In the third model, myosin is incorporated into a fibrous or membranous network or gel extending into the endoplasm. This network is pulled forward as the attached myosin slides along the actin bundles. Using network dimensions estimated from published micrographs of characean endoplasm, the results show that this system can easily generate the observed cytoplasmic streaming.

Actins↗
PubMed1968

The localization of circulating immune complexes in experimental serum sickness. The role of vasoactive amines and hydrodynamic forces.

In serum sickness, mechanisms by which circulating immune complexes become localized in the walls of vessels and glomeruli have been studied. In affected arteries, morphologic observations showed that circulating marker particles of carbon would rapidly deposit along the luminal surface of the internal elastic lamina. This, as in previous studies, suggested an increase in vascular permeability during which large molecules were capable of being trapped by a filtering membrane in the vessel wall. In attempts to prevent the increase in vascular permeability, rabbits were treated with antagonists of histamine and serotonin. Such treatment markedly inhibited the localization of immune complexes in glomeruli, the development of proteinuria, and glomerular endothelial proliferation. Cardiovascular lesions also were largely prevented from developing. Depletion of platelets, the principal reservoir of vasoactive amines, had a similar though less pronounced effect. While the deposition of immune complexes was inhibited, allergic inflammation in general was not, since normal rabbits treated as above were found capable of developing full Arthus reactions and acute nephrotoxic nephritis. Hydrodynamic factors were noted to be important in determining the location of arterial lesions. Studies of aortas from unmodified rabbits and from those with surgically induced coarctations of the abdominal aorta revealed intimal lesions concentrated at areas of high turbulence, such as at branches, bifurcations, outflows and zones of configurational change. Lesions in these areas were also largely inhibitable by depletion of platelets or by antagonists of histamine and serotonin.

Animals↗
PubMed2000

Radio Emission from Three-dimensional Relativistic Hydrodynamic Jets: Observational Evidence of Jet Stratification.

We present the first radio emission simulations from high-resolution three-dimensional relativistic hydrodynamic jets; these simulations allow us to study the observational implications of the interaction between the jet and the external medium. This interaction gives rise to a stratification of the jet in which a fast spine is surrounded by a slow high-energy shear layer. The stratification (in particular, the large specific internal energy and slow flow in the shear layer) largely determines the emission from the jet. If the magnetic field in the shear layer becomes helical (e.g., resulting from an initial toroidal field and an aligned field component generated by shear), the emission shows a cross section asymmetry, in which either the top or the bottom of the jet dominates the emission. This, as well as limb or spine brightening, is a function of the viewing angle and flow velocity, and the top/bottom jet emission predominance can be reversed if the jet changes direction with respect to the observer or if it presents a change in velocity. The asymmetry is more prominent in the polarized flux because of field cancellation (or amplification) along the line of sight. Recent observations of jet cross section emission asymmetries in the blazar 1055+018 can be explained by assuming the existence of a shear layer with a helical magnetic field.

Journal Article↗
PubMed2000

Hydrodynamic effects on the solute transport across endothelial pores and hepatocyte membranes.

In this short note we propose a simple and rapid procedure to calculate the net quantity of metabolites absorbed by hepatocytes from blood plasma. The blood movement through sinusoids determines an opposed circulation of plasma through the space of Disse. Hydrodynamic considerations lead to the conclusion that hepatocytes absorb for their own synthesis processes a quantity of metabolites in a volume flow of the order of 10(-12) nl s(-1) through a sieve plate surface with an area of 1 microm2. At pathological temperature (40 degrees C), the excess of the net absorbed volume flow for the entire sinusoidal surface of the mammalian liver may be as high as 1.9 nl s(-1). Some observations on the effect of red and white blood cells on the chylomicron traffic through endothelial pores are made.

Animals↗