NMR of petrochemical-type chemical reactions.

A simple technique is presented for NMR of chemically reacting systems at conditions of high temperature and pressure. The method can follow reactions that are typical of refinery operations - hydrogenation, transfer dehydrogenation, methanol synthesis, and isomerization. All of the reacting materials are flame-sealed into a glass capillary.

Helicopter-borne NMR for detection of oil under sea-ice.

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.

Rapid focused sequencing: a multiplexed assay for simultaneous detection and strain typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis.

Background: The intentional release of Bacillus anthracis in the United States in 2001 has heightened concern about the use of pathogenic microorganisms in bioterrorism attacks. Many of the deadliest bacteria, including the Class A Select Agents Bacillus anthracis, Francisella tularensis, and Yersinia pestis, are highly infectious via the pulmonary route when released in aerosolized form. Hence, rapid, sensitive, and reliable methods for detection of these biothreats and characterization of their potential impact on the exposed population are of critical importance to initiate and support rapid military, public health, and clinical responses.

A multiplexed microfluidic PCR assay for sensitive and specific point-of-care detection of Chlamydia trachomatis.

Background: Chlamydia trachomatis (Ct) is the most common cause of bacterial sexually transmitted diseases (STD) worldwide. While commercial nucleic acid amplification tests (NAAT) are available for Ct, none are rapid or inexpensive enough to be used at the point-of-care (POC). Towards the first Ct POC NAAT, we developed a microfluidic assay that simultaneously interrogates nine Ct loci in 20 minutes.

Electric field driven flow in natural porous media.

Electric fields were applied to fluid-saturated packed sand beds (0.23+/-0.03 mm average pore diameter), and the effects on the mobility of the water molecules were monitored using stimulated echo (STE) and pulsed field gradient (PFG) experiments.

Internal magnetic gradient fields in glass bead packs from numerical simulations and constant time diffusion spin echo measurements.

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.

Observation of electro-osmotic flow echoes in porous media by nuclear magnetic resonance.

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.

Escherichia coli glutamyl-tRNA reductase. Trapping the thioester intermediate.

In the first step of tetrapyrrole biosynthesis in Escherichia coli, glutamyl-tRNA reductase (GluTR, encoded by hemA) catalyzes the NADPH-dependent reduction of glutamyl-tRNA to glutamate-1-semialdehyde. Soluble homodimeric E. coli GluTR was made by co-expressing the hemA gene and the chaperone genes dnaJK and grpE.

Optically detected magnetic resonance in the photoexcited triplet states of Ti(IV) and Zr(IV) cylopentadienyl complexes.

The class of compounds (RCp)2MX2, where M is a group IV metal, Cp is cyclopentadienyl, R is an alkyl, and X is a halide, has been of continuing interest as precursors for olefin coordination polymerization catalysts. In this communication, we demonstrate that the technique of optically detected magnetic resonance (ODMR) reveals subtle differences in the composition of the frontier molecular orbitals associated with the nature of the alkyl substituents on the Cp rings.

NMR T2 distributions and two phase flow simulations from x-ray micro-tomography images of sandstones.

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.

Transfer RNA-dependent cognate amino acid recognition by an aminoacyl-tRNA synthetase.

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.

Functional connectivity between tRNA binding domains in glutaminyl-tRNA synthetase.

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.

Homologous expression and purification of mutants of an essential protein by reverse epitope-tagging.

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.

A broadly applicable continuous spectrophotometric assay for measuring aminoacyl-tRNA synthetase activity.

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.

Substrate selection by aminoacyl-tRNA synthetases.

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.

A point mutation in Euglena gracilis chloroplast tRNA(Glu) uncouples protein and chlorophyll biosynthesis.

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).

Combined proton T1N and CPMG T2N studies of water saturated sandstone core plugs.

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 recognition of E. coli glutamine tRNA by glutaminyl-tRNA synthetase.

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.

The first human genes for tRNA(ArgICG), tRNA(GlyUCC), and tRNA(ThrIGU) and more tRNA(Val) pseudogenes: expression and pre-tRNA maturation in HeLa cell-free extracts.

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.