Biomedical subjects

L C Davis

Publications and source records attributed to L C Davis.

At least 19 recordsLinked to original sources

PubMed2004

Effect of adaptive cruise control systems on traffic flow.

The flow of traffic composed of vehicles that are equipped with adaptive cruise control (ACC) is studied using simulations. The ACC vehicles are modeled by a linear dynamical equation that has string stability. In platoons of all ACC vehicles, perturbations due to changes in the lead vehicle's velocity do not cause jams. Simulations of merging flows near an onramp show that if the total incoming rate does not exceed the capacity of the single outgoing lane, free flow is maintained. With larger incoming flows, a state closely related to the synchronized flow phase found in manually driven vehicular traffic has been observed. This state, however, should not be considered congested because the flow is maximal for the density. Traffic composed of random sequences of ACC vehicles and manual vehicles has also been studied. At high speeds (approximately 30 m/s ) jamming occurs for concentrations of ACC vehicles of 10% or less. At 20% no jams are formed. The formation of jams is sensitive to the sequence of vehicles (ACC or manual). At lower speeds (approximately 15 m/s ), no critical concentration for complete jam suppression is found. Rather, the average velocity in the pseudojam region increases with increasing ACC concentration. Mixing 50% ACC vehicles randomly with manually driven vehicles on the primary lane in onramp simulations shows only modestly reduced travel times and larger flow rates.

Journal Article↗

PubMed2004

Multilane simulations of traffic phases.

The optimal velocity model, as modified by the author, is used in simulations of traffic on a dual-lane highway and a single-lane highway with an on-ramp. The equilibrium solutions of the modified model cover a two-dimensional region of flow-density space beneath the fundamental-diagram curve, rather than just lying on the curve as in the original model. Thus it satisfies a requirement of the three-phase model of Kerner [Phys. Rev. Lett. 81, 3797 (2002)]. Synchronization of velocity across dual lanes due to frequent lane changes is observed in free flow. True synchronized flow, as determined by the region of density-flow space it occupies, is obtained in on-ramp simulations with typical driver reaction times. A gradual change to the formation of a jam is observed for increasing delay times.

Journal Article↗

PubMed2003

Technical note: fate and transport of jet fuel (JP-8) in soils with selected plants.

Remediation of soil and groundwater contaminated by leaking fuel storage tanks may be assisted by plants, although plant effects on abiotic and biotic removal processes remain unclear. The objectives of this study were to investigate abiotic and biotic removal of JP-8, a kerosene-based jet fuel, in soils with plants, and to determine the effects of plant-induced water movement. Loss of JP-8 in a dry-soil, control column was 25% after 5 months, primarily due to volatilization and gas-phase diffusion. By comparison, managed treatments with simulated surface spills averaged 86% mass reduction at 5 months, indicating an important contribution of biodegradation. Overall JP-8 mass reduction was similar in surface and subsurface-irrigated systems, indicating water content, not mode of water application, influences bioremediation in near-surface systems. The JP-8 concentration reductions in soil columns contaminated above a simulated watertable were 36% after 3 months and 50% after 12 months for vegetated columns compared to 26% and 34% in unplanted columns. Downward movement of JP-8 in unplanted columns was double that in planted columns. Near the groundwater table, JP-8 persists longer than near the soil surface. Plants promote upward movement of water and help draw spilled JP-8 to aerobic near-surface soil.

Armoracia↗

PubMed2003

Modeling jet fuel (JP-8) fate and transport in soils with plants.

Vegetation is often used to clean up soils and groundwater contaminated with organic contaminants. Plant-induced upward water movement may draw organic contaminants spilled near the watertable to the more aerated near-surface soil. The objective of this study was to develop and verify a 1-D model of fate and transport of JP-8, a kerosene-based jet fuel, in soil. The modeling approach considered the advective and dispersive transport of jet fuels dissolved in groundwater, which may undergo simple first-order decay or linear adsorption. The governing partial differential advection dispersion equation was solved in one dimension. Data from an experiment of fate and transport of JP-8 with plant-induced upward water movement were used to verify the model. Simulated results with different scenarios described the experimental results well for different depths above the contaminated zone in both vegetated and unvegetated columns. Advection was the dominant mechanism near the contaminated zone and advection with retardation and decay was used to fit the data away from the contaminated zone. Results indicated that the soil water movement impacted the transport and concentration of JP-8 in the soil columns. This model can be used to simulate the fate of JP-8 associated with phytoremediation and evapotranspiration.

Humans↗

PubMed2002

Comment on "Analysis of optimal velocity model with explicit delay".

The effect of including an explicit delay time (due to driver reaction) on the optimal velocity model is studied. For a platoon of vehicles to avoid collisions, many-vehicle simulations demonstrate that delay times must be well below the critical delay time determined by a linear analysis for the response of a single vehicle. Safe platoons require rather small delay times, substantially smaller than typical reaction times of drivers. The present results do not support the conclusion of Bando et al. [M. Bando, K. Hasebe, K. Nakanishi, and A. Nakayama, Phys. Rev. E 58, 5429 (1998)] that explicit delay plays no essential role.

Journal Article↗

PubMed2001

Transport of methyl tert-butyl ether through alfalfa plants.

Concentrations measured in alfalfa plant stem segments indicated that plants grown in methyl tert-butyl ether (MTBE)-contaminated soil took up the chemical through their roots. Assuming a cylindrical shape for the plant stem, a mathematical model was developed to describe the transport of MTBE through the stems. Simulation results from uniform and nonuniform initial concentration distributions across the stem radius were compared with steady-state experimental data. With known values of plant stem radius, water usage, water content, and the distance over which the concentration decreased by 50%, the diffusion coefficient of MTBE radial transport across the plant stem was estimated with 95% confidence to be in the range of 8.43-16.2 x 10(-8) cm2/s with a mean of 1.23 x 10(-7) cm2/s. When the diffusion coefficient was calculated based on transient experimental data, the values with 95% confidence interval ranged from 4.14 x 10(-7) to 8.00 x 10(-7) cm2/s with a mean value of 6.07 x 10(-7) cm2/s. The difference between these two results can be reduced by more accurate estimation of the water flow velocity through plant stems. The model is applicable to other species including sunflowers and poplars upon substitution of appropriate parameters.

Carcinogens↗

PubMed2000

Using electrophoresis to observe the interaction of nitrogenase with ions.

The two protein components of nitrogenase from Klebsiella pneumoniae were shown to interact with metal ions and ADP, altering their electrophoretic mobility in polyacrylamide gel electrophoresis. Both Mg+2 and Mn+2 caused reduced mobility of Fe protein relative to other proteins. The effect was about 50% complete at concentrations around 0.2 mM. Other ions including Fe+2, Ni+2 and Co+2 had no observable effect at levels up to 1 _mM. Both Cd+2 and Zn+2 appeared to interact with the protein; Cd+2 at 0.5 mM dramatically destabilized the protein. The effects of more than a dozen different mutations of the Fe protein on Mg+2 interaction were examined. All mutated proteins appeared to interact with Mg+2 similarly to wild-type. Using relative mobility differences of charge-changed mutants it was estimated that two to three Mg+2 interact with each Fe protein monomer. The MoFe protein also showed interaction with metal ions but the alteration of mobility was much smaller than for the Fe protein because it is larger and less acidic, so that it runs much more slowly than the Fe protein in standard gels. The interaction of ADP with Fe protein was examined in the presence of Mg+2. Increasing ADP partially reversed the mobility decrease observed on Mg+2 binding, and produced a more diffuse protein band indicative of a reaction zone of interconverting conformers. No alteration of MoFe protein mobility was observed with ADP added during electrophoresis.

Adenosine Diphosphate↗

PubMed2000

Interaction with magnesium and ADP stabilizes both components of nitrogenase from Klebsiella pneumoniae against urea denaturation.

The nitrogenase enzyme of Klebsiella pneumoniae consists of two separable proteins, each with multiple subunits and one or more oxygen sensitive metallocenters. The wild-type nitrogenase proteins are stable to electrophoresis in high concentrations of urea under anaerobic conditions. Addition of Mg+2 and ADP greatly increases the stability of the smaller Fe protein (from <4 to >6 M for full unfolding), an effect directly analogous to stabilization in p21ras induced by Mg+2 and GDP. Stabilization by Mg+2 is slight for the holo MoFe protein (from approximately 1.5 to approximately 2.4 M) but more dramatic for the apo protein form of the MoFe protein accumulated by certain Fe protein (nifH gene) mutants. The potent product inhibitor of nitrogenase function, MgADP, increases stability of the MoFe protein more than Mg+2 alone, to approximately 3.6 M, showing that nucleotides interact with the MoFe protein. Mutations of the nifM gene result in slower accumulation of less stable Fe protein, indicating that NifM is involved in correct folding of the Fe protein. Mutationally altered proteins are often difficult to purify for study because of their inherent instability, low expression level, or oxygen lability. Crude extracts of 11 different mutants of Fe protein (nifH gene) were examined by transverse urea gradient gels to rapidly screen for stabilizing interactions in the presence or absence of substrate or inhibitor analogs. Amino acid alterations D44N and R188C, at the interface of the dimer, in the vicinity of the nucleotide binding site(s), have significantly lower stability than the wild-type enzyme in the absence of Mg+2 but comparable stability in its presence, showing the importance of Mg+2 in the subunit interactions. Mutations N163S and E266K, in which residues normally involved in hydrogen bonding far from the active site were altered, are more labile than the wild-type even with Mg+2 added. Seven other mutants, though nonfunctional, did not appear altered in stability compared to the wild-type.

Adenosine Diphosphate↗

PubMed1993

Sideport incision paracentesis versus antiglaucoma medication to control postoperative pressure rises after intraocular lens surgery.

Twenty-eight patients who had an intraocular pressure greater than 30 mm Hg within 24 hours after cataract surgery were randomly assigned to be treated with medication or by paracentesis through a sideport incision. Paracentesis provided an immediate reduction in intraocular pressure, but within one hour pressures rebounded. Within two to three hours after treatment, the medication group had significantly greater mean reductions in intraocular pressure than the paracentesis group.

Acetazolamide↗

PubMed1992

Systematics and body size: implications for feeding adaptations in New World monkeys.

The relationship between body size and feeding ecology is well established for primates. It is argued that the evolutionary history of modern New World monkeys and, in particular, the path to attainment of current body size is significant in understanding the similarities and differences between dietary strategies and other ecological parameters of similar-sized monkeys. Current interpretations of New World monkey evolutionary relationships are reviewed. Based on a synthesis of available body weights and the assumption that the earliest New World monkeys weighed close to 1 kg, similar to modern Aotus and Callicebus, predicted patterns of body size change in each lineage are given. Restrictions on directions of body size change in primates are discussed, and it is shown that "Stanley's Rule" offers a good explanation for differing body size ranges in New and Old World anthropoids. Predicted ecological correlates to body size drawn from the mammalian literature are offered and tested using data on New World monkeys, which show some concurrence and several interesting departures from predicted patterns. Sexual dimorphism in body weight of New World monkey species is reviewed, based on the new summary of body weight data given.

Adaptation, Physiological↗

PubMed1990

Two-step isolation of bacterial ribonucleic acid without using a chaotropic agent or cesium chloride centrifugation.

A simple RNA isolation method was developed to purify bacterial RNAs from a large number of samples simultaneously in an hour. The method is based on boiling the cells in the presence of Triton X-100 and lysozyme, and then preferential RNA precipitation with ammonium acetate. There is no CsCl centrifugation required. For the nitrogen-fixing bacterium Klebsiella pneumoniae, the depression condition can be maintained during the cell-harvesting process. The intact isolated RNAs appeared to be free of protein, with a yield of 100 micrograms RNA from a 4-ml cell culture of 100 Klett units (10(9) cells/ml). Any DNA present was in a form that did not react with a nifH probe following Northern blotting to nitrocellulose (i.e., was not single-stranded).

Acetates↗

PubMed1990

Kinetics of protease hydrolysis of extended peptide substrates: measurement by flow-injection analysis.

A flow-injection analysis (FIA) system was developed to study the enzyme-catalyzed hydrolysis of synthetic peptides, each of which contained one scissile bond. The concentrations of alpha-amino groups in reactions mixtures were determined by FIA with o-phthalaldehyde as a fluorescence reagent. The method allows a rapid, precise, and sensitive determination of kinetic constants for proteases acting on extended peptide substrates.

Chromatography, High Pressure Liquid↗

PubMed1989

Substitution of histidine for arginine-101 of dinitrogenase reductase disrupts electron transfer to dinitrogenase.

Dinitrogenase reductase from Klebsiella pneumoniae strain UN1041 has a histidine residue substituted for arginine at position 101. The mutant dinitrogenase reductase was purified and characterized in order to determine the importance of arginine-101 in the interaction between dinitrogenase and dinitrogenase reductase during electron transfer. Purified dinitrogenase reductase from UN1041 is a dimer of 67 kDa, contains a functional 4Fe-4S cluster, undergoes a MgATP-dependent conformational change, and is competent for ATP hydrolysis uncoupled from substrate reduction in the presence of dinitrogenase. However, the mutant protein is unable to support the reduction of protons or acetylene by dinitrogenase. A 100-fold molar excess of Kp2 from UN1041 does not inhibit electron transfer from wild-type dinitrogenase reductase to dinitrogenase. It is concluded that the interaction of dinitrogenase reductase with dinitrogenase during reductant-independent ATP hydrolysis is different than the interaction between the two proteins during electron transfer; the substitution of histidine for arginine at position 101 disrupts only the latter interaction. The same conclusions are reached using wild-type dinitrogenase reductase which has been ADP-ribosylated at arginine-101.

Adenosine Triphosphate↗

PubMed1989

Estimation of nitrogenase activity in the presence of ethylene biosynthesis by use of deuterated acetylene as a substrate.

Nitrogenase reduces deuterated acetylene primarily to cis dideuterated ethylene. This can be distinguished from undeuterated ethylene by the use of Fourier transform infrared spectroscopy. Characteristic bands in the region from 800 to 3,500 cm-1 can be used to identify and quantitate levels of these products. This technique is applicable to field studies of nitrogen fixation where ethylene biosynthesis by plants or bacteria is occurring. We have verified the reaction stoichiometry by using Klebsiella pneumoniae and Bradyrhizobium japonicum in soybeans. The most useful bands for quantitation of substrate purity and product distribution are as follows: acetylene-d0, 3,374 cm-1; acetylene-d1, 2,584 cm-1; acetylene-d2, 2,439 cm-1; cis-ethylene-d2, 843 cm-1; trans-ethylene-d2, 988 cm-1; ethylene-d1, 943 cm-1; ethylene-d0, 949 cm-1. (The various deuterated ethylenes and acetylenes are designated by a lowercase d and subscript to indicate the number, but not the position, of deuterium atoms in the molecule.) Mass spectrometry coupled to a gas chromatograph system has been used to assist in quantitation of the substrate and product distributions. Significant amounts of trans-ethylene-d2 were produced by both wild-type and nifV mutant K. pneumoniae. Less of this product was observed with the soybean system.

Acetylene↗

PubMed1988

Characterization of nifH mutations of Klebsiella pneumoniae.

Nucleotide changes in the nifH gene of Klebsiella pneumoniae were identified by DNA cloning and sequencing of six selected mutant strains. The strains were UN60, C-640-GC----TGC; UN116, C-67-TC----TTC; UN117, G-688-AG----AAG; UN1041, CG-302-C----CAC; UN1678, GC-713-C----GTC; and UN1795, G-439-AG----AAG. Their corresponding amino acid substitutions were UN60, Arg-214----Cys; UN116, Leu-23----Phe; UN117, Glu-230----Lys; UN1041, Arg-101----His; UN1678, Ala-238----Val; and UN1795, Glu-147----Lys. Results from Western and Northern blots of the mutant strains showed significant reductions in both steady-state levels of the accumulated Fe protein and nifH mRNA during derepression in the presence of serine. The relative specific activities of the nitrogenases in strains UN60, UN1041, and UN1795 were less than 2% of the wild type, whereas those in UN116, UN117, and UN1678 were between 28 and 40% of the wild type during enhanced derepression with serine. The residues of Arg-101 (UN1041), Glu-147 (UN1795), and Arg-214 (UN60) were invariant in sequences of a dozen diazotrophs that have been examined thus far. In UN1041, in which Arg-101 of the Fe protein was replaced by His, the Fe protein had a larger apparent molecular weight than that of the other strains on sodium dodecyl sulfate-gel electrophoresis, as detected with rabbit antiserum raised against the C-terminal peptide of the wild-type Fe protein. The reduced levels of nifH mRNA in point mutant strains suggests that nifH (the gene or gene product) may be involved in self-regulation. mRNA transcripts of different sizes were detected when a nifH-specific probe, CCKp2003, was used in the Northern blot hybridization.

DNA, Bacterial↗

PubMed1987

Measurement of protein using flow injection analysis with bicinchoninic acid.

We have used the bicinchoninic acid reagent developed by Pierce Chemical Co. to measure proteins in a simple flow injection analyzer. The sensitivity is comparable to that of the Lowry method and no pipetting of reagents is needed. Results are obtained in less than 1 min and samples may be run at a rate of 60/h. The response is linear over a range of protein concentration (0-10 micrograms) and sample size (5-20 microliters) convenient for most analytical requirements. A peristaltic pump, a controlled-temperature water bath, and a spectrophotometer with flow cuvette are the only special apparatus required.

Proteins↗

PubMed1986

C-terminal peptides of rhodopsin. Determination of the optimum sequence for recognition of retinal transducin.

In vertebrate retinal rod outer segments, transducin, a guanine-nucleotide-binding protein, mediates signal coupling between rhodopsin and cyclic GMP phosphodiesterase. Whereas the T alpha subunit (39 kDa) of transducin binds guanine nucleotides and is the activator of the phosphodiesterase, the T beta gamma subunits (35 and 10 kDa) may function to physically link T alpha with photolysed rhodopsin. We have previously reported that a site of binding of transducin is on the C-terminus of bovine rhodopsin. By using competition with synthetic peptides, the recognition region was localized to bovine opsin amino acid residues 317-339. Further studies are detailed which determine the boundaries of this binding site on rhodopsin, as well as some of the critical amino acids needed for transducin binding. These results suggest that the serine and threonine residues in the rhodopsin C-terminal peptides Rhod-1 and Rhod-3 are critical for reconstitution of transducin GTPase activity.

Amino Acid Sequence↗

PubMed1986

Rhizobium trifolii 0403 Is Capable of Growth in the Absence of Combined Nitrogen.

Rhizobium trifolii 0403 was treated with 16.6 mM succinate and other nutrients and thereby induced to grow in nitrogen-free medium. The organism grew microaerophilically on either semisolid or liquid medium, fixing atmospheric nitrogen to meet metabolic needs. Nitrogen fixation was measured via N incorporation (18% N enrichment in 1.5 doublings) and acetylene reduction. Nitrogen-fixing cells had a K(m) for acetylene of 0.07 atm (ca. 7.09 kPa), required about 3% oxygen for optimum growth in liquid medium, and showed a maximal specific activity of 5 nmol of acetylene reduced per min per mg of protein at 0.04 atm (ca. 4.05 kPa) of acetylene. The doubling time on N-free liquid medium ranged from 1 to 5 days, depending on oxygen tension, with an optimum temperature for growth of about 30 degrees C. Nodulation of white clover by the cultures showing in vitro nitrogenase activity indicates that at least part of the population maintained identity with wild-type strain 0403.

Journal Article↗