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PubMed1994

High-sensitivity sequencing of large proteins: partial structure of the rapamycin-FKBP12 target.

We report on studies leading to refinements of various steps of the protein internal sequencing process. Specifically, the developments comprise (1) higher-sensitivity chemical sequencing through background reduction; (2) improved peptide recovery from rapid in situ digests of nanogram amount, nitrocellulose-bound proteins; and (3) accurate UV spectroscopic identification of Trp- and Cys-containing peptides. In addition, we describe strategies for 2-dimensional liquid chromatographic peptide isolation from complex mixtures and a multi-analytical approach to peptide sequence analysis (Edman sequencing, matrix-assisted laser desorption mass spectrometry, and UV spectroscopy). Both strategies were applied in tandem to the primary structural analysis of a gel-purified, 250-kDa protein (mammalian target of rapamycin-FKBP12 complex), available in low picomolar quantities only. More than 300-amino acids worth of sequence was obtained in mostly uninterrupted stretches, several containing Trp, Cys, His, and Ser. That information has allowed the matching of a biological function of a mammalian protein to a yeast gene product with a well-characterized mutant phenotype. The results also demonstrate that extended chemical sequencing analysis (e.g., 26 successive amino acids) is now feasible, starting with initial yields well below 1 pmol.

Amino Acid Sequence↗
PubMed2002

Mathematical method for the prediction of retention times of fatty acid methyl esters in temperature-programmed capillary gas chromatography.

An accurate method for identification of fatty acids in complex mixtures analyzed by temperature-programmed capillary gas chromatography is described. The method is based on a mathematical approach using regression curves obtained by plotting the relative retention times of fatty acid methyl esters (FAMEs) analyzed in isothermal and gradient temperature conditions. The method was applied to a complex biological sample (human milk), and it was possible to identify 64 fatty acids, including branched-chain and other fatty acids for which reference standards were not readily available. The identities of the majority of the peaks were confirmed by mass spectrometry. The relative residuals and the relative differences between estimated and measured relative retention times of individual FAMEs varied from 0.03 to 3.15% and from 0.0 to 2.9%, respectively. The method is useful for identification of fatty acids in routine analysis.

Chromatography, Gas↗
PubMedDate not supplied

Exposure of humans to a volatile organic mixture. I. Behavioral assessment.

Exposure to a low-level mixture of volatile organic compounds, typical of those found in new buildings, has been reported to impair neurobehavioral function in persons who have experienced sick building syndrome (SBS). Sixty-six healthy young males who had no history of chemical sensitivity were exposed for 2.75 h to a complex mixture of volatile organic compounds at 0 and 25 mg/m3. Even though subjects reported more fatigue and more mental confusion following exposure to volatile organic compounds than to clean air, performance on 13 neurobehavioral tests was not affected. Practice or learning effects were observed if administration of many behavioral tests were repeated. Further studies are needed to clarify the relationship of exposure to volatile organic chemicals, neurobehavioral performance, and subject characteristics, e.g., age, gender, and chemical sensitivity.

Adolescent↗
PubMed1990

Studies on the potential mutagenicity of p-phenylenediamine in oxidative hair dye mixtures.

An aqueous mixture of p-phenylenediamine dihydrochloride, resorcinol and hydrogen peroxide, incubated for 30 min at 37 degrees C, was not mutagenic in the Ames test and in the mouse lymphoma assay and did not produce chromosome aberrations in human lymphocytes, whereas the same mixture without resorcinol was mutagenic in the Ames test and the chromosome aberration assay, probably due to the formation of Bandrowski's base. The formation of mutagenic Bandrowski's base and other reactive products could be demonstrated by thin-layer chromatography and subsequent Ames testing. Preincubation for 0-7 h of 5 different oxidative mixtures of p-phenylenediamine dihydrochloride and various couplers at 37 degrees C resulted in mutagenicities in the Ames test ranging from 'very strong effects' at 0 or 0.5 h for 2,4-diaminoanisole dihydrochloride to 'not mutagenic' at up to 7 h preincubation time for a recently developed alternative coupler. A comparable ranking of mutagenic potencies of the same mixtures could be obtained by Ames tests with dyed buffalo hair strands, either tested directly on the agar plates or by testing the solvent extracts of the colored strands. The optimal combination without any sign of mutagenic tendency was finally tested in a commercially available hair dye formulation. This complex mixture was also not mutagenic in the Ames test. Our main conclusions are as follows. (I) Oxidative hair dye mixtures of p-phenylenediamine dihydrochloride and non-mutagenic couplers are not mutagenic if tested under normal conditions of use; the formation of mutagenic reaction products (such as Bandrowski's base) can be prevented if the oxidative reaction time is limited to 30 min and if about equimolar proportions of para to meta compounds are used. (II) Optimal non-mutagenic combinations of primary intermediates (such as p-phenylenediamine dihydrochloride) and couplers can be evaluated in the Ames test by either time-dependent preincubation of the mixtures or the described test protocol with hair strands.

Animals↗
PubMed2005

Aqueous stability of gadolinium in surface waters receiving sewage treatment plant effluent, Boulder Creek, Colorado.

In many surface waters, sewage treatment plant (STP) effluent is a substantial source of both regulated and unregulated contaminants, including a suite of complex organic compounds derived from household chemicals, pharmaceuticals, and industrial and medical byproducts. In addition, STP effluents in some urban areas have also been shown to have a positive gadolinium (Gd) anomaly in the rare earth element (REE) pattern, with the Gd derived from its use in medical facilities. REE concentrations are relatively easy to measure compared to many organic wastewater compounds and may provide a more widely utilized tracer of STP effluents. To evaluate whether sewage treatment plant-associated Gd is a useful tracer of treatment plant effluent, an investigation of the occurrence, fate, and transport of rare earth elements was undertaken. The rare earth element patterns of four of five STP effluents sampled display positive Gd anomalies. The one site that did not have a Gd anomaly serves a small community, population 1200, with no medical facilities. Biosolids from a large metropolitan STP are not enriched in Gd even though the effluent is, suggesting that a substantial fraction of Gd remains in the aqueous phase through routine treatment plant operation. To evaluate whether STP-derived Gd persists in the fluvial environment, a 14-km study reach downstream of an STP was sampled. Gadolinium anomalies were present at all five downstream sites, but the magnitude of the anomaly decreased. Effluent from STPs is a complex mixture of organic and inorganic constituents, and to better understand the chemical interactions and their effect on REEs, the aqueous speciation was modeled using comprehensive chemical analyses of water samples collected downstream of STP input. These calculations suggest that the REEs will likely remain dissolved because phosphate and carbonate complexes dominate over free REE ions. This study supports the application of Gd anomalies as a useful tracer of urban wastewater.

Cations↗
PubMed2004

Characterization of nanostructure phenomena in airborne particulate aggregates and their potential for respiratory health effects.

Airborne aggregates of nanoparticulates were collected on carbon/form-coated, 100-mesh Ni TEM grids in a thermal precipitator and observed in an analytical TEM utilizing a BF-SAED-DF-EDS characterization protocol to identify the nanocrystalline or nanoparticulate components, especially their degree of crystallinity, size, structural/morphologic features, and chemistries. Reference aggregates of TiO2 rutile and anatase as well as Si3N4 nanoparticles were used to establish these characterization protocols, which were applied to several hundred individual particulates: homogeneous aggregates of carbonaceous/diesel particulate matter, complex mixtures of carbonaceous matter, including carbon nanocrystals, and inorganic nanocrystals; and heterogeneous, nanocrystal/nanoparticulate aggregates. Most airborne particulates were aggregates ranging in aerodynamic diameters from a few nanometers to a few microns; containing as few as 2 nanocrystals to several thousand nanocrystals or nanoparticulates such as carbonaceous spherules arranged in complex branched homogeneous aggregates composing diesel exhaust, with spherule diameters ranging from 10 to 30 nm. The potential for ultrafine airborne aggregates to fragment into hundreds or thousands of nanoparticulate components in human airways and act as toxic agents in deep lung tissue is demonstrated.

Air Pollutants↗
PubMed2004

Systematic investigation of protein phase behavior with a microfluidic formulator.

We demonstrated a microfluidic device for rapidly generating complex mixtures of 32 stock reagents in a 5-nl reactor. This "formulation chip" is fully automated and allows thousands of experiments to be performed in a single day with minimal reagent consumption. It was applied to systematically study the phase behavior of the protein xylanase over a large and complex chemical space. For each chemical formulation that demonstrated a pronounced effect on solubility, the protein phase behavior was completely mapped in the chip, generating a set of empirical phase diagrams. This ab initio phase information was used to devise a rational crystallization screen that resulted in 72-fold improvement in successful crystallization hits compared with conventional sparse matrix screens. This formulations tool allows a physics-based approach to protein crystallization that may prove useful in structural genomics efforts.

Biophysical Phenomena↗
PubMed1981

[Lateralization thresholds for two-tone complexes in man with various interaural differences in stimulation].

With the aid of dichotic stimulation, one-tone signals (1 and 2 kHz) and two--tone complexes (mixture of these frequencies) were presented to subjects with interaural differences simulating shift of the sound image for azimuth angle alpha = 45 and 60 degrees in respect to situation of this image at the midline (alpha = 0 degree). At alpha = 0 degree, the lateralization threshold of the two--tone complex for interaural delay of the low-frequency component tone (1 kHz) is lesser by half than the lateralization threshold for the one--tone signal of the same frequency, whereas the lateralization threshold of the two--tone complex for interaural differences of the higher (2 kHz) tone intensity is somewhat greater than the analogous lateralization threshold for the one--tone signal of the same frequency. At alpha = 45 degrees, the differences between respective lateralization thresholds of the two--tone complex and one--tone signals become less obvious, and quite insignificant at alpha = 60 degrees.

Auditory Perception↗
PubMedDate not supplied

Analysis and screening of combinatorial libraries using mass spectrometry.

Mass spectrometry is a highly selective and high throughput analytical technique that is ideally suited for the identification and purity determination of large numbers of compounds prepared using combinatorial chemistry or for the dereplication of natural products. Compounds may be characterized based on molecular weight, elemental composition and structural features based on fragmentation patterns. When coupled to a separation technique such as high-performance liquid chromatography (HPLC) or capillary electrophoresis, mass spectrometric applications may be expanded to include analysis of complex mixtures. However, the slower speed of the separation step reduces the throughput of the analysis. This review concerns the application of mass spectrometry to the characterization of combinatorial libraries and the screening of library and natural product mixtures. Strategies to enhance the throughput of LC-MS are discussed including fast HPLC and parallel LC-MS. Also, mass spectrometry-based screening methods are described including frontal affinity chromatography-mass spectrometry, gel permeation chromatography LC-MS, direct electrospray mass spectrometry of receptor-ligand complexes, affinity chromatography-mass spectrometry, and pulsed ultrafiltration mass spectrometry.

Chromatography, Affinity↗
PubMed1986

Site-directed antisera to the chromophore binding site of phytochrome: characterization and cross-reactivity.

The preparation and characterization of antisera to a synthetic undecapeptide which encompasses the chromophore binding site on oat phytochrome are described. By direct enzyme-linked immunosorbent assay, this antiserum recognizes bilin-linked peptides in proteolytic digestion mixtures of phytochrome from several plant species including the monocot species, oat and maize, and the dicot species, pea. Competitive enzyme-linked immunosorbent assays have been used to establish the specificity of the site-directed antisera for those peptides homologous with the synthetic undecapeptide which are present in complex mixtures. These results show that the local environment of the phytochromobilin prosthetic group is structurally conserved.

Antibody Specificity↗
PubMedDate not supplied

Contributions of subdiaphragmatic activity, attenuation, and diaphragmatic motion to inferior wall artifact in attenuation-corrected Tc-99m myocardial perfusion SPECT.

BACKGROUND: Subdiaphragmatic activity and diaphragmatic motion both contribute to inferior wall artifacts in technetium 99m myocardial perfusion single photon emission computed tomography (SPECT). METHODS AND RESULTS: We used an anthropomorphic phantom with ventricular wall activity, liver/spleen inserts containing variable Tc-99m activity, and variable vertical (diaphragmatic) motion amplitude. SPECT and transmission scans were obtained on a GE Optima NX camera. Data were processed by use of filtered backprojection or attenuation correction (AC). Resulting myocardial activity maps were analyzed with standardized inferior-anterior and anterior-lateral wall ratios. At a subdiaphragmatic-myocardial activity ratio of 0.5:1, inferior wall attenuation predominates, producing a cold artifact. AC corrects inferior wall activity to the level of the anterior wall irrespective of diaphragmatic motion. At a subdiaphragmatic-myocardial activity ratio of 1:1, inferior wall counts vary widely depending on the proximity of subdiaphragmatic activity to the ventricle. With increasing diaphragmatic amplitude, the overlap of subdiaphragmatic activity and inferior wall worsens, leading to a complex mixture of cold and hot artifacts, not corrected by AC. CONCLUSIONS: Concentration and proximity of subdiaphragmatic Tc-99m activity relative to myocardium comprise a major factor in the nature and severity of inferior wall artifacts. If the subdiaphragmatic Tc-99m concentration is equivalent to that in the myocardium, complex, potentially uninterpretable hot and cold inferior wall artifacts are produced.

Artifacts↗
PubMed2001

Oligosaccharides: application in infant food.

Oligosaccharides are a complex mixture of approximately 130 compounds present in human milk. It has been shown that human milk oligosaccharides induce an increase in the number of bifidobacteria of colonic flora in breast-fed infants, accompanied with a significant reduction in the number of pathogenic potential bacteria, due to their bifidogenic activity. Complex oligosaccharides have the capacity of inhibiting the binding of pathogens to cell surface because they act as competitive receptors. They are associated with a lower risk of infections and diarrhoea and an improvement of the immune system response. Due to the decrease of the pH intestinal caused by their fermentation, oligosaccharides provoke a reduction of the flora pathogens, an increase of bifidobacteria and an increase of the availability of minerals. In the food industry, simple oligosaccharides such as fructooligosaccharides and galactooligosaccharides are used as bifidogenic oligosaccharides and some infant products contain them in the hope that this might provide some of the benefits attributed to oligosaccharides in human milk. This paper reviews characteristics of oligosaccharides, their beneficial effects and use of oligosaccharides in the food industry. In adults, the benefits of some of the oligosaccharides have been established in several clinical trials, but in infants more fundamental research is needed to establish the metabolic role of these components and the daily intake with bifidogenic activity.

Bifidobacterium↗
PubMed1990

Preparative separation of small molecular weight peptides from casein hydrolysate using gel filtration and immobilized metal ion affinity chromatography.

A two step method consisting of a gel filtration step, followed by a Immobilized Metal Affinity Chromatography (IMAC) step using a IDA-Cu coupled Sephadex G-25 column, on a preparative scale is described for the group separation of peptides from a casein hydrolysate. The 48 groups of peptides thus separated are further characterised by RP-HPLC and amino acid analysis. Some peptides after the analytical RP-HPLC step are further characterised by sequencing. An insight into the mechanism of retention on IMAC of the peptides is attempted. In such complex mixtures as casein hydrolysate, the peptide-peptide interaction can mask the potential sites of interactions in a single peptide. The results obtained using volatile buffers as eluents show the possibility of using IMAC step as an alternative to obtain gram quantities of group of peptides free of salts from complex protein hydrolysates.

Amino Acid Sequence↗
PubMed1996

Enzyme induction and acute endocrine effects in prepubertal female rats receiving environmental PCB/PCDF/PCDD mixtures.

Air, subsurface soil, and superficial dust from a National Priorities List landfill located in southern Illinois were sampled to determine their potential toxicities. The major components of these landfill extracts were polychlorinated biphenyls (PCBs), with significant amounts of polychlorinated dibenzofurans (PCDFs) and small amounts of polychlorinated dibenzodioxins (PCDDs). The 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxic equivalency factor approach has been proposed to estimate the toxic potency of complex mixtures of chlorinated aromatics for environmental risk assessment. However, most components of environmental residues are nonplanar and do not act as aryl hydrocarbon (Ah) receptor agonists, so there is a great risk of not identifying adverse responses that are not dioxinlike. We used a 2-day prepubertal female rat bioassay to examine multiple biological responses, including both dioxinlike and nondioxinlike effects from these landfill extracts. As expected, both types of effects were detected. The soil and dust extracts produced similar dose-response relationships for 7-ethoxyresorufin O-deethylase, 7-pentoxyresorufin O-depentylase, 7-benzyloxyresorufin O-debenzylase, and 4-nitrophenol UDP-glucuronyltransferase induction; the dose response for the air extract deviated from the other two extracts. Soil, dust, and air extracts effectively reduced serum total thyroxine (T4) with similar dose-response relationships, despite the significantly different TCDD toxic equivalent (TEQ) values of these three extracts. Both soil (346 mg PCB/kg) and air (175 mg PCB/kg) extracts caused a greater than 30% increase in uterine wet weight. This study suggests that a more comprehensive approach is required to improve current risk assessment of environmental mixtures. TCDD TEQs reflect only a portion of effects and may especially underpredict effects on T4.

Air Pollutants↗
PubMed2004

Fast high-performance liquid chromatography method for quality control of soy extracts.

Soy extracts contain a mixture of isoflavones belonging to the group of phytoestrogens. In the quality control of soy the amount of isoflavones, both aglycones and glycosides, is usually determined by means of reversed-phase HPLC-UV. On conventional C18-material columns, long analysis times are required in order to separate this complex mixture. In order to speed up analysis, the separation was optimized using two linked monolithic silica-based reversed-phase C18 columns. A spectacular decrease of the analysis time, i.e. almost three-fold, was achieved by applying a flow rate of 3-4 ml/min without loosing any separation efficiency. This analysis method for determination of isoflavones in soy extracts in less than 25 min was fully validated according to the ICH guidelines.

Chromatography, High Pressure Liquid↗
PubMed2002

Comparative measurements of multicomponent phospholipid mixtures by electrospray mass spectroscopy: relating ion intensity to concentration.

Electrospray mass spectrometry allows direct identification and sensitive detection of multiple phospholipids in non-derivatized cell extracts. However, quantitative analyses are not straightforward, and are confounded by analyte and mass discrimination effects, and non-linear dependence of the ion intensity on concentration. This non-linearity is particularly severe in the negative mode and precludes even comparative measurements of anion concentrations. Herein, we report a general method for relating negative electrospray ion intensity to concentration when analyzing multicomponent phospholipid samples. In this method, the intensity of individual ions is measured at several different concentrations of the total mixture and the slope (n(E)) of the double log plot of sample concentration vs. intensity for each analyte is determined. The n(E) is then used to map intensity data to a quantity proportional to concentration for each analyte. The method allows facile and accurate comparison of negative spectra of complex mixtures containing structurally different anions.

Animals↗
PubMed1975

DNA-RNA hybridization.

Interest in nucleic acid hybridization stems mainly from its great power as a tool in biological research. It is used in several quite distinct ways. Because of the high degree of specificity that they show, hybridization techniques can be used to measure the amount of one specific sequence within a very heterogeneous mixture of sequences. Measurements of 1/10(6)-10(7) have been recorded. In extension of this, various properties of a specific sequence can often be studied. Secondly, because the kinetics of nucleic acid hybridization are quite well understood, it can be used to characterize both a pure sequence and a very complex mixture of sequences, like the genome of a vertebrate. Thirdly, again because of its specificity, it can be used to measure homologies between different populations of nucleic acids. Lastly, in conjunction with other techniques, it can be used as a basis for the fractionation of nucleic acid populations and the purification of specific sequences. Specific examples of these applications are given, with special reference to the organization of the genome in higher eukaryotes.

Animals↗
PubMed2005

Mapping protein interfaces by a trifunctional cross-linker combined with MALDI-TOF and ESI-FTICR mass spectrometry.

Chemical cross-linking of protein complexes has gained renewed interest in combination with mass spectrometric analysis of the reaction products as it allows a rapid mapping of protein interfaces, which is crucial for understanding protein/protein interactions. The identification of cross-linking products from the complex mixtures created after the cross-linking reaction, however, remains a daunting task. To facilitate the identification of cross-linking products, we explore the use of the commercially available biotinylated cross-linking reagent sulfo-SBED (sulfosuccinimidyl-2-[6-(biotinamido)-2-(p-azidobenzamido)-hexanoamido]ethyl-1,3'-dithiopropionate). This trifunctional cross-linker possesses one amine-reactive and one photo-reactive site and, additionally, allows an affinity-based enrichment of cross-linker containing species. As a model system, we chose the Ca(2+)-dependent complex between calmodulin and its target peptide M13, which represents a part of the C-terminal sequence of the skeletal muscle myosin light chain kinase. After the cross-linking reaction, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and one-dimensional gel electrophoresis were employed to check for the extent of cross-linking product formation. The cross-linking reaction mixtures were subjected to tryptic in-solution digestion. Biotinylated peptides, e.g., peptides that had been modified by the cross-linker as well as cross-linked peptides, were enriched on monomeric avidin beads after several washing steps had been performed. Peptide mixtures were analyzed by MALDI-TOFMS, nano-high-performance liquid chromatography (HPLC)/nano-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS), and tandem MS. We demonstrate that an enrichment of cross-linker containing species allows a more efficient identification of interacting amino acid sequences in protein complexes. This strategy is expected to be especially beneficial for investigating large protein assemblies.

Binding Sites↗