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Mobile nuclear magnetic resonance (NMR) operating in Earth's magnetic field is adapted to detect leaked or spilled oil trapped in or under sea ice without the need to place any personnel on the ice. A helicopter placed a 6-meter diameter NMR coil system weighing approximately 1000 kg on 92 cm-thick ice surrogate and detected the equivalent of 1 cm thick oil under the ice surrogate in 3-1/2 min.

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Internal magnetic field gradients in water saturated glass bead packs were studied by numerical simulations and a constant time spin echo (CTSE) experiment. The CTSE is comprised of two spin echo refocusing periods where each of the two evolution periods, tau1 and tau2, is varied so that the total evolution, 2(tau1 + tau2), is held constant. The experiment is similar to that introduced by Norwood and Quilter and allows the effects of dephasing due to diffusion in a magnetic field gradient to be separated from other relaxation mechanisms. In our experiments, the magnetic susceptibility difference between the pore fluid and glass beads creates the internal field gradient. CTSE measurements were performed at 7 T (300 MHz 1H) for water saturated in 50 microm diameter glass bead pack. We find that the internal gradients in the center of the pore bodies, where free diffusion applies, is in the range of 10 to 100 G/cm. This fluid volume accounts for < or =10% of the total pore volume. From direct numerical simulations of the internal magnetic field based on a first principles calculation, we find that the major fraction, >90%, of the pore volume has internal gradients of order 500 to 5,000 G/cm. Signals from water in these large gradients is not observed in our CTSE measurements.

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A method for assessing the time reversibility of molecular displacements in fluids is presented. The method utilizes pulsed field gradient NMR experiments, in which the flow driving force is inverted during the magnetization lifetime in each measurement cycle. The method is suitable for opaque three-dimensional systems and short displacements, and provides inherent separation between thermal diffusion and displacements driven by externally controlled forces. This approach was applied to study the time reversibility of an electric-field-driven flow of water in natural sand samples, over time scales of up to 0.4 s and displacement scales of the order of one particle diameter. It is demonstrated that the intensity loss of the NMR signal, caused by flow-induced phase dispersion, is fully refocused upon inversion of the polarity of the applied electric field, resulting in flow echoes.

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The distribution of fluids in the pore space of a series of sandstones is calculated as a function of capillary pressure using a two phase flow simulation model. The pore space is represented by a system of channels and nodes which are derived from x-ray micro-tomography images of sandstones. The sandstones studied varied in permeability from approximately 40 to 3,000 mD. The simulation results illustrate the significance of the pore level by-pass phenomena in controlling the location of fluids within the pore structure. The implications of these results on the interpretation of NMR T(2) distributions to determine the irreducible water saturation are discussed.

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An investigation of the role of tRNA in the catalysis of aminoacylation of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) has revealed that the accuracy of specific interactions between GlnRS and tRNAGln determines amino acid affinity. Mutations in GlnRS at D235, which makes contacts with nucleotides in the acceptor stem of tRNAGln, and at R260 in the enzyme's active site were found to be independent during tRNA binding but interactive for aminoacylation. Characterization of mutants of GlnRS at position 235, showed amino acid recognition to be tRNA mediated. Aminoacylation of tRNA(CUA)Tyr [tyrT (UAG)] by GlnRS-D235H resulted in a 4-fold increase in the Km for the Gln, which was reduced to a 2-fold increase when A73 was replaced with G73. These and previous results suggest that specific interactions between GlnRS and tRNAGln ensure the accurate positioning of the 3' terminus. Disruption of these interactions can change the Km for Gln over a 30-fold range, indicating that the accuracy of aminoacylation is regulated by tRNA at the level of both substrate recognition and catalysis. The observed role of RNA as a cofactor in optimizing amino acid activation suggests that the tRNAGln-GlnRS complex may be partly analogous to ribonucleoprotein enzymes where protein-RNA interactions facilitate catalysis.

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The structure of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) in complex with tRNAGln and ATP has identified a number a sequence-specific protein-tRNA interactions. The contribution to glutamine identity has previously been determined for the nucleotides in tRNAGln. Here, we report the mutational analysis of residues in all three tRNA recognition domains of GlnRS, thus completing a survey of the major sequence-specific contacts between GlnRS and tRNAGln. Specifically, we analyzed the GlnRS determinants involved in recognition of the anticodon which is essential for glutamine identity and in the communication of anticodon recognition to the acceptor binding domain in GlnRS. A combined in vivo and in vitro approach has demonstrated that Arg341, which makes a single sequence-specific hydrogen bond with U35 in the anticodon of tRNAGln, is involved in initial RNA recognition and is an important positive determinant for this base in both cognate and non- cognate tRNA contexts. However, Arg341, as well as Arg402, which interacts with G36 in the anticodon, are negative determinants for non-cognate nucleotides at their respective positions. Analysis of acceptor-anticodon binding double mutants and of a mutation of Glu323 in the loop-strand-helix connectivity subdomain in GlnRS has further implicated this domain in the functional communication of anticodon recognition. The better than expected activity (anticooperativity) of these double mutants has led us to propose an "anticodon-independent" mechanism, in which the removal of certain synthetase interactions with the anticodon eliminates structural constraints, thus allowing the relaxed specificity mutants in the acceptor binding domain ot make more productive interactions.

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Purification of mutant enzymes is a prime requirement of biophysical and biochemical studies. Our investigations on the essential Escherichia coli enzyme glutaminyl-tRNA synthetase demand mutant enzymes free of any wild-type protein contamination. However, as it is not possible to express noncomplementing mutant enzymes in an E. coli glnS-deletion strain, we developed a novel strategy to address these problems. Instead of following the common tactic of epitope-tagging the mutant protein of interest on an extrachromosomal genetic element, we fused a reporter epitope to the 5' end of the chromosomal glnS-gene copy: this is referred to as 'reverse epitope-tagging.' The corresponding strain, E. coli HAPPY101, displays a normal phenotype, and glutaminyl-tRNA synthetase is exclusively present as an epitope-tagged form in cell-free extracts. Here we report the use of E. coli HAPPY101 to express and purify a number of mutant glutaminyl-tRNA synthetases independently of their enzymatic activity. In this process, epitope-tagged wild-type protein is readily separated from mutant enzymes by conventional chromatographic methods. In addition, the absence of wild-type can be monitored by immunodetection using a monoclonal antibody specific for the epitope. The strategy described here for expression and purification of an essential enzyme is not restricted to glutaminyl-tRNA synthetase and should be applicable to any essential enzyme that retains sufficient activity to sustain growth following reverse epitope-tagging.

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We describe a convenient, simple and novel continuous spectrophotometric method for the determination of aminoacyl-tRNA synthetase activity. The assay relies upon the measurement of inorganic pyrophosphate generated in the first step of the aminoacylation of a tRNA. Pyrophosphate release is coupled to inorganic pyrophosphatase, to generate phosphate, which in turn is used as the substrate of purine nucleoside phosphorylase to catalyze the N-glycosidic cleavage of 2-amino 6-mercapto 7-methylpurine ribonucleoside. Of the reaction products, ribose 1-phosphate and 2-amino 6-mercapto 7-methylpurine, the latter has a high absorbance at 360 nm relative to the nucleoside and hence provides a spectrophotometric signal that can be continuously followed. The non-destructive nature of the spectrophotometric assay allowed the re-use of the tRNAs in question in successive experiments. The usefulness of this method was demonstrated for glutaminyl-tRNA synthetase (GlnRS) and tryptophanyl-tRNA synthetase. Initial velocities measured using this assay correlate closely with those assayed by quantitation of [3H]Gln-tRNA or [14C]Trp-tRNA formation respectively. In both cases amino acid transfer from the aminoacyl adenylate to the tRNA represents the rate determining step. In addition, aminoacyl adenylate formation by aspartyl-tRNA synthetase was followed and provided a more sensitive means of active site titration than existing techniques. Finally, this novel method was used to provide direct evidence for the cooperativity of tRNA and ATP binding to GlnRS.

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The integration of genetic and biochemical approaches to study the crystal structure of the glutaminyl-tRNA synthetase (GlnRS):tRNA(Gln):ATP complex has elucidated the mechanism by which GlnRS selects its cognate tRNA for aminoacylation. Three principal types of interaction have been identified: interaction with specific bases in the cognate tRNA, rejection of non-cognate tRNAs, and activation of the active site upon cognate tRNA binding. The recent solving of the crystal structure of tryptophanyl-tRNA synthetase (TrpRS) has allowed comparable studies to be initiated in an aminoacyl-tRNA synthetase which, unlike GlnRS, does not require tRNA binding prior to amino acid activation.

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The universal precursor of tetrapyrrole pigments (e.g., chlorophylls and hemes) is 5-aminolevulinic acid (ALA), which in Euglena gracilis chloroplasts is derived via the two-step C5 pathway from glutamate charged to tRNA(Glu). The first enzyme in this pathway, Glu-tRNA reductase (GluTR) catalyzes the reduction of glutamyl-tRNA(Glu) (Glu-tRNA) to glutamate 1-semialdehyde (GSA) with the release of the uncharged tRNA(Glu). The second enzyme, GSA-2,1-aminomutase, converts GSA to ALA. tRNA(Glu) is a specific cofactor for the NADPH-dependent reduction by GluTR, an enzyme that recognizes the tRNA in a sequence-specific manner. This RNA is the normal tRNA(Glu), a dual-function molecule participating both in protein and in ALA and, hence, chlorophyll biosynthesis. A chlorophyll-deficient mutant of E. gracilis (Y9ZNalL) does not synthesize ALA from glutamate, although it contains GluTR and GSA-2,1-aminomutase activity. The tRNA(Glu) isolated from the mutant can still be acylated with glutamate in vitro and in vivo. Furthermore, it supports chloroplast protein synthesis; however, it is a poor substrate for GluTR. Sequence analysis of the tRNA and of its gene revealed a C56-->U mutation in the resulting gene product. C56 is therefore an important identity element for GluTR. Thus, a point mutation in the T loop of tRNA uncouples protein from chlorophyll biosynthesis.

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Diffusion dynamics for water in a series of sandstone core plugs with a broad range of permeabilities was studied using both the Carr-Purcell-Meiboom-Gill (CPMG) and inversion recovery experiments. Both the transverse and longitudinal magnetization curves were found to fit well to stretched exponential relaxation kinetics. At short times, the transverse magnetization is well described by an expression for free diffusion averaged over a distribution of pore sizes. The stretch exponents for the transverse and longitudinal magnetization are shown to be simply related to the width of the pore size distribution. A cross over from free to restricted diffusion is evident in the dependence of T2 with increasing diffusion time set by the interpulse spacing tau in the CPMG experiment. The T2(tau) data is fit to a model which interpolates between the limits of free and restricted diffusion. A length derived from this model is shown to provide a simple estimate of the absolute fluid flow permeability.

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A variety of genetic, biochemical and structural studies have been used to determine factors ensuring the accuracy of recognition by aminoacyl-tRNA synthetases for tRNA. The identity elements of Escherichia coli tRNA(Gln) are located mainly in the anticodon and acceptor stem, and ensure the accurate recognition of the tRNA by glutaminyl-tRNA synthetase. We summarize a number of experimental techniques to define the accuracy of aminoacylation in vivo and in vitro.

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A functional tRNA(Val) gene, which codes for the major tRNA(ValIAC) isoacceptor species, and three new tRNA(Val) pseudogenes have been isolated from human genomic DNA. Two tRNA(Val) pseudogenes and a tRNA(Val) variant gene were found to be associated with tRNA genes encoding tRNA(ArgICG), tRNA(GlyUCC), and tRNA(ThrIGU), respectively, on distinct DNA fragments. All tRNA genes, including the pseudogenes, are actively transcribed in HeLa nuclear extract. Pre-tRNAs of tRNA(Val), tRNA(Arg), tRNA(Thr), and tRNA(Gly) genes are correctly processed to mature-sized tRNAs, whereas the three tRNA(Val) pseudogenes yield stable pre-tRNAs in vitro. These findings reveal that, together with the three known pseudogenes, half of the members of the human tRNA(Val) gene family are pseudogenes, all of which are active in homologous nuclear extracts in vitro and presumably also in vivo.

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Several neurokinins, namely substance P, neurokinin A, neurokinin B, [beta-Ala8]neurokinin A-(4-10) and senktide, were tested on noradrenaline-precontracted rabbit aortic rings to characterize the receptor mediating their endothelium-dependent relaxant effect in this preparation. CP-96,345, the new nonpeptide antagonist selective for the NK1 receptor, was also studied. Substance P, neurokinin A and neurokinin B, in that order of potency, were effective in relaxing precontracted rings, indicating the involvement of the NK1 receptor; [beta-Ala8]neurokinin A-(4-10) and senktide, which are selective agonists for NK2 and NK3 receptors, respectively, had no significant relaxant effect. The relaxant effects of substance P, neurokinin A and neurokinin B were competitively antagonized by nanomolar concentrations of CP-96,345. These findings support the view that the NK1 receptor mediates the endothelium-dependent relaxant effect of the neurokinins in rabbit aorta.

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