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PubMed2003

In-field spatial variability in the degradation of the phenyl-urea herbicide isoproturon is the result of interactions between degradative Sphingomonas spp. and soil pH.

Substantial spatial variability in the degradation rate of the phenyl-urea herbicide isoproturon (IPU) [3-(4-isopropylphenyl)-1,1-dimethylurea] has been shown to occur within agricultural fields, with implications for the longevity of the compound in the soil, and its movement to ground- and surface water. The microbial mechanisms underlying such spatial variability in degradation rate were investigated at Deep Slade field in Warwickshire, United Kingdom. Most-probable-number analysis showed that rapid degradation of IPU was associated with proliferation of IPU-degrading organisms. Slow degradation of IPU was linked to either a delay in the proliferation of IPU-degrading organisms or apparent cometabolic degradation. Using enrichment techniques, an IPU-degrading bacterial culture (designated strain F35) was isolated from fast-degrading soil, and partial 16S rRNA sequencing placed it within the Sphingomonas group. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial community 16S rRNA revealed two bands that increased in intensity in soil during growth-linked metabolism of IPU, and sequencing of the excised bands showed high sequence homology to the Sphingomonas group. However, while F35 was not closely related to either DGGE band, one of the DGGE bands showed 100% partial 16S rRNA sequence homology to an IPU-degrading Sphingomonas sp. (strain SRS2) isolated from Deep Slade field in an earlier study. Experiments with strains SRS2 and F35 in soil and liquid culture showed that the isolates had a narrow pH optimum (7 to 7.5) for metabolism of IPU. The pH requirements of IPU-degrading strains of Sphingomonas spp. could largely account for the spatial variation of IPU degradation rates across the field.

Biodegradation, Environmental↗
PubMed1994

Inhibition of leukotriene B4 synthesis does not prevent development of acute renal failure following storage and transplantation.

Compound BW B70C, a selective 5-lipoxygenase inhibitor was tested for its ability to reduce inflammatory damage in an in vivo rabbit model of renal storage and transplantation. Kidneys were stored at 0-2 degrees C for 48 hr prior to autografting. In controls, renal vein LTB4 levels rose significantly after 30 min reperfusion but fell after 2 hr to baseline. TxB2 levels remained at baseline for the 6 hr measured. 6-k-PGF1 alpha levels rose significantly after 1 hr of reperfusion and remained elevated thereafter. Histology after 6 hr reperfusion showed moderate-to-severe cortical edema and mild congestion. Infused colloidal carbon was retained in the perivascular area in a narrow band at the corticomedullary junction, indicating a zone of vascular permeability. At 3 days after transplant, kidneys exhibited widespread tubular necrosis and calcification but little inflammation. Serum creatinine and urea peaked between days 3 and 5. 3/6 rabbits showed no symptoms of renal failure after 3 weeks. Pretreatment with BW B70C prevented the increase in LTB4 but had little effect on TxB2 and 6-k-PGF1 alpha levels. Histology showed no amelioration of cortical edema at 6 hr and congestion and hemorrhage were exacerbated. BW B70C had no effect on either colloidal carbon retention or distribution but did significantly reduce tubular necrosis and calcification at day 3. There was very little inflammatory infiltrate. BW B70C treatment did not improve the long-term viability of transplanted kidneys: 2/6 rabbits showed no symptoms of renal failure after 3 weeks. These data indicate that inhibition of LTB4 synthesis by BW B70C does not prevent the development of acute renal failure following 48 hr hypothermic storage and transplantation.

Acute Kidney Injury↗
PubMed1996

Detection of DNA-crosslinking agents with the alkaline comet assay.

The single cell gel electrophoresis, or comet assay, under alkaline conditions is a sensitive, simple and rapid method for the detection of DNA damage at the individual cell level. Its applicability as an indicator for the DNA crosslinking potency of a test substance was investigated in human white blood cells by combined treatment with the DNA damaging agent methyl methanesulphonate (MMS) for 2 hr at 37 degrees C. The known crosslinking agents cisplatinum, mitomycin C and formaldehyde, and the formaldehyde releasers diazolidinyl urea and dimethylol urea, were shown to reduce MMS-induced DNA migration in the comet assay in a concentration-dependent manner. Two other protocols, adding MMS to the cells before or after treatment with a crosslinking agent, were carried out and achieved similar results. The results of this study indicate that the comet assay is a useful tool for the detection of crosslinking agents. Advantages and limitations of this method compared to the alkaline elution technique are discussed.

Adult↗
PubMed1999

Electrically driven microseparation methods for pesticides and metabolites. II: on-line and off-line preconcentration of urea herbicides in capillary electrochromatography.

Capillary electrochromatography (CEC) was introduced to the separation of nine important urea herbicides using octadecyl-silica (ODS) capillary columns that were specially designed to allow the realization of a relatively strong electroosmotic flow (EOF) and, in turn, fast separations. The ODS stationary phase was intentionally prepared to have a low surface coverage in octadecyl ligands in order to ensure a strong EOF. This ODS stationary phase of low surface coverage exhibited the usual reversed-phase chromatographic behavior as was manifested by the linearity of plots of log kappa versus the percent organic modifier in the mobile phase. The nature of the organic modifier of the mobile phase influenced the order of elution as well as the separation efficiency of the nine urea herbicides. Mobile phases containing acetonitrile yielded higher separation efficiency (by a factor of 1.5) than methanol-containing mobile phases. This was attributed to the higher mass transfer resistances of the solute in and out of the pores in the presence of the more viscous methanol-containing mobile phases. Due to the relatively strong affinity of the urea herbicides to the ODS stationary phase, on-line preconcentration consisting of prolonged injections allowed the determination of 10(-5) M urea herbicide samples using a UV detector without sacrificing separation efficiency. This was further decreased to 10(-7) M when the prolonged injection was preceded by the injection of a plug of water. The plug of water (the more retentive mobile phase) brought about an enhanced accumulation of the dilute samples into a narrow band at the inlet of the CEC column. When this on-column sample enrichment approach was combined with an off-line sample preconcentration step, which consisted of a solid-phase extraction process, ultra dilute samples of 10(-10) M (0.1 ppb) could be detected.

Chromatography, High Pressure Liquid↗
PubMed2000

Improved matrix-assisted laser desorption/ionization mass spectrometric analysis of tryptic hydrolysates of proteins following guanidination of lysine-containing peptides.

Analysis of tryptic digests of proteins using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry commonly results in superior detection of arginine-containing peptides compared with lysine-containing counterparts. The effect is attributable in part to the greater stability of the arginine-containing peptide ions associated with the sequestration of the single ionizing proton on the arginine side-chain. Reaction of peptides with O-methylisourea resulted in conversion of lysine to homoarginine residues with consequent improved detection during MALDI-MS. Analysis of the underivatized tryptic digest of the yeast protein, enolase, revealed peptides representing 20% of the protein; the corresponding figure after derivatization was 46%.

Alcohol Dehydrogenase↗
PubMed2000

Enhancing the intensities of lysine-terminated tryptic peptide ions in matrix-assisted laser desorption/ionization mass spectrometry.

Tryptic digests of three proteins are reacted with O-methylisourea in order to convert lysine residues to homoarginines. The resulting homoarginine-terminated peptides exhibit more intense MALDI mass spectral peaks than their lysine-terminated predecessors. This simple chemical reaction should therefore facilitate protein sequencing and mass mapping.

Amino Acid Sequence↗
PubMed2000

Derivatization procedures to facilitate de novo sequencing of lysine-terminated tryptic peptides using postsource decay matrix-assisted laser desorption/ionization mass spectrometry.

Guanidination of the epsilon-amino group of lysine-terminated tryptic peptides can be accomplished selectively in one step with O-methylisourea hydrogen sulfate. This reaction converts lysine residues into more basic homoarginine residues. It also protects the epsilon-amino groups against unwanted reaction with sulfonation reagents, which can then be used to selectively modify the N-termini of tryptic peptides. The combined reactions convert lysine-terminated tryptic peptides into modified peptides that are suitable for de novo sequencing by postsource decay matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The guanidination reaction is very pH dependent. Product yields and reaction kinetics were studied in aqueous solution using either NaOH or diisopropylethylamine as the base. Methods are reported for derivatizing and sequencing lysine-terminated tryptic peptides at low pmole levels. The postsource decay (PSD) MALDI tandem mass spectra of a model peptide (VGGYGYGAK), the homoarginine analog and the sulfonated homoarginine analog are compared. These spectra show the influence that each chemical modification has on the peptide fragmentation pattern. Finally, we demonstrate that definitive protein identifications can be achieved by PSD MALDI sequencing of derivatized peptides obtained from solution digests of model proteins and from in-gel digests of 2D-gel separated proteins.

Amino Acid Sequence↗
PubMed2001

Fluorescent Pseudomonas isolates from Mississippi Delta oxbow lakes: in vitro herbicide biotransformations.

Fluorescent pseudomonads were a major component [log (10) 4.2-6.1 colony-forming units mL-1] of the culturable heterotrophic gram-negative bacterioplankton observed in three Mississippi Delta oxbow lakes in this study. Pure cultures of fluorescent pseudomonads were isolated from three Mississippi Delta oxbow lakes (18 per lake), using selective media S-1. Classical physiological tests and Biolog GN plates were used in criteria for taxonomic identification. Most isolates were identified as biotypes of Pseudomonas fluorescens 55% (II), 7% (III), and 25% (V). About 7% of the isolates were identified as P. putida and 7% as non-fluorescent Pseudomonas-like. Cell suspensions of these isolates were tested for their ability to metabolize/co-metabolize six 14C-radiolabeled herbicides (2,4-dichlorophenoxyacetic acid (2,4-D), cyanazine, fluometuron, metolachlor, propanil, and trifluralin) that are commonly used for crop production in this geographical area. Almost all (53 of 54) isolates transformed trifluralin via aromatic nitroreduction. Most isolates (70%) dechlorinated metolachlor to polar metabolites via glutathione conjugation. About 60% of the isolates hydrolyzed the amide bond of propanil (a rice herbicide) to dichloroaniline, with the highest frequency of propanil-hydrolyzing isolates observed in the lake from the watershed with rice cultivation. All propanil-hydrolyzing isolates were identified as P. fluorescens biotype II. No metabolism of cyanazine or fluometuron was observed by any isolates tested, indicating little or no potential for N-dealkylation among this group of bacterioplankton. No mineralization of 2,4-D labeled in either the carboxyl or ring position was observed. These results indicate that reductive and hydrolytic pathways for herbicide co-metabolism (aromatic nitroreduction, aryl acylamidase, and glutathione conjugation) are common in Mississippi Delta aquatic fluorescent pseudomonads; however, the potential for certain oxidative transformations (N-dealkylation, cyano group oxidation) may be rare in this group of bacterioplankton.

2,4-Dichlorophenoxyacetic Acid↗
PubMed2006

Solvent-induced lysozyme gels: effects of system composition and temperature on structural and dynamic characteristics.

The gelation process of lysozyme in water/tetramethylurea in the presence of salt was investigated as a function of temperature and system composition by rheology, infrared spectroscopy, and microcalorimetry. Times and temperatures of gelation were determined from the variation of the storage (G') and loss (G'') moduli. It was found that gelation times follow exponential decays with both protein and tetramethylurea (TMU) concentrations and with temperature. The activation energy for the overall process shows a linear dependence on TMU mass fraction. A strongly increased beta-sheet content and reduced alpha-helix occur with the increase of TMU concentration in the binary solvent. Also, a linear decrease of lysozyme denaturation temperature and enthalpy on TMU concentration is found for the TMU mass fraction up to 0.5, above which no denaturation signal can be detected.

Calorimetry, Differential Scanning↗
PubMed2004

A method for determination of dimethyl benzoylphenyl urea (BPU) in human plasma by using LC/UV.

Dimethyl benzoylphenyl urea (BPU) inhibited tubulin polymerization, caused microtubule depolymerization in vitro and demonstrated activity against solid tumors. BPU is being tested in phase I clinical trials. A rapid and specific method using LC/UV has been developed for quantitation of BPU in human heparin-containing plasma to perform pharmacokinetic and pharmacodynamic studies. BPU is extracted from plasma into acetonitrile:n-butyl-chloride using paclitaxel as the internal standard and separated on a Waters Symmetry C18 (3.9 x 150 mm, 5 microm) column with acetonitrile-water mobile phase (70:30, v/v) using isocratic flow at 1 mL/min for a run time of 5 min. Ultraviolet detection was utilized and performed at 225 nm for BPU and paclitaxel. The retention times were 1.9 min for paclitaxel and 4.1 min for BPU. Calibration curves were generated over the range of 0.01-10 microg/mL with coefficient of determination of > 0.99. The values for within-day and between-day precision were < or = 17.0% at the LLOQ and < or = 7.4% at the low, medium and high quality controls; accuracy was +/- 5.4%. Following administration of BPU 320 mg as a weekly oral dose to a patient with advanced solid tumor malignancies, the maximum plasma concentration was 2 micro g/mL and concentrations were quantifiable up to 168 h after administration. The lower limit of quantitation of 0.01 microg/mL allows for successful measurement of plasma concentrations in patients.

Calibration↗
PubMedDate not supplied

'Laterally aggregated' polyacrylamide gels for electrophoresis.

A new method is described for producing highly porous polyacrylamide matrices: polymerization in presence of a preformed hydrophilic polymer. If a standard mixture of monomers (e.g., 5%T, 4%C) is polymerized in presence of, e.g., polyethylene glycol (PEG) 10 kDa, lateral chain aggregation occurs, with formation of large pore sizes. In PEG 10 kDa, the transition from a small- to a large-pore gel is clearly apparent at 0.5% PEG addition and reaches a plateau already at 2.5% PEG. Even with shorter PEG fragments (6.2 and 1 kDa) this transition occurs, but with progressively larger amounts of PEG in solution (up to 25% for the 1 kDa species). Other polymers such as hydroxymethyl cellulose (1000 kDa) and polyvinyl-pyrrolidone (360 kDa and 25 kDa) are also able to elicit this phenomenon. It appears that lateral chain aggregation (before the cross-linking event) is induced via intra-chain hydrogen bonding, since urea and temperature strongly inhibit it, whereas tetramethylurea (an agent quenching hydrophobic interactions) does not hamper it. By scanning electron microscope, it is found that the maximum pore size obtained in a 5%T, 4%C gel in presence of 2.5% PEG 10 kDA is of the order of 0.5 micron, whereas the same 5%T, 4%C control gel would have an average pore diameter of 5 nm. Thus, an increment of pore size of about 2 orders of magnitude is obtained: in these new matrices, a 21000 bp DNA fragment exhibits a much greater migration than in a control gel in which the sample is entrapped at the application site.

Acrylic Resins↗
PubMed1991

Role of the extracellular matrix on the growth and differentiated phenotype of murine colonic adenocarcinoma cells in vitro.

The growth and differentiation characteristics of MAC 15 murine adenocarcinoma cells, derived from routine passage in vivo for growth in vitro on a plastic substrate (MAC15j cells), were compared under conditions in which the cells were seeded onto a substrate of type-I collagen which was either attached to plastic or was released to float free in medium. Cells grown on a plastic substrate consisted of a heterogeneous, largely anaplastic population with a putative enterocytic morphology but with no evidence of junctional complexes or cell polarity typical of an epithelial phenotype. MAC 15j cells from cultures grown on a plastic substrate reestablished a moderate to well-defined degree of differentiation when transplanted back into NMRI mice. When MAC 15j cells were seeded from plastic onto type-I collagen, either attached to plastic or free-floating, tight junctional complexes were formed and the cells began to attain a more recognizable, columnar and polarised epithelial morphology. Cells grown on a type-I collagen gel which was free-floating showed a selective expression of alkaline phosphatase at the apical surfaces of approximately 10% of the cells. This expression was detectable by electron microscope histochemistry but could not be detected biochemically. Treatment of MAC 15j cells grown on a released collagen matrix with tetramethyl-urea (20mM) accelerated the expression of alkaline phosphatase activity at the apical surface as detected by microscopy.

Adenocarcinoma↗
PubMedDate not supplied

Influence of methylamine and N,N'-dimethylurea, the hydrolysis products of methyl isocyanate, on its systemic toxicity.

Subcutaneous administration of the LD50 dose of methyl isocyanate (MIC) to rats induced severe hyperglycaemia, lactic acidosis and uraemia in rats. Neither methylamine (MA) nor N,N'-dimethylurea (DMU), the hydrolysis products of MIC, administered in equimolar doses had any influence on these parameters except for a marginal transient increase in plasma urea by DMU. Methyl isocyanate administration led to haemoconcentration, resulting in an increase in the plasma concentration of total proteins and a decrease in both the plasma concentration of albumin and the plasma cholinesterase activity. The hydrolysis products of MIC had no influence on any of these parameters. Thus, it seems reasonable to suggest that the systemic effects of MIC are caused by MIC per se, in spite of its high hydrolytic instability.

Animals↗
PubMedDate not supplied

Subchronic oral toxicity of a combination of insecticide (HCH) and herbicide (ISP) in male rats.

Rats were treated orally with technical hexachlorocyclohexane (HCH, 12.5, 25 and 50 mg kg-1 day(-1)) and technical isoproturon (ISP 22.5. 45 and 90 mg kg-1 day(-1)) daily for a period of 90 days alone and in combination. Treatment with HCH alone showed mild to severe toxicity and death. Significant changes occurred in liver weight, clinical enzyme profiles, haematological parameters and pathomorphological changes. Treatment with ISP alone did not produce such changes. The combination of HCH and ISP produced changes not suggestive of synergism.

Administration, Oral↗
PubMed2003

Pharmacophore-based molecular docking to account for ligand flexibility.

Rapid computational mining of large 3D molecular databases is central to generating new drug leads. Accurate virtual screening of large 3D molecular databases requires consideration of the conformational flexibility of the ligand molecules. Ligand flexibility can be included without prohibitively increasing the search time by docking ensembles of precomputed conformers from a conformationally expanded database. A pharmacophore-based docking method whereby conformers of the same or different molecules are overlaid by their largest 3D pharmacophore and simultaneously docked by partial matches to that pharmacophore is presented. The method is implemented in DOCK 4.0.

Algorithms↗
PubMed2003

Automated generation of MCSS-derived pharmacophoric DOCK site points for searching multiconformation databases.

All docking methods employ some sort of heuristic to orient the ligand molecules into the binding site of the target structure. An automated method, MCSS2SPTS, for generating chemically labeled site points for docking is presented. MCSS2SPTS employs the program Multiple Copy Simultaneous Search (MCSS) to determine target-based theoretical pharmacophores. More specifically, chemically labeled site points are automatically extracted from selected low-energy functional-group minima and clustered together. These pharmacophoric site points can then be directly matched to the pharmacophoric features of database molecules with the use of either DOCK or PhDOCK to place the small molecules into the binding site. Several examples of the ability of MCSS2SPTS to reproduce the three-dimensional pharmacophoric features of ligands from known ligand-protein complex structures are discussed. In addition, a site-point set calculated for one human immunodeficiency virus 1 (HIV1) protease structure is used with PhDOCK to dock a set of HIV1 protease ligands; the docked poses are compared to the corresponding complex structures of the ligands. Finally, the use of an MCSS2SPTS-derived site-point set for acyl carrier protein synthase is compared to the use of atomic positions from a bound ligand as site points for a large-scale DOCK search. In general, MCSS2SPTS-generated site points focus the search on the more relevant areas and thereby allow for more effective sampling of the target site.

Binding Sites↗