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PubMed2002

Hydrodynamic properties of rigid macromolecules composed of ellipsoidal and cylindrical subunits.

A procedure is devised for the calculation of hydrodynamic properties of rigid macromolecules composed subunits that are modeled as ellipsoids of revolution and cylinders. Owing to the axial symmetry of these shapes, smooth shell models can be constructured for the subunit structure. The bead shell model so constructed is employed for the calculation of the properties. A computer program, HYDROSUB, has been written implementing both the model building and the hydrodynamic calculation. A detailed example of the use of this methodology is presented for the case of the solution properties of the human antibody molecule immunoglobulin G3 (IgG3). Finally, hints are given on other uses and applications of the procedure.

Biophysical Phenomena↗
PubMed2003

Modeling HIV-1 integrase complexes based on their hydrodynamic properties.

We present a model structure of a candidate tetramer for HIV-1 integrase. The model was built in three steps using data from fluorescence anisotropy, structures of the individual integrase domains, cross-linking data, and other biochemical data. First, the structure of the full-length integrase monomer was modeled using the individual domain structures and the hydrodynamic properties of the full-length protein that were recently measured by fluorescence depolarization. We calculated the rotational correlation times for different arrangements of three integrase domains, revealing that only structures with close proximity among the domains satisfied the experimental data. The orientations of the domains were constrained by iterative tests against the data on cross-linking and footprinting in integrase-DNA complexes. Second, the structure of an integrase dimer was obtained by joining the model monomers in accordance with the available dimeric crystal structures of the catalytic core. The hydrodynamic properties of the dimer were in agreement with the experimental values. Third, the active sites of the two model dimers were placed in agreement with the spacing between the sites of integration on target DNA as well as the integrase-DNA cross-linking data, resulting in twofold symmetry of a tetrameric complex. The model is consistent with the experimental data indicating that the F185K substitution, which is found in the model at a tetramerization interface, selectively disrupts correct complex formation in vitro and HIV replication in vivo. Our model of the integrase tetramer bound to DNA may help to design anti-integrase inhibitors.

Base Sequence↗
PubMedDate not supplied

Computer simulation of hydrodynamic properties of semiflexible macromolecules: randomly broken chains, wormlike chains, and analysis of properties of DNA.

The translational and rotational diffusion coefficients and the intrinsic viscosity of semiflexible, randomly broken, and wormlike chains have been obtained by Monte Carlo simulation in the context of the rigid-body treatment. Both approximate and rigorous rigid-body hydrodynamics are used, so that the error introduced by the approximate methods can be evaluated. A randomly broken chain and a wormlike chain having the same contour length and persistence length have the same radius of gyration but different values for any of the hydrodynamic properties. The two types of chains are compared in this regard. Considering that the cross section of the chain is represented by a cylinder better than by a string of spheres, we devise a cylindrical correction to be applied to the results simulated for chains of beads. Application is made to the analysis of experimental data for the translational and rotational coefficients of DNA fragments with up to 10(3) base pairs, obtaining the persistence length for each model. The values for the wormlike chain agree well with model-independent values obtained from radii of gyration and with other literature data at varying ionic strength. The randomly broken chain is equally able to reproduce the experimental length dependence of the properties, but the resulting persistence length may be too high.

Chemical Phenomena↗
PubMed1990

A hydrodynamic study with quasielastic light scattering and sedimentation of bacterial elongation factor EF-Tu.guanosine-5'-diphosphate complex under nonassociating conditions.

The hydrodynamics of the bacterial elongation factor EF-Tu have been studied in the presence of its ligand guanosine-5'-diphosphate (GDP) by sedimentation in the ultracentrifuge and quasielastic light scattering. Sedimentation studies have made it possible to establish experimental conditions under which only negligible aggregation of the protein occurs (neutral pH, concentration less than 3 mg/mL). Analysis of the light intensity autocorrelation functions under these conditions revealed two independent scattering species with diffusion coefficients of 0.71 X 10(-6) and 0.04 X 10(-6) cm2 s-1. The material with the lower diffusion coefficient, i.e., the aggregates, represented less than 1% of the total number of EF-Tu particles. The other 99% diffused as monomeric molecules with a molar mass corresponding to the value calculated from the known primary structure of the protein. The hydrodynamic parameters derived from the experimental data suggest that EF-Tu.GDP in solution is close to a spherical particle.

Escherichia coli↗
PubMed2003

Hydrodynamic characteristics of immobilized cell beads in a liquid-solid fluidized-bed bioreactor.

This study examined the hydrodynamic characteristics of a liquid-solid fluidized-bed bioreactor using elastic particles (PVA gel beads) of various diameters as carriers. The drag coefficient-Reynolds number, velocity-voidage, and expansion index-Reynolds number relationships observed during fluidization of PVA gel beads in a fluidized bed in our experiments were compared with the published results. Predictions made from previous correlations were examined with our new experimental findings, revealing the inadequacy of most of these correlations. Thus, new correlations describing the above-mentioned relationships are suggested. The drag coefficient of immobilized cell beads is larger than that of free cell ones at the same Reynolds number because the surface of the immobilized cell beads is rougher. For multiparticle systems, the correction factor, f(epsilon), is a function of the falling gel bead properties (Reynolds number) as well as the fluidized gel bead properties (Archimedes number), and depend strongly on the bed voidage (epsilon). A new simple relation was developed to predict easily the epsilon value from 0.5-0.9 at 4,986 < A(r) < 40,745 or 34 < Re(t) < 186. For all the immobilized cell beads used in this study, the prediction error of the bed voidage was less than 5% at epsilon > 0.5. The prediction equations in this study can be further applied to analyzing the hydrodynamic characteristics of a fluidized-bed reactor using similar entrapped elastic particles as carriers.

Acinetobacter baumannii↗
PubMed2004

Analyzing and modeling of photobioreactors by combining first principles of physiology and hydrodynamics.

Mixing in photobioreactors is known to enhance biomass productivity considerably, and flow dynamics play a significant role in the reactor's performance, as they determine the mixing and the cells' movement. In this work we focus on analyzing the effects of mixing and flow dynamics on the photobioreactor performance. Based on hydrodynamic findings from the CARPT(Computer Automated Radioactive Particle Tracking) technique, a possible mechanism for the interaction between the mixing and the physiology of photosynthesis is presented, and the effects of flow dynamics on light availability and light intensity fluctuation are discussed and quantitatively characterized. Furthermore, a dynamic modeling approach is developed for photobioreactor performance evaluation, which integrates first principles of photosynthesis, hydrodynamics, and irradiance distribution within the reactor. The results demonstrate the reliability and the possible applicability of this approach to commercially interesting microalgae/cyanobacteria culture systems.

Bioreactors↗
PubMed2004

Physical and hydrodynamic properties of flocs produced during biological hydrogen production.

Dense flocs readily form in continuous culture bioreactors used for hydrogen production, but the fractal and hydrodynamic properties of these flocs have not been previously analyzed. We therefore examined the size distribution, fractal dimension, and hydrodynamic properties of flocs formed in a continuous flow, well-mixed reactor treating synthetic wastewater at a fixed condition of a 4.5 h hydraulic detention time (23 degrees C, pH 5.5). The reactor was operated for a total of 3 months at three different organic loading rates (27, 53, and 80 g-COD/L-d) with influent glucose concentrations of 5, 10, and 15 g-COD/L. At all three loading rates the removal of glucose was nearly complete (98.6-99.4%) and biomass was produced in proportion to the organic loading rate (0.86 +/- 0.11, 2.40 +/- 0.26, and 4.59 +/- 1.55 g/L of MLVSS in the reactor). Overall conversion efficiencies of glucose to hydrogen, evaluated on the basis of a maximum of 4 mol-H2/mol-glucose, increased with organic loading rates in the order 17.7%, 23.1%, and 25.6%. The gas contained 56.1 +/- 4.9% hydrogen, with the balance as carbon dioxide. No methane gas was detected. Under these conditions, flocs were produced with mean sizes that increased with organic loading, in the order 0.12 cm (5 g-COD/L), 0.35 cm (10 g-COD/L), and 0.58 cm (15 g-COD/L). As the average floc size increased, the flocs became on average denser and less fractal, with fractal dimensions increasing from 2.11 +/- 0.17 to 2.48 +/- 0.13. Floc porosities ranged from 0.75-0.96, and resulted in aggregate densities that allowed little intra-aggregate flow through the floc. As a result, average settling velocities were not appreciably larger than those predicted by Stokes' law for spherical, impermeable flocs. Our results demonstrate that dense, relatively impermeable flocs are produced in biohydrogen reactors that have settling properties in reasonable agreement with Stokes' law.

Bacteria, Anaerobic↗
PubMed2005

Relationships between hydrodynamics and rheology of flocculating yeast suspensions in a high-cell-density airlift bioreactor.

In this article a hydrodynamic and rheological analysis of a continuous airlift bioreactor with high-cell-density system is presented. A highly flocculating recombinant strain of Sacharomyces cerevisiae containing genes for lactose transport (lactose permease) and hydrolysis (beta-galactosidase) was exploited to ferment lactose from cheese whey to ethanol. The magnetic particle-tracer method was used to assess the effect of operational conditions (air-flow rate, biomass concentration) on hydrodynamic behavior of an airlift bioreactor during the fermentation process. Measurements of liquid circulation velocity showed the existence of a critical value of biomass concentration at which a dramatic deceleration of net liquid flow appeared with increasing biomass quantity. Rheological analysis revealed exponential increase of viscosity of the yeast floc suspension at the same biomass concentration of about 73 g/dm3 corresponding to 42.8% v/v of solid fraction. These facts have a particular importance for the successful processing of a high-cell-density airlift bioreactor as only a circulated flow regime will be favorable to keep the solid particles in suspension state and evenly distributed throughout the bioreactor.

Bioreactors↗
PubMed2005

Hydrodynamics and mass transfer coefficient in activated sludge aerated stirred column reactor: experimental analysis and modeling.

The aerated stirred reactor (ASR) has been widely used in biochemical and wastewater treatment processes. The information describing how the activated sludge properties and operation conditions affect the hydrodynamics and mass transfer coefficient is missing in the literature. The aim of this study was to investigate the influence of flow regime, superficial gas velocity (U(G)), power consumption unit (P/V(L)), sludge loading, and apparent viscosity (mu(ap)) of activated sludge fluid on the mixing time (t(m)), gas hold-up (epsilon), and volumetric mass transfer coefficient (k(L)a) in an activated sludge aerated stirred column reactor (ASCR). The activated sludge fluid performed a non-Newtonian rheological behavior. The sludge loading significantly affected the fluid hydrodynamics and mass transfer. With an increase in the U(G) and P/V(L), the epsilon and k(L)a increased, and the t(m), decreased. The epsilon, k(L)a, and t(m), were influenced dramatically as the flow regime changed from homogeneous to heterogeneous patterns. The proposed mathematical models predicted the experimental results well under experimental conditions, indicating that the U(G), P/V(L), and mu(ap) had significant impact on the t(m), epsilon, and k(L)a. These models were able to give the t(m), epsilon, and k(L)a values with an error around +/-8%, and always less than +/-10%.

Bioreactors↗
PubMed2007

Characterization of the localized hydrodynamic shear forces and dissolved oxygen distribution in sparged bioreactors.

Detailed, high-resolution numerical simulations of the bubbly flows, used for oxygen delivery and mixing in mammalian cell suspensions, have been performed. The hydrodynamics, shear and normal forces, mass transfer and mass transport from and around individual bubbles and bubble clusters were resolved for different operating conditions, that is, Weber, Morton, and Schmidt numbers. Suspended animal (e.g., mammalian, insect) cells are known to be susceptible to damage potentially leading to cell death, caused by hydrodynamic stresses and oxygen deprivation. Better knowledge of the magnitude of the shear forces and the extent of mixing of the dissolved oxygen in sparged bioreactors can have a significant impact on their future design and optimization. Therefore, the computed liquid-phase velocity fields were used to calculate and compare the local shear in different types of single bubble wakes and in bubble clusters. Oxygen mass transfer and dissolved oxygen transport were resolved to examine oxygen supply to the cells in the different types of flows.

Animals↗
PubMed2006

Hydrodynamic flow and electroosmotic flow in zirconia-packed capillaries.

Fused-silica capillaries were packed with Zirchrom-PBD stationary phase for application in CEC, nanoLC and pseudoelectrochromatography (PEC). Acido-basic properties of zirconia can be used to control the EOF even if the zirconia particles were coated by polybutadiene. As for native zirconia, the EOF is pH-dependent and the pI is close to pH 5. The mixed-mode pressure-voltage technique induced a modulation of the mobile-phase velocity as well as an electrophoretic migration of the solutes in order to improve the resolution of the separation. A significant increase of the flow appeared when both hydrodynamic and EOFs were in the same direction. But an important reduction of the electroosmotic velocity was observed when the hydrodynamic flow and EOF were opposed in Zirchrom-PBD columns. This behaviour has been observed at high or low pH on several columns. Separations of neutral and charged compounds have been performed with these columns in PEC mode.

Chromatography↗
PubMed1993

Effect of polymer additives on hydrodynamics and oxygen transfer in a bubble column bioreactor.

The influence of polymer additives (polyethylene oxide and polyacrylamide) on the hydrodynamics and oxygen transfer in a bubble column bioreactor was examined. The addition of small amounts of these polymers has been known to cause significant drag reduction in turbulent flow circumstances. The gas hold-up was slightly decreased and the liquid-phase mixing was somewhat enhanced due to the addition of the polymers. The addition of polymer additives brought about a reduction of the volumetric oxygen transfer coefficient by about 40%. In dilute polymer solutions, large bubbles formed by bubble coalescence moved with high rise velocities in the presence of many small bubbles and the bubble size distributions were less uniform compared with those in water. The complicated changes in bubble hydrodynamic characteristics were examined to give possible explanations for oxygen transfer reduction.

Acrylic Resins↗
PubMed2003

Long-term control of food intake and body weight by hydrodynamics-based delivery of plasmid DNA encoding leptin or CNTF.

BACKGROUND: Obesity contributes to many common diseases, including cardiovascular and metabolic disorders such as diabetes, hypertension, and stroke. Leptin and ciliary neurotrophic factor (CNTF), two members of the cytokine family, play important roles in controlling food intake and body weight in rodents. Here, we used the hydrodynamics-based gene delivery technique to introduce leptin and CNTF expression plasmids, pCAGGS-leptin and pCAGGS-CNTF, into mice and to assess whether they could induce high expression of leptin or CNTF and reduce food intake and body weight in the mice. METHODS: Plasmid DNA (50 microg) in lactated Ringer's solution (0.1 ml/g body weight) was rapidly injected into the tail vein of 4-week-old male MCH-ICR mice. RESULTS: After a single injection, serum leptin peaked (at 32.0 +/- 3.1 ng/ml) 2 days after the injection, and serum CNTF peaked (at 22.0 +/- 0.8 microg/ml) 1 day after the injection. The high expression of either leptin or CNTF was sustained and dramatically reduced food intake (CNTF and leptin group vs. control group; 2.3 +/- 0.5 and 3.1 +/- 0.5 g/day vs. 4.8 +/- 0.6 g/day; p < 0.001) and body weight (3 weeks after the injection; CNTF and leptin group vs. control group; -19.5% and +3.3% vs. +33.3-47.5%; p < 0.001) in the mice, suggesting potent in vivo activities for these exogenously expressed proteins. CONCLUSIONS: These results suggest that hydrodynamics-based gene delivery could have broad applications in the study of appetite regulation and metabolism.

Animals↗
PubMed2006

Stimulatory effect of polyethylene glycol (PEG) on gene expression in mouse liver following hydrodynamics-based transfection.

BACKGROUND: Rapid intravenous injection of a large volume of plasmid DNA (pDNA), i.e. a transfection procedure based on hydrodynamics, is known to be an efficient and liver-specific method of in vivo gene delivery. However, the gene expression is transient. METHODS: We investigated the effect of addition of polyethylene glycol (PEG) to a solution of naked pDNA (luciferase) on the expression of the gene in mouse liver following transfection by the hydrodynamics-based technique. In addition, the mechanism leading to the enhancement of the gene expression was studied. RESULTS: The addition of 1% (w/v) PEG2000 to the pDNA solution enhanced the resulting gene expression in the liver. Increasing the PEG2000 concentration to more than 1 and up to 10% (w/v) rather diminished the gene expression level. By contrast, increasing the molecular weight of PEG to over 2000 up to 10 000 did not affect the level of gene expression. Histopathological and serum-chemistry examinations indicated that hydrostatic or osmotic pressure increased tissue and hepatocellular damage in a PEG-concentration-dependent manner, and resulted in a decrease in gene expression. Quantitative evaluation showed that the enhanced gene expression resulted from stabilization of the pDNA introduced into the hepatocytes and an enhancement of the transport of intact pDNA to the nucleus. CONCLUSIONS: For most gene therapy applications and gene function studies, sustained expression of the introduced gene(s) is necessary. This simple method to achieve enhanced gene expression in liver may have a great potential for a wide variety of laboratory studies in molecular and cellular biology as well as possibly for future clinical applications in humans.

Animals↗
PubMed2006

Mechanism of plasmid delivery by hydrodynamic tail vein injection. II. Morphological studies.

BACKGROUND: The efficient delivery of plasmid DNA (pDNA) to hepatocytes by a hydrodynamic tail vein (HTV) procedure has greatly popularized the use of naked nucleic acids. The hydrodynamic process renders onto the tissue increased physical forces in terms of increased pressures and shear forces that could lead to transient or permanent membrane damage. It can also trigger a series of cellular events to seal or reorganize the stretched membrane. Our goal was to study the uptake mechanism by following the morphological changes in the liver and correlate these with the fate of the injected plasmid DNA. METHODS: We utilized both light microscopic (LM) and electron microscopic (EM) techniques to determine the effect of the HTV procedure on hepatocytes and non-parenchymal cells at various times after injection. The LM studies used paraffin-embedded livers with hematoxylin and eosin (H&E) staining. The immune-EM studies used antibodies labeled with sub-nanometer gold particles followed by silver enhancement to identify the location of injected pDNA at the subcellular level. The level of overall damage to liver cells was estimated based on alanine aminotransferase (ALT) release and clearance. RESULTS: Both the LM and EM results showed the appearance of large vesicles in hepatocytes as early as 5 min post-injection. The number of vesicles decreased by 20-60 min. Plasmid DNA molecules often appeared to be associated with or inside such vesicles. DNA could also be detected in the space of Disse, in the cytoplasm and in nuclei. Non-parenchymal cells also contained DNA, but HTV-induced vesicles could not be observed in them. CONCLUSIONS: Our studies suggest an alternative or additional pathway for naked DNA into hepatocytes besides direct entry via membrane pores. It may be difficult to prove which of these pathways lead to gene expression, but the membrane pore hypothesis alone appears insufficient to explain why expression happens preferentially in hepatocytes. Further study is needed to delineate the importance of each of these putative pathways and their interrelationship in enabling oligonucleotide (siRNA) activity and pDNA expression.

Alanine Transaminase↗
PubMed1990

Resistance of a defect of the supraspinatus tendon to intraarticular hydrodynamic pressure: an experimental study on rabbits.

The healing of a standardized defect of the supraspinatus tendon in a time-related series on rabbits was monitored with arthrography and simultaneous determination of the intra-articular hydrodynamic pressure of the glenohumeral joint. All normal glenohumeral joints produced a biphasic pressure versus volume curve. Rupture of a normal glenohumeral joint occurred at a pressure level of 140-170 mm Hg and was located in the area around the biceps tendon sheath. In joints with a defect of the supraspinatus tendon, leakage of the contrast medium was evident up to the sixth week, at an intra-articular pressure varying from 40 to 100 mm Hg. After week 6, no leakage of the cuff was seen during the determination of the intraarticular pressure. This was in accordance with the histological findings: the defect was covered with solid scar tissue from the ninth week onward. Resistance to hydrodynamic intraarticular pressure proved a reliable method of determining the strength of the healing of the supraspinal defects.

Animals↗
PubMed1976

Effects of various hydrodynamic conditions on dissolution rate determinations.

An automated potentiometric procedure was used in dissolution rate studies to determine the effects of various hydrodynamic conditions on dissolution rate determinations. Changes in the hydrodynamics of the system resulted from using various sizes and shapes of dissolution vessels. Dissolution rate constants for benzoic acid prills in distilled water at pH-stat 6.2 were used as a measure of the agitation intensities present in the different shaped vessels. Great variations in the dissolution rates occurred in vessels with the same diameter and stirrer blade position when the shapes of the bottom of the vessel were varied. A similar order of dissolution rates was obtained at 100 and 150 rpm for the individual vessels at various propeller heights. The order differed from one vessel to another, depending on the shape of the bottom (concave, convex, or flat) of the vessel. In some cases, a change in the type of bottom resulted in the opposite order of rates for vessels with the same diameter.

Benzoates↗
PubMed1999

Kinetic analysis of analyte binding by optical biosensors: hydrodynamic penetration of the analyte flow into the polymer matrix reduces the influence of mass transport.

I examined the penetration of the hydrodynamic flow into a polymer matrix immobilized by grafting to a surface, such as used in optical biosensors designed to measure binding reactions in real time. I show that the flow penetrates with an appreciable velocity into a region located at the tip of such a polymer brush, corresponding to about 10 to 15% of the total mass of the grafted polymer. Furthermore, under the conditions recommended for kinetic measurements, the concentrations of both polymer and immobilized ligands are low in these regions of the matrix, where crowding effects are negligible. Under such conditions, the hydrodynamic flow penetrating into the dextran matrix flow will bring the analytes close to their targets, thus considerably reducing transport problems.

Biosensing Techniques↗