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PubMedDate not supplied

Application of a semi-automated SOS chromotest for measuring genotoxicities of complex environmental mixtures containing polycyclic aromatic hydrocarbons.

Soxhlet-extracted samples of standard reference materials (SRMs) 1649 (PAR1: urban dust/organics) and 1650 (PAR2: diesel particulate matter) from the U.S. Institute of Standards and Technology were tested for induction of SOS functions using a semi-automated version of the SOS chromotest with Escherichia coli PQ37. Concentrations of 10 polycyclic aromatic hydrocarbons in the extracts were determined using reversed-phase HPLC. Only the diesel particulate matter (PAR2) extracts expressed SOS induction activity, which decreased when metabolic activation was used. Mutagenic PAH compounds (e.g., chrysene) were found in higher concentrations in the PAR2 extracts than in the PAR1 extracts but this could not explain the genotoxicity while it was mainly exhibited without metabolic activation. The direct genotoxic activity of the diesel particulate matter sample PAR2 is probably caused by nitroaromatic compounds; this was also supported by parallel studies with the Ames/Salmonella assay.

Air Pollutants↗
PubMed1989

Immunotoxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin in a complex environmental mixture from the Love Canal.

The organic phase of the leachate (OPL) from the Love Canal chemical dump site contains more than 100 organic compounds including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The immunotoxic potential of OPL was determined in two mouse strains which differ in their sensitivity to aromatic hydrocarbon (Ah) receptor-mediated toxicity. OPL was administered in corn oil in a single oral gavage to male BALB/cByJ (Ahb/Ahb) mice (0.5, 0.8, or 1.1 g/kg) and DBA/2J (Ahd/Ahd) mice (0.6, 0.9, or 1.3 g/kg). TCDD was similarly administered at 0.25, 1.0, 4.0, or 16.0 micrograms/kg. Two days later all mice were immunized with sheep erythrocytes (SRBC). The antibody response (PFC) and organ weights were evaluated 4 days later. OPL produced thymic atrophy and hepatomegaly in both strains at all dose levels. The PFC/spleen in BALB/cByJ mice was significantly reduced at the three doses to 34, 13, and 15%, respectively, of the control response. Serum anti-SRBC antibody levels and relative spleen weights were also reduced. The only immune effect in the DBA/2J mice was a decrease of the PFC/spleen to 58% of the control at the highest dose. TCDD decreased the relative thymus and spleen weights only in BALB/cByJ mice. However, TCDD produced hepatomegaly, a decrease in serum antibody, and a decrease in PFC/spleen in both BALB/cByJ and DBA/2J mice to 3 and 15%, respectively, at 16 micrograms/kg. Thus, the TCDD dose required to cause a 50% suppression (ED50) of PFC/spleen for the BALB/cByJ and DBA/2J strains was 1.84 and 3.89 micrograms/kg, respectively. The ED50 for OPL was 0.24 g/kg in BALB/cByJ mice. The TCDD concentration in the OPL was estimated to be 7.6 ppm, which agrees closely with the chemical analysis (3 ppm). The results suggest that the immunosuppression caused by OPL in BALB/cByJ mice was primarily due to TCDD, that the non-TCDD components of OPL diminished the TCDD immunotoxicity in the DBA/2J strain, and that the thymic atrophy and hepatomegaly were caused primarily by the non-TCDD components of the OPL.

Animals↗
PubMed1987

Chromatography of complex protein mixtures.

This review has shown that a variety of chromatographic techniques are available for fractionating proteins. Fortunately, high-quality columns of every type described in this review are commercially available. Most water-soluble proteins may be eluted from size-exclusion, hydrophobic-interaction, ion-exchange, metal chelate, and bioaffinity columns with ease. When this is the case, high recovery and retention of biological activity are the norm. The exception is reversed-phase chromatography where the organic solvents and acids used in polypeptide elution denature many proteins. When problems do occur, they are generally the result of unique structural features of the protein. Very hydrophobic proteins have presented the biggest problem in that they are difficult to solubilize, particularly with retention of biological activity. It has been found that zwitterionic and non-ionic detergents are the most suitable solubilizing agents, but urea has also been used in cases where hydrophobic interacts are not as strong. Unfortunately, there is still an element of trial-and-error in selecting the most suitable solubilizing agent. Heterogeneous glycosylation of proteins also presents a problem. Both neutral and charged monosaccharides can be incorporated into proteins through multiple steps at several sites. Thus, there is the potential in a sample for a large number of glycoprotein species which have the same polypeptide backbone and differing amounts of oligosaccharide. A problem arises when size-exclusion, ion-exchange, hydrophobic-interaction, reversed-phase and bioaffinity systems begin to discriminate between these very similar glycoprotein species. Chromatographic peaks can become very broad, due to incomplete fractionation, and the polypeptide chain of interest can be associated with multiple peaks. The separation of glycoproteins requires much more study before logical procedures can be suggested for column selection and operation. Aggregated species are another class of proteins which present occasional problems. Multimeric proteins are adsorbed to sorbents by a series of forces, among which are hydrogen bonding, hydrophobic interactions, and electrostatic forces. These forces are also responsible for the maintenance of quaternary structure in proteins. When the same forces dominate both retention of protein structure and adsorption at the sorbent surface, the quaternary structure of the protein can be disrupted during elution. Very basic proteins also present a problem in some cases. Columns with residual negative charges, such as a silica-based reversed-phase column, adsorb anionic species so strongly that they are difficult to elute.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2004

Implications of column peak capacity on the separation of complex peptide mixtures in single- and two-dimensional high-performance liquid chromatography.

Column peak capacity was utilized as a measure of column efficiency for gradient elution conditions. Peak capacity was evaluated experimentally for reversed-phase (RP) and cation-exchange high-performance liquid chromatography (HPLC) columns, and compared to the values predicted from RP-HPLC gradient theory. The model was found to be useful for the prediction of peak capacity and productivity in single- and two-dimensional (2D) chromatography. Both theoretical prediction and experimental data suggest that the number of peaks separated in HPLC reaches an upper limit, despite using highly efficient columns or very shallow gradients. The practical peak capacity value is about several hundred for state-of-the-art RP-HPLC columns. Doubling the column length (efficiency) improves the peak capacity by only 40%, and proportionally increases both the separation time and the backpressure. Similarly, extremely shallow gradients have a positive effect on the peak capacity, but analysis becomes unacceptably long. The model predicts that a 2D-HPLC peak capacity of 15,000 can be achieved in 8 h using multiple fraction collection in the first dimension followed by fast RP-HPLC gradients employing short, but efficient columns in the second dimension.

Chromatography, High Pressure Liquid↗
PubMed2004

The use of enzyme mixtures for complex biosyntheses.

Biocatalysis is currently employed to produce known substances more economically and for the synthesis of new compounds. Increased production or novel product synthesis can be achieved through the use of mutant organisms, tailored enzymes or novel combinations of enzymes in reactors. These complex biosyntheses, once only in the realm of the biopharmaceutical industry, have now been embraced by the food and textile industries and are finding geochemical and environmental applications. New uses are dictating novel methods of manufacture that utilize knowledge of systems level biology. Increased understanding of the functional interaction of proteins and protein-protein networks is also altering the practice of in vitro biosynthesis.

Biotechnology↗
PubMed2004

Amplified fragment length polymorphism measures proportions of malaria parasites carrying specific alleles in complex genetic mixtures.

We are interested in developing a method for the identification of those genes in malaria parasites which underlie a variety of selectable phenotypes of the parasites including drug resistance and strain-specific immunity. A key aspect of our approach is to subject a genetically mixed population of malaria parasites to a specific phenotypic selection pressure such as the administration of an antimalarial drug and then identify genetic markers affected by the selection. Our aim, therefore, is to be able to identify those genetic markers carried by sensitive parasites which disappear from the population after selection as they should be closely linked to the locus determining the phenotype involved. We have previously identified more than 800 amplified fragment length polymorphisms (AFLP) distinguishing two cloned strains of the rodent malaria parasite Plasmodium chabaudi chabaudi and distributed across the whole of the parasites' genome. Here we evaluate the possibility that the intensities of these AFLP bands are quantitatively related to the proportions of parasite DNA which bear these markers in mixtures of genetically different parasites. We prepared mixtures of DNA and parasitised blood from different mixtures of two genetically distinct clones (AS and AJ) of P. c. chabaudi and analysed AFLP markers amplified from them. The results show that the relative band intensities of AFLP markers are, indeed, linearly related to the proportions of parasite DNA in a genetically mixed sample. The precision of the method is sufficient to detect reliably the effects of phenotypic selection at loci closely linked to a genetic locus under selection.

Alleles↗
PubMed2003

Direct observation of lipid domains in free standing bilayers: from simple to complex lipid mixtures.

The direct observation of temperature-dependent lipid phase equilibria, using two-photon excitation fluorescence microscopy on giant unilamellar vesicles (GUVs) composed of different lipid mixtures, provides novel information about the physical characteristics of lipid domain coexistence. Physical characteristics such as shape, size, and time evolution of different lipid domains are not directly accessible from the traditional experimental approaches that employ either small and large unilamellar vesicles or multilamellar vesicles. In this short presentation, I will address the most relevant findings reported from our laboratory, regarding the direct observation of lipid domain coexistence at the level of single vesicles in artificial and natural lipid mixtures. In addition, key points concerning our experimental approach will be discussed. The unique advantages of the fluorescent probe 6-dodecanoyl-2-dimethylamino-naphthalene (LAURDAN) under the two-photon excitation fluorescence microscopy will be particularly addressed, especially, the possibility to obtain information about the phase-state of different lipid domains directly from the fluorescent images.

2-Naphthylamine↗
PubMed1985

Automated tandem high-performance liquid chromatographic system for separation of extremely complex peptide mixtures.

We have developed an automated tandem chromatography system, which consists of a combination of ion-exchange column chromatography and reversed-phase column chromatography. The system is composed of two independent high-performance liquid chromatography assemblies, in each of which programmed elution is carried out by a computer-assisted controller. A peptide mixture is applied to an ion-exchange column and is eluted in a stepwise manner. The eluent from the first column is introduced directly into the second, reversed-phase column, which is connected in tandem through a tee tube. After application of two column volumes of the eluent, reversed-phase chromatography is performed by linear gradient elution. Stepwise elution for ion-exchange chromatography and the gradient elution for reversed-phase chromatography are synchronized by a computer program. The resolving power and the reproducibility of the method were tested by using a tryptic digest of human ceruloplasmin [molecular weight 132 000 daltons (132 kDa)]. By this method, the digest was resolved reproducibly into several hundred peaks within 16 h. All of the four glycopeptides expected to be obtained by tryptic digestion were purified easily from the whole digest of the protein. Comparison of the peptide maps between a single-chain and a degraded form of ceruloplasmin facilitated the identification of two tryptic peptides, derived from the carboxyl-terminal regions of 67 kDa and 50 kDa fragments of the degraded form, which lack the carboxyl-terminal arginine and lysine residues, respectively. The method may be applicable to comparative peptide mapping of very large proteins exhibiting molecular microheterogeneity, such as carbohydrate or genetic variants; it also can be used complementarily for sequence support of DNA sequencing as well as for preparative purification of peptides as a strategy of protein sequencing of very large proteins.

Ceruloplasmin↗
PubMed1983

Reversed-phase high-performance liquid chromatography of Escherichia coli ribosomal proteins. Characteristics of the separation of a complex protein mixture.

We have previously reported the application of reversed-phase high-performance liquid chromatography (RP-HPLC) to the separation of Escherichia coli ribosomal proteins (A. R. Kerlavage, L. Kahan and B. S. Cooperman, Anal. Biochem., 123 (1982) 342-348; A. R. Kerlavage, T. Hasan and B. S. Cooperman, J. Biol. Chem., in press). In the present studies RP-HPLC is shown to yield much greater resolution of these proteins than does size-exclusion HPLC. In addition, we report on various aspects of RP-HPLC of ribosomal proteins including column capacity, resolution, reproducibility, recovery, separation of irreversibly denatured protein, and analysis of affinity-labeled ribosomal protein. The capacity of analytical columns was found to range from several micrograms to several milligrams with minimal loss in resolution and highly reproducible retention values. Recovery varied from protein to protein and ranged from 27% to 91%, with an average total protein recovery of 70%. The partitioning of several proteins between two peaks was shown to be due to irreversible denaturation of a small fraction. Finally, the utility of RP-HPLC in the study of the ribosome was demonstrated by analyses of [3H]puromycin-labeled ribosomal proteins, and the demonstration that labeling slightly alters protein elution.

Bacterial Proteins↗
PubMed1990

Simple method for the analysis of glycerol enol ethers derived from plasmalogens in complex lipid mixtures and subsequent determination of the aldehydic components by gas chromatography-mass spectrometry.

Glycerol enol ethers, obtained by the reduction of plasmalogens with lithium aluminum hydride, can be converted into glycerol alk-(1)-enyl ether bismethyl ethers with diazomethane in the presence of silica gel. Their mass spectra allow the position of the enol ether group in glycerol unit to be deduced. Branches in the aldehydic components of the glycerol alk-(1)-enyl ether bismethyl ethers can be identified unequivocally by preparation of the 2-alkyl-1,3-dithiolanes, desulphurization with Raney nickel and deuterium to hydrocarbons and subsequent analysis by gas chromatography-mass spectrometry.

Aldehydes↗
PubMed1995

A microscale electrospray interface for on-line, capillary liquid chromatography/tandem mass spectrometry of complex peptide mixtures.

A microcapillary liquid chromatography (HPLC) system designed for the gradient elution of peptide and protein samples at flow rates < 1 microL/min has been coupled to a triple-sector quadrupole mass spectrometer via a simple sheathless electrospray interface (microspray). The microspray interface used a flame-drawn, uncoated, fused silica needle with tip outer diameters in the range of 15-20 microm and an opening less than 5 microm in diameter. Online sample filtration to prevent clogging of the drawn needle was accomplished by using a hydrophilic PVDF membrane filter integrated into the needle assembly. The spray potential (0.5-1 kV) was applied directly to the sample stream through the capillary union. Stable electrospray conditions were obtained over the full range of the gradient (0-90% acetonitrile in water) and was generally independent of flow rate. Both off-line and online analyses of proteins and peptide digest mixtures were performed at sample levels less than 10 fmol. HPLC parameters could be optimized for either rapid LC/MS analysis or enhanced performance in LC/MS/MS experiments by modulation of the eluting peak widths. Additionally, flow could be greatly reduced as selected components pass through the interface to prolong the time available to collect mass spectral data. The reduced spectral background and peak width manipulation facilitated the acquisition of peptide production spectra (MS/MS) using real-time, automated instrument control procedures.

Chromatography, High Pressure Liquid↗
PubMed2002

Acid-labile isotope-coded extractants: a class of reagents for quantitative mass spectrometric analysis of complex protein mixtures.

Quantitative mass spectrometry using stable isotope-labeled tagging reagents such as isotope-coded affinity tags has emerged as a powerful tool for identification and relative quantitation of proteins in current proteomic studies. Here we describe an integrated approach using both automated two-dimensional liquid chromatography/ mass spectrometry (2D-LC/MS) and a novel class of chemically modified resins, termed acid-labile isotope-coded extractants (ALICE), for quantitative mass spectrometric analysis of protein mixtures. ALICE contains a thiol-reactive group that is used to capture all cysteine (Cys)-containing peptides from peptide mixtures, an acid-labile linker, and a nonbiological polymer. The acid-labile linker is synthesized in both heavy and light isotope-coded forms and therefore enables the direct relative quantitation of peptides/proteins through mass spectrometric analysis. To test the ALICE method for quantitative protein analysis, two model protein mixtures were fully reduced, alkylated, and digested in solution separately and then Cys-containing peptides covalently captured by either light or heavy ALICE. The reacted light and heavy ALICE were mixed and washed extensively under rigorous conditions and the Cys-containing peptides retrieved by mild acid-catalyzed elution. Finally, the eluted peptides were directly subjected to automated 2D-LC/MS for protein identification and LC/MS for accurate relative quantitation. Our initial study showed that quantitation of protein mixtures using ALICE was accurate. In addition, isolation of Cys-containing peptides by the ALICE method was robust and specific and thus yielded very low background in mass spectrometric studies. Overall, the use of ALICE provides improved dynamic range and sensitivity for quantitative mass spectrometric analysis of peptide or protein mixtures.

Amino Acid Sequence↗