Microbial source tracking by DNA sequence analysis of the Escherichia coli malate dehydrogenase gene.

Criteria for sub-typing of microbial organisms by DNA sequencing proposed by Olive and Bean were applied to several genes in Escherichia coli to identify targets for the development of microbial source tracking assays. Based on the aforementioned criteria, the icd (isocitrate dehydrogenase), and putP (proline permease) genes were excluded as potential targets due to their high rates of horizontal gene transfer; the rrs (16S rRNA) gene was excluded as a target due to the presence of multiple gene copies, with different sequences in a single genome. Based on the above criteria, the mdh (malate dehydrogenase) gene was selected as a target for development of a microbial source tracking assay.

Automated template quantification for DNA sequencing facilities.

The quantification of plasmid DNA by the PicoGreen dye binding assay has been automated, and the effect of quantification of user-submitted templates on DNA sequence quality in a core laboratory has been assessed. The protocol pipets, mixes and reads standards, blanks and up to 88 unknowns, generates a standard curve, and calculates template concentrations. For pUC19 replicates at five concentrations, coefficients of variance were 0.

Primer design for automated DNA sequencing in a core facility.

We assessed the quality of nine standard primers for automated fluorescent dye terminator DNA sequencing by whether their melting temperatures (Tms) were in the optimal range for DNA sequencing, and the degree to which their sequences matched the sequences of 36 common vectors. The M13F (-21/-20), M13F (-41/-40), M13R, and T7R primers showed optimal physicochemical characteristics and were not redesigned. The M13R (-41/-40), T3, and SP6 primers showed mismatches and/or Tm values outside of the optimal range and were redesigned by these two criteria.

Biotechnology core laboratories: An overview.

An assessment of the capabilities of biotechnology core facilities requires access to current data on state-of-the-art technologies, personnel, space, services, financial issues, and the demand for such facilities. Data on these topics should be useful to researchers, facility personnel, administrators, and granting agencies.To obtain such data, the Association of Biomolecular Resource Facilities (ABRF) conducted a general survey on the operation and technical capabilities of core facilities.

Automated purification and quantification of oligonucleotides.

We have developed automated methods for the trityl-on purification and quantification of synthetic oligonucleotides. Oligonucleotide purification is by solid-phase extraction cartridges using Amberchrom CG-50 resin on an XYZ-axis robotic system. Quantification is by OD260nm using an online UV-visible spectrophotometer with sipper.

Molecular recognition of tRNA by tRNA pseudouridine 55 synthase.

Escherichia coli tRNA pseudouridine 55 synthase catalyzes pseudouridine formation at U55 in tRNA. A 17 base oligoribonucleotide analog of the T-arm was equivalent to intact native tRNA as a substrate for pseudouridine 55 synthase, viz., the features for substrate recognition by this enzyme are completely contained within the T-arm.

Recognition of the T-arm of tRNA by tRNA (m5U54)-methyltransferase is not sequence specific.

tRNA (m5U54)-methyltransferase (RUMT) catalyzes the methylation of U54 of tRNAs. In contrast to enzymes which recognize a particular tRNA, RUMT recognizes features common to all tRNAs. We have shown that these features reside in the T-arm of tRNA and constructed a minimal consensus sequence for RUMT recognition and catalysis (Gu et al.

Interaction of tRNA (uracil-5-)-methyltransferase with NO2Ura-tRNA.

tRNA in which uracil is completely replaced by 5-nitro-uracil was prepared by substituting 5-nitro-UTP for UTP in an in vitro transcription reaction. The rationale was that the 5-nitro substituent activates the 6-carbon of the Ura heterocycle towards nucleophiles, and hence could provide mechanism-based inhibitors of enzymes which utilize this feature in their catalytic mechanism. When assayed shortly after mixing, the tRNA analog, NO2Ura-tRNA, is a potent competitive inhibitor of tRNA-Ura methyl transferase (RUMT).

Delta 6-desaturase: improved methodology and analysis of the kinetics in a multi-enzyme system.

A new method of assay for the delta 6-desaturation of linoleic acid was developed. This method, which uses HPLC for separation of the fatty acid substrate and product, exhibited a lower coefficient of variation (0.3%) than the reported TLC method (3.

Construction of a synthetic gene for the metalloregulatory protein MerR and analysis of regionally mutated proteins for transcriptional regulation.

The transcriptional control protein MerR is a metalloregulatory switch, activating transcription of a mercury resistance operon in the presence of mercuric ions and repressing transcription in their absence. We report here the construction and utilization of a synthetic merR gene and a single-copy merT'-lacZ fusion reporter for mutagenic analysis of the MerR protein's function. Site-directed mutagenesis of clustered acidic residues within the central region of the MerR protein indicated that these residues are important to the protein's ability to repress transcription.

Kinetic mechanism of human erythrocyte acidic isoenzyme rho.

The kinetic mechanism has been determined for human glutathione S-transferase rho (rho), an isoenzyme related to the human pi (pi) isoenzyme. The kinetic mechanism was investigated by both non-linear regression studies and the analysis of primary and secondary plots, utilizing initial rate and product inhibition data. It was concluded that human isoenzyme rho obeys a random sequential Bi-Bi rapid equilibrium mechanism with the formation of an enzyme-substrate-product (enzyme-CDNB-conjugate) dead-end complex.

Biotechnology core facilities: trends and update.

A survey of 128 biotechnology core facilities has provided data on the finances, services, space requirements, and personnel. An average facility had four full-time personnel and 7.5 major instrument systems, and occupied 969 sq.

Automated purification of synthetic oligonucleotides.

We have automated the trityl-on purification of oligonucleotides by use of an XYZ axis robotic solid-phase extraction system. This greatly decreased the preparation time required for oligonucleotide purification. After about 15 min for set up of the samples and instrument, the oligonucleotides are automatically purified with a 15-min run time per sample.

Reversible inhibition of rat hepatic glutathione S-transferase 1-2 by bilirubin.

The inhibition of rat hepatic glutathione (GSH) S-transferase 1-2 by bilirubin exhibited pseudo first-order kinetics with k(obs) values of 0.0214 +/- 0.0005 and 0.

Explanation of the non-hyperbolic kinetics of the glutathione S-transferases by the simplest steady-state random sequential Bi Bi mechanism.

We have demonstrated that the simplest steady-state random sequential Bi Bi mechanism is sufficient to explain the previously reported non-hyperbolic kinetics of glutathione S-transferase 3-3 [Pabst MJ et al., J Biol Chem 249: 7140-7150, 1974; Jakobson I et al., Biochem J 177: 861-868, 1979].

Bifunctional thymidylate synthase-dihydrofolate reductase in protozoa.

Protozoa contain thymidylate synthase (TS) and dihydrofolate reductase (DHFR) on the same polypeptide. In the bifunctional protein, the DHFR domain is on the amino terminus, TS is on the carboxyl terminus, and the two domains are separated by a junction peptide of varying size depending on the source. The native protein is composed of a dimer of two such subunits and is 110-140 kDa.

Thymidylate synthase-dihydrofolate reductase in protozoa.

In protozoa, thymidylate synthase (TS) and dihydrofolate reductase (DHFR) exist on the same polypeptide. The DHFR domain is on the amino terminus, TS is on the carboxy terminus, and the domains are separated by a junction peptide of varying size depending on the source. The native protein is a dimer of two such subunits and is 110-140 kDa.

A rapid equilibrium random sequential bi-bi mechanism for human placental glutathione S-transferase.

Double-reciprocal plots of initial-rate data for the conjugation of 1-chloro-2,4-dinitrobenzene (CDNB) and GSH by human placental GSH S-transferase pi were linear for both substrates. Computer modelling of the initial-rate data using nonlinear least-squares regression analysis favoured a rapid equilibrium random sequential bi-bi mechanism, over a steady-state random sequential mechanism or a steady-state or rapid equilibrium ordered mechanism. KGSH was calculated as 0.

Site-directed inactivation of human lung acidic glutathione S-transferase by 1-chloro-2,4-dinitrobenzene in the absence of glutathione.

Human lung acidic glutathione S-transferase is irreversibly inhibited by 1-chloro-2,4-dinitrobenzene (CDNB) in the absence of the co-substrate glutathione (GSH). The time-dependent inactivation is pseudo-first-order and demonstrates saturation kinetics, suggesting that inactivation occurs from an EI complex. The Ki was 0.

Halothane: inhibition and activation of rat hepatic glutathione S-transferases.

Multiple halothane anesthesias (1.25 MAC for 1 hr on 3 alternate days) of male Long-Evans rats initially decreased by up to 30% and subsequently increased to up to 185% liver cytosolic glutathione S-transferase activity toward 1-chloro-2,4-dinitrobenzene, 3,4-dichloro-1-nitrobenzene and trans-4-phenyl-3-buten-2-one and glutathione peroxidase activity. Halothane rapidly and reversibly activated hepatic cytosolic glutathione S-transferases and purified isoenzyme 1-2 but not isoenzymes 1-1 and 3-3.

Kinetics and thermodynamics of the interaction of 5-fluoro-2'-deoxyuridylate with thymidylate synthase.

Thymidylate synthase (TS), 5-fluorodeoxyuridylate (FdUMP), and 5,10-methylenetetrahydrofolate (CH2-H4folate) form a covalent complex in which a Cys thiol of TS is attached to the 6-position of FdUMP and the one-carbon unit of the cofactor is attached to the 5-position. The kinetics of formation of this covalent complex have been determined at several temperatures by semirapid quench methods. Together with previously reported data the results permit calculation of every rate and equilibrium constant in the interaction.