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Results for “Complex Mixtures”

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PubMed1981

Quantitative profiling analysis of organic acids in complex mixtures.

The simultaneous detection and quantitative determination of a very large number of metabolites in physiological fluids or tissues, and the subsequent comparison of these data with reference values, is a process which has commonly been called 'metabolic profiling' analysis. Profiles generated by gas-liquid chromatography on packed or capillary columns are readily analyzed by mass spectrometry, utilizing reverse library search procedures to identify individual components. Emphasis will be given here to procedures for the pre-purification of organic acids from plasma, to the use of quartz capillaries for metabolic profiling analysis, and to the sensitivity of this method for trace components.

Carboxylic Acids↗
PubMed2005

Discovery of complex mixtures of novel long-chain quorum sensing signals in free-living and host-associated marine alphaproteobacteria.

More than 100 bacterial isolates from various marine habitats were screened for AHL production by using gfp reporter constructs based on the lasR system of Pseudomonas aeruginosa and the luxR system of Vibrio fischeri. Of the 67 Alphaproteobacteria tested, most of which belonged into the so-called Roseobacter clade, 39 induced fluorescence in either one or both sensor strains up to 103-fold compared to controls. Acylated homoserine lactones were identified by GC-MS analysis and shown to have chain lengths of C8, C10, C13-C16, and C18. One or two double bonds were often present, while a keto or hydroxyl group occurred only rarely in the side chain. Most strains produced several different AHLs. C18-en-HSL and C18-dien-HSL were produced by Dinoroseobacter shibae, an aerobic anoxygenic phototrophic bacterium isolated from dinoflagellates, and are among the longest AHLs found to date. Z7-C14-en-HSL, which has previously been detected in Rhodobacter sphaeroides, was produced by Roseovarius tolerans and Jannaschia helgolandensis. This signal molecule was synthesised and shown to induce a similar response to the culture supernatant in the respective sensor strain. The widespread occurrence of quorum-sensing compounds in marine Alphaproteobacteria, both free-living strains and those associated to eukaryotic algae, points to a great importance of this signalling mechanism for the adaptation of the organisms to their widely different ecological niches.

Alphaproteobacteria↗
PubMed2003

Nanoelectrospray-based detection and sequencing of substoichiometric amounts of phosphopeptides in complex mixtures.

A novel immobilized metal affinity chromatography (IMAC)-based protocol was successfully used for sample preparation prior to nanoelectrospray-based sequencing of phosphopeptides. In a first step, phosphorylated peptides are detected in an unseparated peptide mixture using precursor ion scanning in the negative ion mode on a triple-quadrupole mass spectrometer. Then the phosphorylated peptides are enriched by passing the sample over an IMAC column and sequenced in the positive ion mode. The IMAC-based enrichment allows the sequencing of phosphorylated peptides even if other, much more abundant, peptides are present at the same m/z value in the original mixture. Using this two-step approach, we are able to combine the simplicity, sensitivity and specificity of precursor ion scanning-based detection of phosphopeptides using the nanoelectrospray ion source with the ability to sequence phosphorylated peptides even if they are present in substoichiometric amounts.

Animals↗
PubMed1995

HIV-1 protease specificity derived from a complex mixture of synthetic substrates.

A rapid and semiquantitative method is described for determining the relative kcat/Km for individual peptides in defined substrate mixtures. The method utilizes electrospray ionization/mass spectrometry alone to semiquantitatively determine relative peptide substrate turnover rates. Unlike previous studies, in which chromatographic separation of individual peptide species was required, this mass spectrometric-based method relies strictly on the ability to ionize and detect simultaneously all peptide species in a defined mixture. Differences in the ion intensities of the individual components before and after incubation with protease are used to semiquantitatively determine preferred substrates. This method was used to the identify preferred peptide substrates for HIV-1 protease. Optimal substrates were identified from a defined synthetic peptide substrate mixture based on Ser-Gln-Asn-Tyr-Pro-Ile-Val, where the P1' proline was substituted with 20 naturally occurring amino acids. The hydrophobic residues Leu, Ile, Val, Phe, and Tyr were preferred in addition to Pro at the P1' site. The results were corroborated by performing the more laborious HPLC/Frit-fast atom bombardment/MS analyses.

Amino Acid Sequence↗
PubMed2002

A strategy for examining complex mixtures of deoxyoligonucleotides using ion-pair-reverse-phase high-performance liquid chromatography, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, and informatics.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and ion-pair-reverse-phase high-performance liquid chromatography (IP-RP HPLC) techniques were combined to determine the sequence identity of short single-stranded deoxyoligonucleotides. This methodology is demonstrated using a commercially available multiplex set of eight primer pairs. The primer pairs were separated and collected by IP-RP HPLC. Partial sequence information for IP-RP HPLC fractions was obtained from analyzing exonuclease digestion products by MALDI-TOF MS. IP-RP HPLC, MALDI-TOF MS, exonuclease digests, and a simple computational algorithm provide an integrated strategy for determining the sequence of short nucleic acid oligomers.

Algorithms↗
PubMed1995

Assessment of the reproductive toxicity of a complex mixture of 25 groundwater contaminants in mice and rats.

The potential reproductive toxicity of a mixture of 25 chemicals (MIX) formulated to simulate contaminated groundwater supplies near hazardous waste dumps was evaluated in CD-1 Swiss mice and Sprague-Dawley rats using the reproductive assessment by continuous breeding protocol. Male and female mice and rats were exposed to MIX in the drinking water at concentrations of 1, 5, and 10% of a technically achievable stock solution. For mice, body weight and feed consumption were not affected by MIX but water consumption was decreased for both the 5 and 10% MIX groups in both F0 and F1 animals. For F0 mice, the number of live pups/litter was decreased at 10% MIX and the number of females/litter was decreased 10 and 17% at the mid and high MIX dose, respectively. Vaginal cytology was normal, as were testis weight and testicular spermatid head count. For F1 mice, fertility was unaffected, but there was a decreased number of female pups/litter (19%) and a decreased adjusted live pup weight at 10% MIX. At necropsy, cauda epididymal sperm concentration and spermatid head count were reduced (20%) in the presence of normal testis, epididymis, prostate, seminal vesicle, liver, and kidney/adrenal weight. Female estrous cyclicity was altered at 5 and 10% MIX with normal kidney/adrenal, uterus, and ovary/oviduct weight. For rats, F0 body weight and feed consumption were not affected by MIX but water consumption was decreased 10, 30, and 40% in the low-, medium-, and high-dose MIX groups, respectively, and 39% in the high-dose MIX F1 animals. Rat fertility was normal but there was a decreased number of male pups/litter (11%) and a decreased live pup weight (6%) at 10% MIX. Male and female (F1) pup weights were decreased on Postnatal Days 0, 4, 7, 14, and 21 (10% MIX) and remained lower through necropsy on Day 120 +/- 10. F1 fertility was normal but F2 pup weights were decreased (10% MIX). At necropsy, F1 (10% MIX) male body weight was decreased 16% and relative kidney, testis, epididymis, and prostate weights were increased in the presence of normal sperm concentration percentage motile sperm and percentage abnormal sperm. Estrous cyclicity was normal as were kidney/adrenal and ovary weight while female liver weight was reduced 14%. In summary, a "cocktail" of 25 chemicals commonly found in contaminated groundwater at or near hazardous waste sites was administered in drinking water at doses which resulted in severely decreased water consumption in both mice and rats.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1998

A three-dimensional DOSY-HMQC experiment for the high-resolution analysis of complex mixtures

A three-dimensional experiment is described in which NMR signals are separated according to their proton chemical shift, 13C chemical shift, and diffusion coefficient. The sequence is built up from a stimulated echo sequence with bipolar field gradient pulses and a conventional decoupled HMQC sequence. Results are presented for a model mixture of quinine, camphene, and geraniol in deuteriomethanol. Copyright 1998 Academic Press.

Journal Article↗
PubMed1998

Estimating the Growth Rate of a Bacterial Species in a Complex Mixture by Hybridization of Genomic DNA

> Abstract Advances in molecular techniques have enabled new approaches to identifying bacteria. However, once identified, there is no quantitative information on the in situ growth rate of the species, mainly because the technology has not been available. The quantitative incorporation of [methyl-3H]thymidine into dividing bacteria is coupled with a molecular (hybridization) method, to determine the growth rate of bacterial species in situ. The basis of this molecular method is a reverse gene probe-natural populations are labeled in situ with [methyl-3H]thymidine. The probe (3H-Tdr-DNA) is captured, using a hybridization procedure, on a positively charged nylon membrane on which is attached non-labeled target DNA. Two bacterial species, Bacillus cereus and Zoogloea ramigera, were used to demonstrate the principle in laboratory cultures and in a municipal activate sludge treatment process. The DNA of the dividing bacteria in activated sludge was radioactively labeled with [methyl-3H]thymidine, and the DNA of Z. ramigera was recovered using a DNA hybridization method. The recovered radioactively-labeled DNA was used to estimate the growth rate (0.03 x 10(9) cells . ml-1 . h-1) of Z. ramigera in situ. Simultaneously applying these two powerful molecular-based methods could potentially be used to study bacterial population dynamics in situ.

Journal Article↗
PubMed1989

Two dimensional benzyldimethyl-n-hexadecylammonium chloride----sodium dodecyl sulfate preparative polyacrylamide gel electrophoresis: a high capacity high resolution technique for the purification of proteins from complex mixtures.

A two dimensional preparative polyacrylamide gel electrophoresis system is described which has both high resolving power and high loading capacity (approximately 100 mg protein). The first dimension is electrophoresis toward the cathode at acid pH in the presence of the cationic detergent benzyldimethyl-n-hexadecylammonium chloride (16-BAC), and the second dimension is electrophoresis toward the anode in the presence of sodium dodecyl sulfate. Proteins purified in this way have been sequenced and used successfully as antigens.

Amino Acid Sequence↗
PubMed1991

Determination of enzyme specificity in a complex mixture of peptide substrates by N-terminal sequence analysis.

A method has been developed to determine preferred residue substitutions in the P' position of peptide substrates for proteolytic enzymes. The method has been validated with four different enzymes; the angiotensin I-converting enzyme, atrial dipeptidyl carboxyhydrolase, bacterial dipeptidyl carboxyhydrolase, and meprin A. A mixture of N-acylated potential peptide-substrates for each of the enzymes was prepared in a single synthesis procedure on the same solid-phase synthesis resin. The peptides were identical in all residue positions except the P' position to be studied, into which numerous amino acid residues were incorporated on a theoretical equimolar basis. After cleavage and extraction of the peptides from the resin, no attempt was made to purify them individually; the exact concentration of each peptide in the mixture was determined by quantitative amino acid analysis. Incubation of an enzyme with its peptide-substrate mixture at [S] much less than Km yielded peptide hydrolytic products with newly exposed N-termini. The identity and amount of each hydrolysis product was determined by automated N-terminal sequence analysis. One cycle of sequencing revealed preferred amino acid substitutions in the P'1 position, two cycles the P'2 position, and so forth. Comparison of the rates of production of the various products indicates the preferred substitution in that particular P' position. New information on the substrate specificities of each of the enzymes tested was obtained and it is clear that this approach can be applied to any protease with a defined (or suspected) point of cleavage in a peptide substrate.

Amino Acid Sequence↗