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At least 775 records · Page 43Linked to original sources
PubMed2006

Top-down approaches for measuring expression ratios of intact yeast proteins using Fourier transform mass spectrometry.

The extension of quantitation methods for small peptides to ions above 5 kDa, and eventually to global quantitative proteomics of intact proteins, will require extensive refinement of current analytical approaches. Here we evaluate postgrowth Cys-labeling and 14N/15N metabolic labeling strategies for determination of relative protein expression levels and their posttranslational modifications using top-down mass spectrometry (MS). We show that intact proteins that are differentially alkylated with acrylamide (+71 Da) versus iodoacetamide (+57 Da) have substantial chromatographic shifts during reversed-phase liquid chromatography separation (particularly in peak tails), indicating a requirement for stable isotopes in alkylation tags for top-down MS. In the 14N/15N metabolic labeling strategy, we achieve 98% 15N incorporation in yeast grown 10 generations under aerobic conditions and determine 50 expression ratios using Fourier transform ion cyclotron resonance MS in comparing these cells to anaerobically grown control (14N) cells. We devise quantitative methods for top-down analyses, including a correction factor for accurate protein ratio determination based upon the signal-to-noise ratio. Using a database of 200 yeast protein forms identified previously by top-down MS, we verify the intact mass tag concept for protein identification without tandem MS. Overall, we find that top-down MS promises work flows capable of large-scale proteome profiling using stable isotope labeling and the determination of >5 protein ratios per spectrum.

Feasibility Studies↗
PubMed2005

Assay of rotenone in river water by high-throughput tandem mass spectrometry and multiple-reaction monitoring methodology.

The high-throughput analytical approach proposed for the assay of rotenone in lake and river waters presented here is based on atmospheric pressure chemical ionization (APCI) multiple-reaction monitoring (MRM) methodology whereby the analyte and internal standard solutions are directly analyzed, without any previous chromatographic separation. The very good accuracy is obtained by the critical choice of a reference compound that shows gas-phase chemistry similar to that of the analyte, by producing the same product ions selected for the MRM-based assay.

Atmosphere↗
PubMed2004

Comment on "A broad frequency range dielectric spectrometer for colloidal suspensions: cell design, calibration, and validation".

Recently, a simple analytical model was derived from the standard electrokinetic theory to deal with electrode polarization in low frequency dielectric measurements [Hollingsworth and Saville, J. Colloid Interface Sci. 257 (2003) 65-76]. Comparisons were made between dielectric constant-frequency relationships extracted from data on electrolyte solutions using the analytical model and the well-known RC-circuit analog. Electrolyte spectra interpreted with the analytical approach remained smooth (and constant) down to much lower frequencies than was the case with the RC model. It was also shown how the RC model arises naturally from the analytical model as an asymptotic expansion in inverse powers of the electrode spacing. Numerical calculations indicated substantial differences between the two models at low frequencies due to higher order terms omitted in the RC model. As it turns out, the comparison contained a numerical error. Here we revisit the methodology to show that although the two formulations disagree, they do so (in a numerical sense) only at much smaller electrode separations than those used in the aforementioned example. The purpose of this Letter is to correct the numerical error and show, explicitly, how the RC-circuit analog coefficients are related to the asymptotic expansion at low frequencies.

Letter↗
PubMed1994

Implicit verbal memory in Alzheimer's disease.

Word stem completion and word identification were used in two repetition priming experiments to evaluate the implicit memory performance of Alzheimer's disease (AD) patients. This issue was also approached using various meta-analyses combining and contrasting previously reported data. While the experimental results suggested that AD patients present preserved repetition priming in both tasks, the meta-analytic approach showed an impairment in stem completion in comparison to word identification. Converging evidence cautiously suggested to accept the results of the meta-analysis. The above dissociation has been interpreted as showing differences in the specific contribution of data- and conceptually-driven processes in the two implicit tasks. A further meta-analysis on the effect of reduced perceptual availability of the study material on the same two tasks indicated that this variable affected repetition priming in word identification more heavily than in stem completion. The impact of such a dissociation on theories of implicit memory is discussed.

Aged↗
PubMedDate not supplied

DNA microarrays in pediatric cancer.

Childhood cancer, like all cancer, is at heart a genetic disease. Consequently, fundamental understanding of the oncogenic process is likely to be beneficially addressed by genetic methodology. Current methods have largely focused on single-gene defects, like chimeric genes, which are present in many sarcomas and leukemias. Real understanding is more likely to derive from a genome-wide analysis of these malignancies. Recent technologic advances have made it possible to simultaneously assess the entire expressed gene profile, or transcriptome, of a given cancer. Foremost among these methods is gene expression profiling using DNA microarrays. Two basic approaches predominate: spotted arrays and photolithography arrays. Regardless of the method, the resulting information can be used to create disease profiles, but only if appropriate bioinformatic solutions are employed. Common analytic approaches include two-way expression comparisons, or scatter analyses; outlier gene analysis, to identify significantly dysregulated genes; dendrogram analyses, as pioneered by Eisen; cluster analyses to identify diagnostic or biologic groups; and various forms of functional analyses to identify relevant genes and biologic pathways. Studies of both adult and pediatric cancer have demonstrated the feasibility of such analyses to identify both diagnostic and prognostic groups of tumors. Acute childhood leukemias have been grouped into myelogenous and lymphoid, and even B- and T-cell subsets. Breast cancer prognostic groups have been identified on the basis of a small subset of expressed genes. In addition, preliminary data on childhood sarcomas appear to identify both diagnostic and prognostic subsets. Specifically, embryonal rhabdomyosarcoma could be distinguished from alveolar rhabdomyosarcoma, and even morphologically mixed embryonal and alveolar rhabdomyosarcoma showed similar gene expression profiles in both histologies. Further, collaborative studies using clustering analyses appear to identify prognostic groups of diverse sarcomas. Larger institutional and cooperative group studies are currently underway to validate these preliminary findings.

Animals↗
PubMed1989

[Compulsion, ego organization and treatment procedure. On the treatment of a patient with chronic compulsive symptoms].

On the basis of a case study, it is shown that traditional approaches to understanding what have been labeled compulsive neuroses are insufficient if the illness is based on a prestructural disturbance. Classical treatment techniques are contraindicated in such a case, and analytical approach oriented toward a response to the structure of the ego is appropriate in its place.

Ego↗
PubMed2002

Magnetic resonance perfusion imaging in patients with coronary artery disease: a qualitative approach.

UNLABELLED: Although contrast-enhanced first pass magnetic resonance imaging (MRI) has potential to quantify blood flow through extensive image post-processing, clinical utility is likely to depend on rapid qualitative analysis. AIMS: To investigate use of an on-line analytical approach for detection of coronary artery disease (CAD). METHODS AND RESULTS: Thirty subjects with CAD underwent contrast-enhanced rest/adenosine stress MRI with basal, mid-papillary and apical short-axis image acquisition. Each short axis was divided into eight regions of interest (ROI). Regional perfusion was visually classified as normal or impaired according to transmural distribution and defect reversibility. MRI and angiographic data were compared. Qualitative MRI reporting was possible for 98% ROI. Eighty-six coronary artery (CA) territories were assessed of which 71 (83%) had stenoses. Sensitivity and specificity for detection of stenoses were 93 and 60%, respectively. The proportion of hypoperfused ROI rose from 31% with < 50% stenosis to 65% with occlusion. More transmural defects were seen in infarction-related territories (75 vs. 54%, p < 0.05). More ROI demonstrated defect reversibility in occluded rather than in stenosed infarction-related vessels (89 vs. 58%, p < 0.05). Occluded vessels with grade 2-3 collaterals contained a higher proportion of normal ROI (44 vs. 25%, p < 0.05). CONCLUSIONS: Qualitative MRI analysis had high sensitivity and moderate specificity for detecting CA stenoses. Additional information was obtained relating to lesion severity, previous infarction, myocardial viability and impact of collateral circulation. The technique has potential for de novo diagnosis of CAD and as a complementary modality to angiography to assess the significance of given angiographic lesions.

Adult↗
PubMedDate not supplied

Ultraviolet-B radiation and plant competition: experimental approaches and underlying mechanisms.

Under realistic stratospheric ozone depletion scenarios, ultraviolet-B radiation (280-320 nm) (UV-B) influences plant morphology and plant competitive interactions. Influence of UV-B on plant competition can be studied using a variety of experimental and analytical approaches including inverse yield-density models and allometric, neighborhood or size-structure analyses that provide links between plant and ecosystem responses. These approaches differ in their abilities to extract information regarding competitive interactions and their morphological underpinnings. Only a limited number of studies have been carried out to investigate UV-B effects on plant competition, and most of these have used the replacement series approach, which has received much criticism. Nonetheless, results to date indicate that slight differences in UV-B-induced morphological responses of species grown within associations can alter canopy structure thereby influencing photosynthetically active radiation (PAR) interception and relative competitive ability. Because the response of individuals of the same species is expected to be uniform, UV-B may influence intraspecific competition less than interspecific competition. Before we can make clear generalizations and predictions concerning the effects of this radiation on plant competition, an understanding is crucial of the mechanisms underlying UV-B-induced shifts in competitive interactions by assessing competition over time.

Ecology↗
PubMed2004

Approach to the comprehensive analysis of glycoproteins isolated from human serum using a multi-lectin affinity column.

Glycosylation is one the most common post-translational modifications (PTM) and glycoproteins play fundamental roles in a diversity of biological processes. The development of an analytical approach to the study of variation of glycosylation patterns in serum samples has been hindered by the structural heterogeneity of this post-translational modification and the complexity of serum proteome. We have used the ability of different lectins to recognize specific glycosylation motifs to develop a specific affinity system that can achieve a comprehensive capture of serum glycoproteins. In a preliminary investigation, we evaluated the ability of five commonly used immobilized lectins to capture glycoproteins from human serum. SDS-PAGE analysis showed each lectin was able to enrich a subset of the serum glycoproteome and overlaps in lectin specificity were indeed observed. Based on these results and with the goal of studying the extent of the human serum glycoproteome, we then developed a multi-lectin affinity column containing Concanavalin A (Con A), Wheat germ and Jacalin lectin. The selection of lectins was also based on the known N-linked and O-linked glycan structures that are considered representative of the serum proteome. We then demonstrated that the capture of glycoproteins was specific, efficient and reproducible with this multi-lectin column. The results obtained with this affinity step indicated that about 10% of human serum proteins are glycosylated (weight/weight) and, after removal of six high abundance proteins, including albumin, at least 50% of the remaining proteins were glycosylated. We then evaluated the use of this affinity column to monitor changes in the pattern of glycosylation in serum samples by a controlled, stepwise release of the captured proteins from the multi-lectin affinity column with specific displacers.

Chromatography, Affinity↗
PubMed2001

Monitoring biogenic volatile compounds emitted by Eucalyptus citriodora using SPME.

A procedure to monitor BVOC emitted by living plants using SPME technique is presented. For this purpose, a glass sampling chamber was designed. This device was employed for the characterization of biogenic volatile compounds emitted by leaves of Eucalyptus citriodora. After extraction with SPME fibers coated with PDMS/ DVB, it was possible to identify or detect 33 compounds emitted by this plant. A semiquantitative approach was applied to monitor the behavior of the emitted BVOC during 9 days. Circadian profiles of the variation in the concentration of isoprene were plotted. Using diffusion-based SPME quantitation, a recently introduced analytical approach, with extraction times as short as 15 s, it was possible to quantify subparts-per-billion amounts of isoprene emitted by this plant.

Butadienes↗
PubMed2001

Linkage analysis of quantitative traits in randomly ascertained pedigrees: comparison of penetrance-based and variance component analysis.

Penetrance-based linkage analysis and variance component linkage analysis are two methods that are widely used to localize genes influencing quantitative traits. Using computer programs PAP and SOLAR as representative software implementations, we have conducted an empirical comparison of both methods' power to map quantitative trait loci in extended, randomly ascertained pedigrees, using simulated data. Two-point linkage analyses were conducted on several quantitative traits of different genetic and environmental etiology using both programs, and the lod scores were compared. The two methods appear to have similar power when the underlying quantitative trait locus is diallelic, with one or the other method being slightly more powerful depending on the characteristics of the quantitative trait and the quantitative trait locus. In the case of a multiallelic quantitative trait locus, however, the variance component approach has much greater power. These findings suggest that one should give careful thought to the likely allelic architecture of the quantitative trait to be analyzed when choosing between these two analytical approaches. It may be the case in general that linkage methods which explicitly or implicitly rely on the assumption of a diallelic trait locus fare poorly when this assumption is incorrect.

Chromosome Mapping↗
PubMed2001

Microarray-based analysis of early development in Xenopus laevis.

In order to examine transcriptional regulation globally, during early vertebrate embryonic development, we have prepared Xenopus laevis cDNA microarrays. These prototype embryonic arrays contain 864 sequenced gastrula cDNA. In order to analyze and store array data, a microarray analysis pipeline was developed and integrated with sequence analysis and annotation tools. In three independent experimental settings, we demonstrate the power of these global approaches and provide optimized protocols for their application to molecular embryology. In the first set, by comparing maternal versus zygotic transcription, we document groups of genes that are temporally regulated. This analytical approach resulted in the discovery of novel temporally regulated genes. In the second, we examine changes in gene expression spatially during development by comparing dorsal and ventral mesoderm dissected from early gastrula embryos. We have discovered novel genes with spatial enrichment from these experiments. Finally, we use the prototype microarray to examine transcriptional responses from embryonic explants treated with activin. We selected genes (two of which are novel) regulated by activin for further characterization. All results obtained by the arrays were independently tested by RT-PCR or by in situ hybridization to provide a direct assessment of the accuracy and reproducibility of these approaches in the context of molecular embryology.

Animals↗
PubMed2004

The prediction of disruptive behaviour disorders in an urban community sample: the contribution of person-centred analyses.

BACKGROUND: Variable- and person-centred analyses were used to examine prediction of middle childhood behaviour problems from earlier child and family measures. METHOD: A community sample of 164 families, initially recruited at antenatal clinics at two South London practices, was assessed for children's behaviour problems and cognitive ability, maternal mental health, and the family environment when the children were 4 years old. At age 11, children, mothers, and teachers reported the child's disruptive behaviour, and mothers and children were interviewed to identify cases of disruptive behaviour disorders (DBD). RESULTS: Neither social class nor ethnicity predicted the child's disruptive behaviour at age 11. Rather, path analyses and logistic regression analyses drew attention to early behavioural problems, maternal mental health and the child's cognitive ability at 4 as predictors of disruptive behaviour at age 11. Cluster analysis extended these findings by identifying two distinct pathways to disruptive symptoms and disorder. In one subgroup children who showed intellectual difficulties at 4 had become disruptive by 11. In a second subgroup mothers and children both showed psychological problems when the child was 4, and the children were disruptive at age 11. The person-centred approach also revealed a high-functioning group of cognitively able 4-year-olds in supportive environments, at especially low risk for DBD. CONCLUSIONS: Combining variable- and person-centred analytic approaches can aid prediction of children's problems, draw attention to pertinent developmental pathways, and help integrate data from multiple informants.

Attention Deficit and Disruptive Behavior Disorder↗
PubMed2005

Multipole-multimode Floquet theory in nuclear magnetic resonance.

In this paper, we present a new analytical approach for describing the spin dynamics of synchronous and asynchronous time-dependent modulations in solid-state nuclear magnetic resonance experiments. The approach, based on multimode Floquet theory, employs the multipole operator basis of Sanctuary for spin description and illustrates the time evolution in the Floquet-Liouville space using the effective Hamiltonians obtained from the contact (or van Vleck) transformation procedure. Since the Hamiltonian and the density operator are expressed in terms of irreducible tensor operators, extensions to higher spin magnitudes (I>12) and multiple spins are quite straightforward and permit analytical treatments for many problems. We outline the general underlying principles involved in this approach with a brief mention of its potential application in other branches of spectroscopy.

Algorithms↗
PubMed2005

Analysis of models for the synapse between the inner hair cell and the auditory nerve.

A general mathematical approach was proposed to study phenomenological models of the inner-hair-cell and auditory-nerve (AN) synapse complex. Two models (Meddis, 1986; Westerman and Smith, 1988) were studied using this unified approach. The responses of both models to a constant-intensity stimulus were described mathematically, and the relationship between model parameters and response characteristics was investigated. The mathematical descriptions of the two models were essentially equivalent despite their structural differences. This analytical approach was used to study the effects of adaptation characteristics on model parameters and of model parameters on adaptation characteristics. The results provided insights into these models and the underlying biophysical processing. This analytical method was also used to study offset adaptation, and it was found that the offset adaptation of both models was limited by the models' structures. A modified version of the synapse model, which has the same onset adaptation but improved offset adaptation, is proposed here. This modified synapse model produces more physiologically realistic offset adaptation and also enhances the modulation gain of model AN fiber responses, consistent with AN physiology.

Acoustic Stimulation↗
PubMed2005

Sexual versus nonsexual workplace aggression and victims' overall job satisfaction: a meta-analysis.

A meta-analytic approach was used to examine whether sexual and nonsexual forms of nonviolent workplace aggression (both verbal and nonverbal) share equivalent or differential relationships with victims' overall job satisfaction. When the meta-analytic comparison was restricted to all-female samples to hold victims' gender constant, nonsexual aggression was found to share a significantly stronger negative relationship with victims' overall job satisfaction than was sexual aggression. In addition, nonsexual aggression was found to share a stronger negative link with women's level of job satisfaction than with men's.

Aggression↗
PubMed2006

Protocols for optimizing MS/MS parameters with an ion-trap GC-MS instrument.

The product ion spectrum allows us to achieve very selective detection of pesticides and to eliminate the ambiguities caused by more conventional analytical approaches. Owing to the enhanced capabilities of GC/MS/MS for multiresidue pesticides, the development of a GC/MS/MS pesticides library will be useful. The aim of this study was to develop a sensitive and specific analytical method for the identification and quantification of compounds without the need of a time-consuming procedure. Two methods were studied in order to optimize the nonresonant conditions of dissociation of five pesticides (deltamethrin, metalaxyl, myclobutanil, procymidone, pirimicarb). The first permits a systematic investigation of the influence of the qz trapping parameter on sensitivity in precursor ion detection and on the efficiency of collision-induced dissociation (CID). The second is more suited for analytical laboratories and less time-consuming and allows us to reach similar results: the experiments were conducted step by step at a constant stability parameter.

Gas Chromatography-Mass Spectrometry↗
PubMed1987

A graphical approach to the identification and estimation of causal parameters in mortality studies with sustained exposure periods.

In observational cohort mortality studies with prolonged periods of exposure to the agent under study, independent risk factors for death commonly determine subsequent exposure to the study agent. For example, in occupational mortality studies, date of termination of employment is both a determinant of subsequent exposure to the chemical agent under study (since terminated individuals receive no further exposure) and an independent risk factor for death (since disabled individuals tend to leave employment). When a risk factor determines subsequent exposure and is determined by previous exposure, standard analyses that estimate age-specific mortality rates as a function of cumulative exposure can underestimate the true effect of exposure on mortality, whether or not one adjusts for the risk factor in the analysis. This observation raises the question, "Which, if any, empirical population parameter can be causally interpreted as the true effect of exposure in observational mortality studies?" In answer, we offer a graphical approach to the identification and estimation of causal parameters in mortality studies with sustained exposure periods. We reanalyze the mortality experience of a cohort of arsenic-exposed copper smelter workers using our approach and compare our results with those obtained using standard methods. We find an adverse effect of arsenic exposure on all cause and lung cancer mortality, which standard methods failed to detect. The analytic approach introduced in this paper may be necessary to control bias in any epidemiologic study in which there exists a risk factor which both determines subsequent exposure and is determined by previous exposure to the agent under study.

Epidemiologic Methods↗