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Misacylation and editing by Escherichia coli valyl-tRNA synthetase: evidence for two tRNA binding sites.

Valyl-tRNA synthetase (ValRS) has difficulty discriminating between its cognate amino acid, valine, and structurally similar amino acids. To minimize translational errors, the enzyme catalyzes a tRNA-dependent editing reaction that prevents accumulation of misacylated tRNA(Val). Editing occurs with threonine, alanine, serine, and cysteine, as well as with several nonprotein amino acids. The 3'-end of tRNA plays a vital role in promoting the tRNA-dependent editing reaction. Valine tRNA having the universally conserved 3'-terminal adenosine replaced by any other nucleoside does not stimulate the editing activity of ValRS. As a result 3'-end tRNA(Val) mutants, particularly those with 3'-terminal pyrimidines, are stably misacylated with threonine, alanine, serine, and cysteine. Valyl-tRNA synthetase is unable to hydrolytically deacylate misacylated tRNA(Val) terminating in 3'-pyrimidines but does deacylate mischarged tRNA(Val) terminating in adenosine or guanosine. Evidently, a purine at position 76 of tRNA(Val) is essential for translational editing by ValRS. We also observe misacylation of wild-type and 3'-end mutants of tRNA(Val) with isoleucine. Valyl-tRNA synthetase does not edit wild-type tRNA(Val)(A76) mischarged with isoleucine, presumably because isoleucine is only poorly accommodated at the editing site of the enzyme. Misacylated mutant tRNAs as well as 3'-end-truncated tRNA(Val) are mixed noncompetitive inhibitors of the aminoacylation reaction, suggesting that ValRS, a monomeric enzyme, may bind more than one tRNA(Val) molecule. Gel-mobility-shift experiments to characterize the interaction of tRNA(Val) with the enzyme provide evidence for two tRNA binding sites on ValRS.

3' Untranslated Regions↗

Determination of interstitial water chemistry and porosity in consolidated aquifer materials by diffusion equilibrium-exchange.

Diffusion equilibrium exchange (DEE) is presented as a novel, practical alternative to centrifugation for the recovery and chemical analysis of interstitial water in contaminated core samples from consolidated rocks and aquifers. The methodology is suitable for sampling organic and inorganic compounds, including redox sensitive species such as SO4(2-), NO3-, NO2-, Mn(II), Fe(II), and sulfide (HS-). DEE also permits analyte extraction from kilogram quantities of core, which avoids extended centrifugation or sample amalgamation and provides analyte masses appropriate for stable isotope analysis. The procedure involves simple and rapid on-site sectioning of representative core samples, which are preserved in the field by storage in airtight bottles filled with deoxygenated deionized water containing a conservative tracer (Br-). Equilibration times for individual solutes can be estimated in advance to reduce the need for time-series analysis; for an effective diffusion coefficient of 2.5 x 10(-10) m2 s(-1) (Br- in chalk rock) equilibration was >90% completed after 30 h, consistent with the predicted equilibration time. The DEE method presented minimizes sampling errors from temperature changes, oxidation of reduced chemical species, and loss of volatile compounds, which can occur with other interstitial water sampling techniques. It also gives superior resolution of in situ solute distributions and geochemical processes in consolidated sediments than centrifugation and can provide estimates of aquifer porosity in core samples. Laboratory experiments using chalk rock core and simulated extraction procedures confirm the superior performance of the DEE method over centrifugation for a range of solutes. The method has been used to generate detailed interstitial water profiles of electron acceptor and contaminant concentrations along the flow path of a petroleum hydrocarbon plume in the U.K. Upper Chalk aquifer as part of a natural attenuation assessment.

Environmental Monitoring↗

Characterization of Actinide Bonding in Th(S(2)PMe(2))(4) by Synchrotron X-ray Diffraction.

Extensive synchrotron (28 K) and conventional sealed-tube (9 K) X-ray diffraction data have been collected on Th(S(2)PMe(2))(4). Modeling of the electron density of the complex shows the bonding is quite ionic with little diffuse f or d type bonding density. Furthermore a large polarization of the Th core is observed revealing some 5d-like involvement in the bonding. High-quality ab initio density functional calculations are not able to reproduce these features and instead predict rather covalent bonding with considerable 6d-5f mixing. The study suggests that this theoretical method exaggerates the covalent nature of actinide bonds. It is shown that the most direct measure of covalence-charge transfer and electron distributions-can be usefully estimated by X-ray diffraction even in this most unfavorable of cases, where many actinide core electrons are present. The use of very low temperature data is crucial in the study of heavy metal complexes in order to minimize systematic errors such as thermal diffuse scattering and anharmonicity. The fact that accurate synchrotron radiation diffraction data can be measured within days makes studies of compounds beyond the first transition series more frequently within reach.

Journal Article↗

Synthesis and dynamic random access memory behavior of a functional polyimide.

The device under testing was a plastic dynamic random access memory based on a donor-functionalized polyimide (TP6F-PI), which exhibited the ability to write, read, erase, and refresh the electrical states. The device had an ON/OFF current ratio up to 105, promising minimal misreading error. Both the on and off states were stable under a constant voltage stress of 1 V and survived up to 108 read cycles at 1 V.

Journal Article↗

Analytic potential energy functions for simulating aluminum nanoparticles.

Potential energy functions (PEFs) parametrized to bulk data are shown to perform poorly for small aluminum nanoparticles and clusters. In contrast, PEFs parametrized to a limited set of cluster and bulk data, but no nanoparticle data, perform well for nanoparticles. This validates a practical scheme for developing PEFs for nanoscale systems. Building on these findings, we optimized five PEFs by minimizing the error in the fit over a broad data set. Two of these PEFs have errors of less than or equal to 0.08 eV/atom for each of three categories of system sizes, i.e., for small clusters, for nanoparticles, and for bulk potential energies.

Journal Article↗

Bond additivity corrections for G3B3 and G3MP2B3 quantum chemistry methods.

We have developed bond additivity correction (BAC) procedures for the G3-based quantum chemistry methods, G3B3 and G3MP2B3. We denote these procedures as BAC-G3B3 and BAC-G3MP2B3. We apply the procedures to compounds containing atoms from the first three rows of the periodic table including H, B, C, N, O, F, Al, Si, P, S, and Cl atoms. The BAC procedure applies atomic, molecular, and pairwise bond corrections to theoretical heats of formation of molecules. The BAC-G3B3 and BAC-G3MP2B3 procedures require parameters for each atom type but not for each bond type. These parameters have been obtained by minimizing the error between the BAC-G3B3 and BAC-G3MP2B3 predictions and the experimental heats of formation for a 155 molecule reference set, containing open and closed shell molecules representing various functional groups, multireference configurations, isomers, and degrees of saturation. As compared to former BAC-MP4, BAC-G2, and BAC-hybrid methods, BAC-G3B3 provides better agreement with experiment for a wider range of chemical moieties, including highly oxidized species involving SOx s, NOx s, POx s, and halogens. The BAC-G3B3 and BAC-G3MP2B3 procedures are applied to an extended test suite involving 273 compounds. We assess the overall quality of BAC-G3B3 with experiments and other theoretical approaches. For the reference set, the average error for the BAC-G3B3 results is 0.44 kcal/mol as compared to 0.82 kcal/mol for the raw G3B3. For the extended test set, the average error for the BAC-G3B3 results is 0.91 kcal/mol as compared to 1.38 kcal/mol for the raw G3B3. As compared to the other BAC procedures, the improved predictive capability of BAC-G3B3 and BAC-G3MP2B3 procedures is, to a large extent, due to the improved quality of G3-based methods resulting in much smaller BAC correction terms.

Journal Article↗

Thermodynamic properties (enthalpy, bond energy, entropy, and heat capacity) and internal rotor potentials of vinyl alcohol, methyl vinyl ether, and their corresponding radicals.

Vinyl alcohols (enols) have been discovered as important intermediates and products in the oxidation and combustion of hydrocarbons, while methyl vinyl ethers are also thought to occur as important combustion intermediates. Vinyl alcohol has been detected in interstellar media, while poly(vinyl alcohol) and poly(methyl vinyl ether) are common polymers. The thermochemical property data on these vinyl alcohols and methyl vinyl ethers is important for understanding their stability, reaction paths, and kinetics in atmospheric and thermal hydrocarbon-oxygen systems. Enthalpies , entropies , and heat capacities (C(p)()(T)) are determined for CH(2)=CHOH, C(*)H=CHOH, CH(2)=C(*)OH, CH(2)=CHOCH(3), C(*)H=CHOCH(3), CH(2)=C(*)OCH(3), and CH(2)=CHOC(*)H(2). Molecular structures, vibrational frequencies, , and C(p)(T) are calculated at the B3LYP/6-31G(d,p) density functional calculation level. Enthalpies are also determined using the composite CBS-Q, CBS-APNO, and G3 methods using isodesmic work reactions to minimize calculation errors. Potential barriers for internal rotors are calculated at the B3LYP/6-31G(d,p) level and used to determine the hindered internal rotational contributions to entropy and heat capacity. The recommended ideal gas phase values calculated in this study are the following (in kcal mol(-1)): -30.0, -28.9 (syn, anti) for CH(2)=CHOH; -25.6, -23.9 for CH(2)=CHOCH(3); 31.3, 33.5 for C(*)H=CHOH; 27.1 for anti-CH(2)=C(*)OH; 35.6, 39.3 for C(*)H=CHOCH(3); 33.5, 32.2 for CH(2)=C(*)OCH(3); 21.3, 22.0 for CH(2)=CHOC(*)H(2). Bond dissociation energies (BDEs) and group additivity contributions are also determined. The BDEs reveal that the O-H, O-CH(3), C-OH, and C-OCH(3) bonds in vinyl alcohol and methyl vinyl ether are similar in energy to those in the aromatic molecules phenol and methyl phenyl ether, being on average around 3 kcal mol(-1) weaker in the vinyl systems. The keto-enol tautomerization enthalpy for the interconversion of vinyl alcohol to acetaldehyde is determined to be -9.7 kcal mol(-1), while the activation energy for this reaction is calculated as 55.9 kcal mol(-1); this is the simplest keto-enol tautomerization and is thought to be important in the reactions of vinyl alcohol. Formation of the formyl methyl radical (vinoxy radical/vinyloxy radical) from both vinyl alcohol and methyl vinyl ether is also shown to be important, and its reactions are discussed briefly.

Computer Simulation↗

Strategies for genetic mapping of categorical traits.

The search for efficient and powerful statistical methods and optimal mapping strategies for categorical traits under various experimental designs continues to be one of the main tasks in genetic mapping studies. Methodologies for genetic mapping of categorical traits can generally be classified into two groups, linear and non-linear models. We develop a method based on a threshold model, termed mixture threshold model to handle ordinal (or binary) data from multiple families. Monte Carlo simulations are done to compare its statistical efficiencies and properties of the proposed non-linear model with a linear model for genetic mapping of categorical traits using multiple families. The mixture threshold model has notably higher statistical power than linear models. There may be an optimal sampling strategy (family size vs number of families) in which genetic mapping reaches its maximal power and minimal estimation errors. A single large-sibship family does not necessarily produce the maximal power for detection of quantitative trait loci (QTL) due to genetic sampling of QTL alleles. The QTL allelic model has a marked impact on efficiency of genetic mapping of categorical traits in terms of statistical power and QTL parameter estimation. Compared with a fixed number of QTL alleles (two or four), the model with an infinite number of QTL alleles and normally distributed allelic effects results in loss of statistical power. The results imply that inbred designs (e.g. F2 or four-way crosses) with a few QTL alleles segregating or reducing number of QTL alleles (e.g. by selection) in outbred populations are desirable in genetic mapping of categorical traits using data from multiple families.

Alleles↗

Cardiovascular reactivity to a naturally occurring stressor: development and psychometric evaluation of a psychophysiological assessment procedure.

Three studies were conducted to examine the feasibility, reactive effects of assessment, stability, sampling parameters, and sensitivity of an assessment procedure designed to measure cardiovascular responses to a discrete, naturally occurring, and replicatable stressor--university course examinations. Undergraduate students monitored their blood pressure and heart rate several times during one or two classroom examinations and for several class sessions preceding each examination. Classroom examinations were generally associated with significant increases in subjective measures of distress and cardiovascular measures. Reactive effects of assessment and other sources of error were minimized and responses were reasonably stable over time. These results support the potential utility, validity, and cost-efficiency of this methodology for assessing cardiovascular reactivity to naturally occurring stressors.

Adolescent↗

Close binding of identity and location in visual feature perception.

The binding of identity and location information in disjunctive feature search was studied. Ss searched a heterogeneous display for a color or a form target, and reported both target identity and location. To avoid better than chance guessing of target identity (by choosing the target less likely to have been seen), the difficulty of the two targets was equalized adaptively; a mathematical model was used to quantify residual effects. A spatial layout was used that minimized postperceptual errors in reporting location. Results showed strong binding of identity and location perception. After correction for guessing, no perception of identity without location was found. A weak trend was found for accurate perception of target location without identity. We propose that activated features generate attention-calling "interrupt" signals, specifying only location; attention then retrieves the properties at that location.

Adult↗

Glomerular filtration dynamics in the dog during elevated plasma colloid osmotic pressure.

To determine if the glomerular filtration coefficient (Kf) of the dog is influenced by changes in plasma colloid osmotic pressure (COP), we conducted micropuncture experiments in dogs given concentrated albumin solutions. In one group (N = 9), filtration dynamics were evaluated following infusion of 450 to 600 ml of a 25% bovine albumin solution. To minimize the effects of acute volume expansion, we also achieved high COP levels in another group (N = 7) by albumin loading on the day prior to the experiment. In all experiments, renal arterial pressure was reduced to approximately 90 mm Hg to minimize potential errors that might lead to overestimation of single nephron filtration rate (SNGFR) and glomerular pressure (GP). In the acutely expanded dogs, COP increased to 23.0 +/- (SEM) 0.9 mm Hg, SNGFR was 59 +/- 6 nl/min, estimated GP was 61.0 +/- 2.0 mm Hg, proximal tubule pressure (PTP) was 23.0 +/- 1.6 mm Hg, and superficial filtration fraction (SFF) was 0.13 +/- 0.02. A similarly reduced whole kidney filtration fraction was also observed, due almost entirely to a marked increase in renal blood flow. When compared to noninfused control dogs (N = 13), Kf was significantly higher in the dogs with elevated COP, being 5.3 +/- 0.6 nl/min/mm Hg as compared to 3.4 +/- 0.3 nl/min/mm Hg. Average effective filtration pressure (EFP) was 12 +/- 1mm Hg, and EFP at the efferent end of the glomerular capillaries was 8.9 +/- 1.2 mm Hg. In the group infused on the prior day, COP was 20.0 +/- 0.8 mm Hg, SFF was 0.26 +/- 0.01, SNGFR was 70 +/-8 nl/min, GP was 59 +/- 2 mm Hg, and PTP was 19.0 +/- 1.5 mm Hg. Average EFP was 15 +/- 1 mm Hg, and EFP at the efferent end of the capillaries was 7.5 +/- 0.7 mm Hg. kf was 4.85 +/- 0.66 nl/min/mm Hg, a value significantly higher than that obtained in control dogs having a COP of 15.0 +/- 0.6 mm Hg. Furthermore, one group of control dogs (N = 4), expanded with an isooncotic albumin solution, did not exhibit significant changes in Kf even though the degree of plasma volume expansion was similar to the group expanded with concentrated albumin solution. These experiments are consistent with previous findings obtained in the rat that Kf is influenced by the COP, although the changes in Kf appear to be less than they are in the rat. The data indicate that even under these conditions of elevated COP, the filtration process in the dog is characterized by positive filtration pressures throughout the length of the glomerular capillaries.

Albumins↗

Causes, kinetics and clinical implications of post-hemodialysis urea rebound.

The rapid increase in end-dialysis urea concentration (Co) immediately after the end of dialysis (HD), which greatly exceeds that expected as an effect of urea generation and defined as "net rebound," was assessed in 21 chronic HD patients. The curve of serial values of net rebound correlated (r = 0.70) with the theoretical curve predicted by the two pool urea kinetics model (UKM). A mean equilibrium concentration (Ce) was achieved in 48 minutes, with a 7.58% increase in Co. Stabilized rebound (Re) was compared after four different HD procedures, and significant correlations were found between the magnitude of Re and the indexes of HD efficiency, dialyzer clearance (r = 0.75) and Kt/V (r = 0.68). The highest values of Re (8.6% and 8.8%) were observed after the procedures with largest urea removal, irrespective of the biocompatibility conditions (new or reused dialyzers). The single pool UKM applied with the stabilized end-HD urea concentration Ce instead of Co resulted in more physiological values of urea distribution volume (56.1% vs. 50.5% of body wt) and in lower values of Kt/V (0.64 vs. 0.73, P less than 0.001) and protein catabolic rate (1.07 vs. 1.17 g/kg/day, P less than 0.001). A reequilibration process, rather than protein hypercatabolism, seems to be responsible for most rebound, the magnitude of which correlated with the efficiency of the procedure. Only by considering Ce as the true end-HD urea concentration it is possible to minimize the errors arising from the application of a single pool analysis to a two pool system.

Body Fluid Compartments↗

General conditions for predictivity in learning theory.

Developing theoretical foundations for learning is a key step towards understanding intelligence. 'Learning from examples' is a paradigm in which systems (natural or artificial) learn a functional relationship from a training set of examples. Within this paradigm, a learning algorithm is a map from the space of training sets to the hypothesis space of possible functional solutions. A central question for the theory is to determine conditions under which a learning algorithm will generalize from its finite training set to novel examples. A milestone in learning theory was a characterization of conditions on the hypothesis space that ensure generalization for the natural class of empirical risk minimization (ERM) learning algorithms that are based on minimizing the error on the training set. Here we provide conditions for generalization in terms of a precise stability property of the learning process: when the training set is perturbed by deleting one example, the learned hypothesis does not change much. This stability property stipulates conditions on the learning map rather than on the hypothesis space, subsumes the classical theory for ERM algorithms, and is applicable to more general algorithms. The surprising connection between stability and predictivity has implications for the foundations of learning theory and for the design of novel algorithms, and provides insights into problems as diverse as language learning and inverse problems in physics and engineering.

Algorithms↗

Hand-held three-dimensional dental X-ray system: technical description and preliminary results.

OBJECTIVE: To design, fabricate, and perform preliminary in vitro testing of a portable, hand-held, three-dimensional (3D) dental X-ray system using options unique to Tuned-Aperture Computed Tomography (TACT). The design allows for task-specific positioning over an unlimited range of user-selected angles and incorporates an integrated laser guidance system to constrain the focal-object distance. METHODS: A prototype system was fabricated consisting of an extremely lightweight X-ray source cantilevered from an aluminum gunstock-type handle to which a transparent radiation scatter shield was attached. Aiming was facilitated by task-specific visual cues used in conjunction with a spherically shaped radiolucent alignment jig coupled to the tissues of interest. Proper range was assured by a laser-assisted guidance system. The image transducer was an extrinsically modified commercially available CMOS device. The irradiated patient was simulated by a DXTTR phantom. RESULTS: The prototype demonstrated automated display of radiographed intra-oral tissues in three dimensions from arbitrary projection geometries and simulated task-specific sequences. Uncontrolled movements between exposures produced no obvious degeneration of 3D image quality. The aiming system minimized technical errors from misangulation. All dental regions in the phantom were imaged without difficulty. Projected risk was observed to be within clinically acceptable limits. CONCLUSIONS: Task-specific 3D images can be generated from as few as three uncontrolled projections. Total exposures can be prorated to levels not greatly exceeding those required for conventional two-dimensional radiographs of comparable image quality. Predicted radiation risks lie well below existing guidelines for occupational exposure.

Dental Equipment↗

Microfluidic devices fabricated in poly(methyl methacrylate) using hot-embossing with integrated sampling capillary and fiber optics for fluorescence detection.

High-aspect-ratio microstructures have been prepared using hot-embossing techniques in poly(methyl methacrylate) (PMMA) from Ni-based molding dies prepared using LIGA (Lithographie, Galvanoformung, Abformung). Due to the small amount of mask undercutting associated with X-ray lithography and the high energy X-ray beam used during photoresist patterning, deep structures with sharp and smooth sidewalls have been prepared. The Ni-electroforms produced devices with minimal replication errors using hot-embossing at a turn around time of approximately 5 min per device. In addition, several different polymers (with different glass transition temperatures) could be effectively molded with these Ni-electroforms and many devices (>300) molded with the same master without any noticeable degradation. The PMMA devices consisted of deep and narrow channels for insertion of a capillary for the automated electrokinetic loading of sample into the microfluidic device and also, a pair of optical fibers for shuttling laser light to the detection zone and collecting the resulting emission for fluorescence analysis. Electrophoretic separations of double-stranded DNA ladders Phi X174 digested with Hae III) were performed with fluorescence detection accomplished using near-IR excitation. It was found that the narrow width of the channels did not contribute significantly to electrophoretic zone broadening and the plate numbers generated in the extended length separation channel allowed sorting of the 271/281 base pair fragments associated with this sizing ladder when electrophoresed in methylcellulose entangled polymer solutions. The dual fiber detector produced sub-attomole detection limits with the entire detector, including laser source, electronics and photon transducer, situated in a single box measuring 3'' x 10" x 14".

Dinitrobenzenes↗

Groundwater monitoring plans at small-scale sites--an innovative spatial and temporal methodology.

An innovative methodology for improving existing groundwater monitoring plans at small-scale sites is presented. The methodology consists of three stand-alone methods: a spatial redundancy reduction method, a well-siting method for adding new sampling locations, and a sampling frequency determination method. The spatial redundancy reduction method eliminates redundant wells through an optimization process that minimizes the errors in plume delineation and the average plume concentration estimation. The well-siting method locates possible new sampling points for an inadequately delineated plume via regression analysis of plume centerline concentrations and estimation of plume dispersivity values. The sampling frequency determination method recommends the future frequency of sampling for each sampling location based on the direction, magnitude, and uncertainty of the concentration trend derived from representative historical concentration data. Although the methodology is designed for small-scale sites, it can be easily adopted for large-scale site applications. The proposed methodology is applied to a small petroleum hydrocarbon-contaminated site with a network of 12 monitoring wells to demonstrate its effectiveness and validity.

Environmental Monitoring↗

The preparation and immunological properties of I-labelled adrenocorticotrophin.

1. A procedure is described for preparing (131)I-labelled adrenocorticotrophin suitable for use in radioimmunoassay. 2. Adsorption of labelled and unlabelled adrenocorticotrophin at low concentrations occurs to various surfaces despite the presence of diluent protein. Adsorption and desorption errors are minimized by low pH and by the use of polystyrene vials. 3. Preparations with low initial damage are obtained if the radioiodination is performed rapidly and the separation of (131)I-labelled adrenocorticotrophin from unchanged [(131)I]iodide is carried out on cellulose columns by using dilute acid. 4. The immunological activity of (131)I-labelled alpha(1-24)-adrenocorticotrophin, but not of (131)I-labelled porcine adrenocorticotrophin, decreases with increasing specific radioactivity. The involvement of tyrosine residues in the immunological specificity of the alpha(1-24)-adrenocorticotrophin only is suggested to explain this finding.

Journal Article↗

Computed resolution and relative specific radioactivities of radiolabelled proteins synthesized by isolated gastric mucosal cells.

1. By radiolabelling, polyacrylamide-gel electrophoresis in the presence of sodium dodecyl sulphate and fluorography, more than 50 soluble proteins in the molecular-weight range 15000-100000 were shown to continue to be synthesized after cells had been isolated from rat gastric mucosa. 2. Densitometric measurements of stained gels and fluorographic films were processed by computer to resolve individual overlapping Gaussian peaks corresponding to the protein bands. 3. Comparison of resolved peak areas of radioactivity and staining showed certain bands to have characteristically high relative specific radioactivities. 4. The computer programs (in FORTRAN) permit the analysis of a single densitometric trace or the simultaneous comparison of a corresponding pair of densitometric records of stained gels, or of fluorographic films, or a combination. Central processing unit time is used economically. 5. The programs identify the Gaussian components that contribute to the records and estimate their means, standard deviations and enclosed areas. These estimates are improved by a piecewise iterative method that minimizes the errors between the calculated and the experimental data. 6. Relative specific radioactivities are calculated as the normalized ratio of the area of a fluorographic film peak and the area of the corresponding stained gel peak. The computer programs have been deposited as Supplementary Publication SUP 50094 (55 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms given in Biochem. J. (1978) 169, 5.

Animals↗