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PubMed1998

Measured lung dose correction factors for 50 MV photons.

Some clinically relevant measurements of lung tissue/water equivalent interfaces have been performed for a 50 MV therapeutic x-ray beam. The purpose was to investigate the severity of dose perturbation effects in lung tissue and adjacent tissues using an energy well above the common clinical practice in thoracic irradiations. The phantoms were constructed of solid water, PMMA and white polystyrene as soft tissue (water) equivalents, and cork was used as the lung tissue equivalent. Measurements were performed using radiographic film and a cylindrical ionization chamber. The results show that the degradation of the 20/80% beam penumbra in the lung region is severe, up to 2.5 times the penumbra in water for a 10 cm thick lung with a density of 0.30 x 10(3) kg m(-3). The lack of electronic equilibrium in the low-density region can cause underdosage at the lung/tumour interface of up to 30% of maximum target dose, and the build-up depth to 95% of target dose in unit density tissue behind the lung may be as large as 22 mm. It is also shown that these figures strongly depend on patient anatomy and beam size and why a careful calculation of the individual dose distribution is needed for optimal choice of photon beam energy in thoracic treatments.

Biophysical Phenomena↗
PubMed1997

Factors influencing the extent and selectivity of alkylation within triplexes by reactive G/A motif oligonucleotides.

G/A motif triplex-forming oligonucleotides (TFOs) complementary to a 21 base pair homopurine/homopyrimidine run were conjugated at one or both ends to chlorambucil. These TFOs were incubated with several synthetic duplexes containing the targeted homopurine run flanked by different sequences. The extent of mono and interstrand cross-linking was compared with the level of binding at equilibrium. Covalent modification took place within a triple-stranded complex and usually occurred at guanine residues in the flanking double-stranded DNA. The efficiency of alkylation was dependent upon the sequence of the flanking duplex, the solution conditions, and the rate of triplex formation relative to the rate of chlorambucil reaction. Self-association of the TFOs as parallel duplexes was demonstrated and this did not interfere with triple strand formation. With an optimal target, cross-linking of the triplex was very efficient when incubation was carried in a physiological buffer supplemented with the triplex selective intercalator coralyne.

Adenosine↗
PubMed1982

Aldehyde reductase from Crithidia fasciculata: purification and characterization.

Crithidia fasciculata, a pterin requiring protozoa, contained a NADPH-dependent dihydro-6-formylpterin reducing enzyme. The aldehyde reductase was purified and characterized. This enzyme was soluble and constitutive, and had the ability to catalyze the interconversion between aldehydes and alcohols. The optimal pH was 7.0 for the reductase activity and 9.0 for the dehydrogenase activity. The enzyme had a broad substrate specificity and reduced aromatic and aliphatic aldehydes such as dihydro-6-formylpterin, benzaldehyde, pyridine-3-aldehyde, butyraldehyde, DL-glyceraldehyde, and acetaldehyde. The enzyme was inhibited by sulfhydryl reagents and heavy metals, but not inhibited by chelating reagents. Its molecular weight was determined to be 66,000 and 72,000 by gel filtration and sedimentation equilibrium analysis, respectively. The value of 39,000 was obtained by sodium dodecyl sulfate gel electrophoresis indicating a dimeric structure. The aldehyde reductase of Crithidia may be classified as NADP+-dependent aryl-alcohol dehydrogenase [EC 1.1.1.91].

Alcohol Oxidoreductases↗
PubMed2005

Minimal work principle: proof and counter-examples.

The minimal work principle states that work done on a thermally isolated equilibrium system is minimal for adiabatically slow (reversible) realization of a given process. This principle, one of the formulations of the second law, is studied here for finite (possibly large) quantum systems interacting with macroscopic sources of work. It is shown to be valid as long as the adiabatic energy levels do not cross. If level crossing does occur, counter-examples are discussed, showing that the minimal work principle can be violated and that optimal processes are neither adiabatically slow nor reversible. The results are corroborated by an exactly solvable model.

Journal Article↗
PubMed1996

Load, length, and velocity of load-moving tibialis anterior muscle of the cat.

Three-dimensional relationships of load, length, and velocity of shortening of the tibialis anterior muscle in the cat were derived experimentally and fitted with an analytic model. Gravitational loads were applied to the isolated muscle, which arrived at an equilibrium with the passive forces before supramaximal tetanic stimulation was delivered to its nerve. Recordings of initial passive muscle length at equilibrium and length changes throughout the shortening phase up to the final length at active equilibrium were taken and numerically differentiated to obtain each load's instantaneous velocity. A three-dimensional surface was constructed by using instantaneous length and the corresponding velocity for each of several loads. Maximal velocity of shortening was shown to gradually decrease, occurring earlier in the shortening phase (at larger muscle lengths) as loads increased. Whereas load-velocity curves were hyperbolic for middle and short muscle lengths, they were nonmonotonic during shortening above the optimal length. The model was found to correlate well with the experimental data (R = 0.98) and allowed for prediction of both muscle performance boundaries and instantaneous shortening velocity for a given length across the physiological load spectrum, thus offering a realistic estimation of the contractile properties exhibited by the tibialis anterior muscle in functions similar to naturally occurring movements against gravitational loads, which are accelerated and decelerated during the movement.

Animals↗
PubMed2002

Utility and accuracy of template-directed dye-terminator incorporation with fluorescence-polarization detection for genotyping single nucleotide polymorphisms.

There are little independent data available about how well single nucleotide polymorphism (SNP) genotyping technologies perform in the typical molecular genetics laboratory. We evaluated the utility and accuracy of a widely used technology, template-directed dye-terminator incorporation with fluorescence-polarization detection (FP-TDI), in a sample of 177 SNPs selected solely on the basis of map location. Genotypes were generated without optimization using standard protocols. Overall, 81% of the SNPs we studied generated readable genotypes by FP-TDI. Thirty-two SNPs were genotyped in duplicate by PCR-RFLP orfluorescent dye-terminator sequencing. Out of a total of 631 duplicate genotypes, no true discrepancies were detected. The true error rate has a 95% chance of lying between 0 and 6 out of 1000 genotypes. We also tested for deviations from Hardy-Weinberg Equilibrium in 33 SNPs genotyped in 50 unrelated individuals, and no significant deviations were detected. Our FP-TDI data were readily adaptable to automated genotype calling using our own method of cluster analysis, which assigns a probability score to each genotype call. We conclude that FP-TDI is both efficient and accurate. The method can easily fill the needs of SNP genotyping projects at the scale typically used for regional or candidate-gene association studies.

Fluorescence Polarization↗
PubMed2001

Measurement of Henry's law constant for methyl tert-butyl ether using solid-phase microextraction.

Increasing groundwater contamination with methyl tert-butyl ether (MTBE) requires more efficient remediation technologies. Accurate measurement of MTBE's air-water partitioning coefficient (Henry's law constant, H) is important for the design and optimization of removal efficiency for many treatment systems as well as for predicting its fate and transport. Previously published data for MTBE appear to have some unusual nonlinearity at lower temperatures (15-30 degrees C), and a wide range of values exists for dimensionless H at 25 degrees C, from 0.0216 to 0.1226 in the published literature. We measured H for MTBE using headspace solid-phase microextraction (SPME) and a static method that considers equilibrium partitioning in a closed system, for temperatures between 15 and 4 degrees C. To validate our methods, we measured H for benzene, toluene, and trichloroethylene and compared our results to previously published values, with excellent agreement. The Arrhenius plot for MTBE indicates that ln(HMBTE) = 6.85 - 2,900 T(-1), with T in K. At 25 degrees C, HMBTE = 0.0555 +/- 0.0122.

Carcinogens↗
PubMed1987

Anesthesia for trauma.

Anesthesia of polytraumatized patients represents a considerable risk for them. The proper treatment of a polytraumatized patient comprises the rapid stabilisation of all his vital functions. At the same time, the attempt must be made to achieve a complete picture of all his injuries in order to be able to select a reliable and safe anesthetic procedure. Over and beyond this, a continuation of all intensive care measures, in particular the optimalization of blood volume, the maintenance of gas exchange, the support of the cardiac, and the balancing of the acid-base and electrolytes, is of the greatest importance for an effective treatment of the polytraumatized patient.

Acid-Base Equilibrium↗
PubMed1992

Fuzzy cluster analysis of molecular dynamics trajectories.

We propose fuzzy clustering as a method to analyze molecular dynamics (MD) trajectories, especially of proteins and polypeptides. A fuzzy cluster analysis locates classes of similar three-dimensional conformations explored during a molecular dynamics simulation. The method can be readily applied to results from both equilibrium and nonequilibrium simulations, with clustering on either global or local structural parameters. The potential of this technique is illustrated by results from fuzzy cluster analyses of trajectories from MD simulations of various fragments of human parathyroid hormone (PTH). For large molecules, it is more efficient to analyze the clustering of root-mean-square distances between conformations comprising the trajectory. We found that the results of the clustering analysis were unambiguous, in terms of the optimal number of clusters of conformations, for the majority of the trajectories examined. The conformation closest to the cluster center can be chosen as being representative of the class of structures making up the cluster, and can be further analyzed, for example, in terms of its secondary structure. The CPU time used by the cluster analysis was negligible compared to the MD simulation time.

Amino Acid Sequence↗
PubMed2002

A correlation for establishing solvolysis rates of aqueous Al(III) complexes: a possible strategy for colloids and nanoparticles.

We here examine whether rates of solvolysis for a range of aluminum complexes can be predicted semiempirically by correlating calculated values of Al-O bond lengths with rate coefficients. We focus on a series of mono- and bis-ligated aqueous aluminum monomers and three epsilon-Keggin-like aluminum polyoxocations, and we make no attempt to simulate transition states. The Al-O bond lengths were calculated by performing ab initio geometry optimizations using the polarizable-continuum model to estimate solvation effects. Both Hartree-Fock and density functional methods (B3LYP) were tested using several basis sets up to 6-31+G(d). We find a strong correlation between rate coefficients for mono-ligated aluminum monomers and bond lengths to hydration waters. We cannot extrapolate the correlation, however, to large epsilon-Keggin-like multimers or to bis-ligated complexes, which suggests that the activated equilibrium for exchange of a water molecule in these molecules is different than that in the simple monomers.

Journal Article↗
PubMed1993

Effect of CPT on the calf thymus Topoisomerase I-mediated DNA breakage-reunion reaction: optimal conditions for the formation and reversal of the CPT trapped Topoisomerase I cleavable complex.

The effects of CPT on the calf thymus Topoisomerase I-mediated DNA breakage-reunion reaction were studied at an enzyme concentration range proper for evidencing, at the same time, both DNA relaxation and DNA cleavage/religation. Some of the requirements and the optimal conditions for the formation and reversal of the CPT-trapped Topoisomerase I-DNA cleavable complex are also characterized. We conclude that: 1. Calf thymus (100 kDa) Topoisomerase I requires, for maximal DNA cleavage activity, specific and characteristic reaction conditions. 2. CPT does not affect these optimal conditions, but only stabilizes the normal enzyme-DNA intermediate. In this way, the drug lowers the religation process, becoming responsible for the relaxation inhibition. 3. The optimum of monovalent salt concentration for cleavable complex formation is found between 30 and 70 mM. These values are lower than those required for the relaxation activity optimum (75-125 mM NaCl). 4. The addition of 0.5 M monovalent salt causes reversal of the reaction, and shifts the equilibrium distribution between cleavable intermediate and closed relaxed DNA in the direction of DNA resealing. Therefore, it is suggested that salt affects the cleavage but not the religation reaction.

Animals↗
PubMed2004

Pattern of anterior cruciate ligament force in normal walking.

The goal of this study was to calculate and explain the pattern of anterior cruciate ligament (ACL) loading during normal level walking. Knee-ligament forces were obtained by a two-step procedure. First, a three-dimensional (3D) model of the whole body was used together with dynamic optimization theory to calculate body-segmental motions, ground reaction forces, and leg-muscle forces for one cycle of gait. Joint angles, ground reaction forces, and muscle forces obtained from the gait simulation were then input into a musculoskeletal model of the lower limb that incorporated a 3D model of the knee. The relative positions of the femur, tibia, and patella and the forces induced in the knee ligaments were found by solving a static equilibrium problem at each instant during the simulated gait cycle. The model simulation predicted that the ACL bears load throughout stance. Peak force in the ACL (303 N) occurred at the beginning of single-leg stance (i.e., contralateral toe off). The pattern of ACL force was explained by the shear forces acting at the knee. The balance of muscle forces, ground reaction forces, and joint contact forces applied to the leg determined the magnitude and direction of the total shear force acting at the knee. The ACL was loaded whenever the total shear force pointed anteriorly. In early stance, the anterior shear force from the patellar tendon dominated the total shear force applied to the leg, and so maximum force was transmitted to the ACL at this time. ACL force was small in late stance because the anterior shear forces supplied by the patellar tendon, gastrocnemius, and tibiofemoral contact were nearly balanced by the posterior component of the ground reaction.

Anterior Cruciate Ligament↗
PubMed2003

Modulation of lymphatic distribution of subcutaneously injected poloxamer 407-coated nanospheres: the effect of the ethylene oxide chain configuration.

Lymphatic distribution of interstitially injected poloxamer 407-coated nanospheres (45 nm in diameter) is controlled by surface configuration of the ethylene oxide (EO) segments of the adsorbed copolymer. At low poloxamer surface coverage, EO tails spread laterally on a nanosphere surface and assume a 'flat or mushroom-like' configuration. Such entities drain rapidly from the subcutaneous site of injection into the initial lymphatic, when compared to uncoated nanospheres, and subsequently are captured by scavengers of the regional lymph nodes. In vitro experiments have also confirmed that such entities are prone to phagocytosis. When the equilibrium poloxamer concentration is at 75 microg/ml or greater the EO chains become more closely packed and project outward from the nanosphere surface. These surface-engineered nanospheres drain faster than those with EO chains in mushroom configurations into the initial lymphatic, escape clearance by lymph node macrophages, reach the systemic circulation, and remain in the blood for prolonged periods. These experiments provide a rational approach for the design and engineering of nano-vehicles for optimal lymphatic targeting and are discussed.

Animals↗
PubMed1989

Ionic-strength-dependence of the oxidation of native and pyridoxal 5'-phosphate-modified cytochromes c by cytochrome c oxidase.

The ionic-strength-dependences of the rate constants (log k plotted versus square root of 1) for oxidation of native and pyridoxal 5'-phosphate-modified cytochromes c by three different preparations of cytochrome c oxidase have complex non-linear character, which may be explained on the basis of present knowledge of the structure of the oxidase and the monomer-dimer equilibrium of the enzyme. The wave-type curve (with a minimum and a maximum) for oxidation of native cytochrome c by purified cytochrome c oxidase depleted of phospholipids may reflect consecutively inhibition of oxidase monomers (initial descending part), competition between this inhibition and dimer formation, resulting in increased activity (second part with positive slope), and finally inhibition of oxidase dimers (last descending part of the curve). The dependence of oxidation of native cytochrome c by cytochrome c oxidase reconstituted into phospholipid vesicles is a curve with a maximum, without the initial descending part described above. This may reflect the lack of pure monomers in the vesicles, where equilibrium is shifted to dimers even at low ionic strength. Subunit-III-depleted cytochrome c oxidase does not exhibit the maximum seen with the other two enzyme preparations. This may mean that removal of subunit III hinders dimer formation. The charge interactions of each of the cytochromes c (native or modified) with the three cytochrome c oxidase preparations are similar, as judged by the similar slopes of the linear dependences at I values above the optimal one. This shows that subunit III and the phospholipid membrane do not seem to be involved in the specific charge interaction of cytochrome c oxidase with cytochrome c.

Cytochrome c Group↗
PubMed2005

Essential role for Pro21 in phospholamban for optimal inhibition of the Ca-ATPase.

We have investigated the functional role of the flexible hinge region centered near the sequence TIEMP(21), which connects the N-terminal cytosolic and C-terminal membrane-spanning helical domains of phospholamban (PLB). Specifically, we ask if the conformation of this region is important to attain optimal inhibitory interactions with the Ca-ATPase. A genetically engineered PLB mutant was constructed in which Pro(21) was mutated to an alanine (P21A-PLB(C)); in this construct, all three transmembrane cysteines were substituted with alanines to stabilize the monomeric form of PLB, and a unique cysteine was introduced at position 24 near the hinge element (A24C), permitting the site-specific attachment of fluorescein-5-maleimide (FMal) to monitor structure changes. In agreement with prior measurements in cardiac SR microsomes, the calcium concentration associated with half-maximal activation (Ca(1/2)) of the Ca-ATPase, 290 +/- 10 nM, is shifted to 580 +/- 20 nM when co-reconstituted with PLB(C) (Pro21) as a result of a reduction in the cooperativity associated with the calcium-dependent structural transition. Kinetic simulations indicate that PLB(C) association with the Ca-ATPase results in a 75% reduction in the equilibrium constant associated with the formation of the second high-affinity calcium binding site. In comparison, there is a 43% reduction in KCa(1/2) upon reconstitution of the Ca-ATPase with P21A-PLB(C), which can be simulated by decreasing the equilibrium constant associated with the calcium-dependent structural activation by 50%. The diminished inhibitory action of P21A-PLB(C) is associated with alterations in the structure of the hinge element, as evidenced by the diminished solvent accessibility of FMal relative to the native structure. Likewise, increases in the alpha-helical content and decreases in the mobility of the carboxyl-terminal domain of P21A-PLB(C) are observed using circular dichroism and fluorescence spectroscopy. Collectively, these results indicate that the overall dimensions of the carboxyl-terminal domain of PLB are increased through a stabilization of secondary structural elements upon mutation in P21A-PLB(C) that result in a reduction in the ability of the amino-terminal cytosolic portion of PLB to productively inhibit the Ca-ATPase. Further, these results suggest that the unstructured characteristics of the flexible hinge region in PLB are critical for optimal inhibitory interactions with the Ca-ATPase and suggest its role as a conformational switch.

Alanine↗
PubMed1998

A highly active protein repair enzyme from an extreme thermophile: the L-isoaspartyl methyltransferase from Thermotoga maritima.

We show that the open reading frame in the Thermotoga maritima genome tentatively identified as the pcm gene (R. V. Swanson et al., J. Bacteriol. 178, 484-489, 1996) does indeed encode a protein L-isoaspartate (D-aspartate) O-methyltransferase (EC 2.1.1.77) and that this protein repair enzyme displays several novel features. We expressed the 317 amino acid pcm gene product of this thermophilic bacterium in Escherichia coli as a fusion protein with an N-terminal 20 residue hexa-histidine-containing sequence. This protein contains a C-terminal domain of approximately 100 residues not previously seen in this enzyme from various prokaryotic or eukaryotic species and which does not have sequence similarity to any other entry in the GenBank databases. The C-terminal region appears to be required for enzymatic function as no activity is detected in two recombinant constructs lacking this domain. Sedimentation equilibrium analysis indicated that the enzyme is monomeric in solution. The Km values for measured for peptide and protein substrates were found to be intermediate between those of the high-affinity human enzyme and those of the lower-affinity wheat, nematode, and E. coli enzymes. The enzyme was extremely heat stable, with no loss of activity after 60 min at 100 degreesC. Enzyme activity was observed at temperatures as high as 93 degreesC with an optimal activity of 164 nmol/min/mg protein at 85 degreesC. This activity is approximately 18-fold higher than the maximal activities of mesophilic homologs at 37 degreesC. These data suggest that the Thermotoga enzyme has unique features for initiating repair in damaged proteins containing L-isoaspartyl residues at elevated temperatures.

Amino Acid Sequence↗
PubMed1999

Electrogenic partial reactions of the SR-Ca-ATPase investigated by a fluorescence method.

A fluorescence method was adapted to investigate active ion transport in membrane preparations of the SR-Ca-ATPase. The styryl dye RH421 previously used to investigate the Na,K-ATPase was replaced by an analogue, 2BITC, to obtain optimized fluorescence changes upon substrate-induced partial reactions. Assuming changes of the local electric field to be the source of fluorescence changes that are produced by uptake/release or by movement of ions inside the protein, 2BITC allowed the determination of electrogenic partial reactions in the pump cycle. It was found that Ca2+ binding on the cytoplasmic and on the lumenal side of the pump is electrogenic while phosphorylation and conformational transition showed only minor electrogenicity. Ca2+ equilibrium titration experiments at pH 7.2 in the two major conformations of the protein indicated cooperative binding of two Ca2+ ions in state E1 with an apparent half-saturation concentration, KM of 600 nm. In state P-E2 two KM values, 5 microm and 2.2 mM, were determined and are in fair agreement with published data. From Ca2+ titrations in buffers with various pH and from pH titrations in P-E2, it could be demonstrated that H+ binding is electrogenic and that Ca2+ and H+ compete for the same binding site(s). Tharpsigargin-induced inhibition of the Ca-ATPase led to a state with a specific fluorescence level comparable to that of state E1 with unoccupied ion sites, independent of the buffer composition.

Animals↗
PubMed2005

Templating of multiple ligand metal ion complexation sites in 8-hydroxyquinoline-modified silica sol-gel materials investigated by in situ Raman spectroscopy.

Metal ion templating in a sol-gel synthesis is used to develop multiligand 8-hydroxyquinoline binding sites in porous silica structures. The acid-base equilibria and the metal ion binding equilibria and stoichiometry of these materials are investigated by in situ Raman spectroscopy. This technique is capable of resolving spectral responses of the free ligand and its acid-base forms along the monomeric and dimeric ligand complexes with Cu2+. The proton-transfer equilibrium constants and first ligand binding equilibrium constant to Cu2+ for the metal ion-templated silica are equivalent to surface-immobilized 8HQ on silica gel. The second ligand binding constant to Cu2+, however, is comparable to the first ligand binding constant, which differs from free-solution behavior, where an order of magnitude smaller value is expected. The free energy available for binding the second ligand within the templated material is comparable to the first ligand, probably due to the nearly optimal location of the second ligand for binding, based on the templating that is done during this synthesis. The metal ion concentration responses of sol-gels prepared with varying amounts of metal ion during the syntheses were also tested, and the results indicate control over the fraction of templated binding sites.

Journal Article↗