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PubMed1988

Induction of 3-hydroxy-3-methylglutaryl coenzyme A reductase activity in foetal rats by maternal cholestyramine feeding.

Late gestation foetus from rats fed a non-absorbable bile acid binding resin (cholestyramine) have increased hepatic 3-hydroxy-3-methylglutaryl coenzyme A reductase activity. This was due to increased unphosphorylated (active) as well as total reductase and was accompanied by higher fatty acid synthetase activity. No increase in foetal hepatic cystathionase or tyrosine aminotransferase activity, or changes in plasma insulin, corticosterone or thyroxine were found. The studies demonstrate that foetal hepatic cholesterol metabolism is sensitive to drug-induced perturbation of maternal lipoprotein metabolism. The data suggest induction of foetal cholesterol and fatty acid synthesis by a specific mechanism not involving generalized hormone-induction of hepatic enzyme systems. Cholestyramine appears to have application for in vivo study of the regulation of foetal cholesterologenesis and its coordination to maternal and foetal steroid requirements.

Animals↗
PubMed1984

Differential swelling in compartments of the corneal stroma.

When a hypotonic solution is applied to the corneal surface the stroma swells. This well-known osmotic response masks a surprising hydration change in the posterior stroma. This was studied by measuring thickness changes in the anterior, middle, and posterior stroma of the rabbit cornea. Measurements were made continuously for 1 hour following osmotic perturbation of the epithelial surface. The data revealed that following a hypotonic shift on the epithelial surface, the posterior stroma thinned briefly. This unexpected effect is predicted satisfactorily by Klyce and Russell's mathematical model. The method of measuring fluid flow between stromal compartments will allow further development of the model in describing the dynamics of stromal hydration.

Animals↗
PubMed1983

Resonance Raman spectra of photodissociated carbonmonoxy hemoglobin and deoxy hemoglobin at 10 K.

Resonance Raman data from deoxy hemoglobin and photodissociated carbonmonoxy hemoglobin (Hb*) at low temperature (10 K) are reported. At this temperature with 457.9 nm excitation, the iron-histidine (Fe-His) stretching mode in deoxy hemoglobin disappears, although with 441.6 nm excitation it is detected at 235 cm-1. The intensity change is interpreted as resulting from changes in energy of iron d orbitals induced by the shortening of the Fe-His bond on temperature reduction. The previously reported narrowing of the Fe-His mode with temperature reduction has been found to be artifact. In Hb*, the Fe-His stretching mode is present with 457.9 nm as well as 441.6 nm excitation and is at higher frequency (242-244 cm-1) than it is in the deoxy samples. Several porphyrin skeletal frequencies are also shifted in Hb* with respect to deoxy hemoglobin. These data are interpreted as resulting from perturbations on the ligand-free histidine-porphyrin complex by the liganded conformation of the heme pocket. We find no evidence that the dissociated CO molecule interacts with the heme in Hb*.

Carboxyhemoglobin↗
PubMed1975

Determination of blood serum protein reactivity in children with behavior disturbances.

The researches were carried out on two groups of children: normals and with behavior disturbances. The serum cationic state was determined by an original method, using heparin as cautions exchanger in physiological pH, and the protein reactivity; the electrophoretic mobility of serum proteins at pH 7.4; total soduim and serum proteins. The obtained results show that serum proteins in children with behavior disturbances differ from those of normals, having: 1) smaller number of serotonin-fixing sites, 2) higher strength interaction between the serotonin and proteins, 3) lower resistance to the denaturant agents which has as a consequence the increase of cationic activity in the serum, and an increased electrophoretic mobility. The data are discussed and interpreted as perturbations in the electrolytes exchange (Na+, especially) in the integration centres of the autonomic functions.

Adolescent↗
PubMed1988

Lipid-protein interaction. The incorporation of myelin proteolipid apoprotein into phosphatidylcholine bilayers.

Bovine myelin proteolipid apoprotein (PLA), obtained in high yield and purity by a novel ultrafiltration procedure, has been used to study the perturbations produced by this protein on phosphatidylcholine bilayers, using infrared spectroscopy, nuclear magnetic resonance and fluorescence polarisation. PLA interacts with phospholipids in a similar manner to other intrinsic proteins. For bilayers in the fluid state, the fatty-acyl chain static order, as measured by deuterium NMR, is slightly increased in the presence of the protein, except at very high PLA concentrations. Phosphorus NMR reveals some perturbation of the phospholipid polar group by PLA, but to a smaller degree than occurs with other intrinsic proteins. An increase in static order above tc (the onset temperature for gel-to-fluid transition) is also detected by infrared spectroscopy. Studies using steady-state polarisation of diphenylhexatriene fluorescence indicate that the microviscosity of the bilayer increases as a function of the protein mole fraction. From these data an estimation of the average number of lipids perturbed per protein monomer has been made, and a figure of 37 phospholipid molecules determined. The data are compatible with a picture of a hydrophobic polypeptide, perturbing the phospholipids close to it, but allowing rapid (greater than 10(4) s-1) exchange with all the lipid molecules in the system.

Apoproteins↗
PubMed2006

Information-based modeling of event-related brain dynamics.

We discuss the theory and practice of applying independent component analysis (ICA) to electroencephalographic (EEG) data. ICA blindly decomposes multi-channel EEG data into maximally independent component processes (ICs) that typically express either particularly brain generated EEG activities or some type of non-brain artifacts (line or other environmental noise, eye blinks and other eye movements, or scalp or heart muscle activity). Each brain and non-brain IC is identified with an activity time course (its 'activation') and a set of relative strengths of its projections (by volume conduction) to the recording electrodes (its 'scalp map'). Many non-articraft IC scalp maps strongly resemble the projection of a single dipole, allowing the location and orientation of the best-fitting equivalent dipole (or other source model) to be easily determined. In favorable circumstances, ICA decomposition of high-density scalp EEG data appears to allow concurrent monitoring, with high time resolution, of separate EEG activities in twenty or more separate cortical EEG source areas. We illustrate the differences between ICA and traditional approaches to EEG analysis by comparing time courses and mean event related spectral perturbations (ERSPs) of scalp channel and IC data. Comparing IC activities across subjects necessitates clustering of similar Ics based on common dynamic and/or spatial features. We discuss and illustrate such a component clustering strategy. In sum, continued application of ICA methods in EEG research should continue to yield new insights into the nature and role of the complex macroscopic cortical dynamics captured by scalp electrode recordings.

Brain↗
PubMed2006

Integration of metabolome data with metabolic networks reveals reporter reactions.

Interpreting quantitative metabolome data is a difficult task owing to the high connectivity in metabolic networks and inherent interdependency between enzymatic regulation, metabolite levels and fluxes. Here we present a hypothesis-driven algorithm for the integration of such data with metabolic network topology. The algorithm thus enables identification of reporter reactions, which are reactions where there are significant coordinated changes in the level of surrounding metabolites following environmental/genetic perturbations. Applicability of the algorithm is demonstrated by using data from Saccharomyces cerevisiae. The algorithm includes preprocessing of a genome-scale yeast model such that the fraction of measured metabolites within the model is enhanced, and thus it is possible to map significant alterations associated with a perturbation even though a small fraction of the complete metabolome is measured. By combining the results with transcriptome data, we further show that it is possible to infer whether the reactions are hierarchically or metabolically regulated. Hereby, the reported approach represents an attempt to map different layers of regulation within metabolic networks through combination of metabolome and transcriptome data.

Algorithms↗
PubMedDate not supplied

Statistical variation in progressive scrambling.

The two methods most often used to evaluate the robustness and predictivity of partial least squares (PLS) models are cross-validation and response randomization. Both methods may be overly optimistic for data sets that contain redundant observations, however. The kinds of perturbation analysis widely used for evaluating model stability in the context of ordinary least squares regression are only applicable when the descriptors are independent of each other and errors are independent and normally distributed; neither assumption holds for QSAR in general and for PLS in particular. Progressive scrambling is a novel, nonparametric approach to perturbing models in the response space in a way that does not disturb the underlying covariance structure of the data. Here, we introduce adjustments for two of the characteristic values produced by a progressive scrambling analysis - the deprecated predictivity (Q*2s) and standard error of prediction (SDEPs*) - that correct for the effect of introduced perturbation. We also explore the statistical behavior of the adjusted values (Q*2(0) and SDEP0*) and the sensitivity to perturbation (dq2/dryy'2). It is shown that the three statistics are all robust for stable PLS models, in terms of the stochastic component of their determination and of their variation due to sampling effects involved in training set selection.

Data Interpretation, Statistical↗
PubMed2000

Neural network model for predicting peak photochemical pollutant levels.

In this paper, an attempt is made for the 24-hr prediction of photochemical pollutant levels using a neural network model. For this purpose, a model is developed that relates peak pollutant concentrations to meteorological and emission variables and indexes. The analysis is based on measurements of O3 and NO2 from the city of Athens. The meteorological variables are selected to cover atmospheric processes that determine the fate of the airborne pollutants while special care is taken to ensure the availability of the required input data from routine observations or forecasts. The comparison between model predictions and actual observations shows a good agreement. In addition, a series of sensitivity tests is performed in order to evaluate the sensitivity of the model to the uncertainty in meteorological variables. Model forecasts are generally rather insensitive to small perturbations in most of the input meteorological data, while they are relatively more sensitive in changes in wind speed and direction.

Air Pollutants↗
PubMed2025

Iterative, multimodal, and scalable single-cell profiling for discovery and characterization of signaling regulators.

Cell signaling plays a critical role in regulating cellular state, yet uncovering regulators of signaling pathways and understanding their molecular consequences remains challenging. Here, we present an iterative experimental and computational framework to identify and characterize regulators of signaling proteins, using the mTOR marker phosphorylated RPS6 (pRPS6) as a case study. We present a customized workflow that uses the 10x Flex assay to jointly profile intracellular protein levels, transcriptomes, and CRISPR perturbations in single cells. We use this to generate a "glossary" dataset of paired protein-RNA measurements across targeted perturbations, which we leverage to train a predictive model of pRPS6 levels based solely on transcriptomic data. Applying this model to a genome-wide Perturb-seq dataset enables in silico screening for pRPS6 and nominates novel regulators of mTOR signaling. Experimental validation confirms these predictions and reveals mechanistic diversity among hits, including changes in signaling output driven by anabolic activity, cellular proliferation and multiple stress pathways. Our work demonstrates how integrated experimental and computational approaches provide a scalable framework for multimodal phenotyping and discovery.

Journal Article↗
PubMed1997

Electroperturbation of the human skin barrier in vitro: II. Effects on stratum corneum lipid ordering and ultrastructure.

In transdermal iontophoresis, drugs can be driven across the skin by electrorepulsion, but their transport can also be enhanced by electrical perturbation of the skin barrier. Our objective was to study perturbing effects of electrical current on human stratum corneum lipid fine structure combining techniques including freeze-fracture electron microscopy. Human stratum corneum was subjected to pulsed constant currents, varying from 0.013-13 mA.cm-2. The voltage across the stratum corneum was high-frequency-sampled and s.c. impedence values derived from it. Upon termination of the current, skin samples were rapidly frozen and processed for freeze-fracture electron microscopy or subjected to X-ray diffraction analysis. Initially a rapid decrease of the resistance and, overall, a rapid increase of the capacitances was observed; generally, these effects became more pronounced with increasing current density. Wide- and small-angle X-ray diffractograms of human stratum corneum exposed for 1 h to the highest current indicated a disordering of both the lateral packaging arrangement and long-range lamellar stacking of the intercellular lipids of stratum corneum. Furthermore, an increase in the stratum corneum hydration level as a result of electrical current application was observed. On electron micrographs of freeze-fracture replicas of human stratum corneum, exposed for 1 h to current densities between 0.013 and 13 mA.cm-2, perturbations of the intercellular lipid structure were observed in accordance with the results of X-ray diffraction; these perturbations aggravated with increasing current density. Together, the data suggest that both the lateral and the longitudinal disordering of the intercellular lipids observed with X-ray diffraction may be responsible for the appearance of perturbed structures observed with freeze-fracture electron microscopy. The lipid disordering may be due to polarization of the lipid head groups induced by the electrical field, followed by mutual repulsion.

Adult↗
PubMed1995

In vivo measurements of pulmonary angiotensin-converting enzyme kinetics. I. Theory and error analysis.

We developed a procedure for measuring pulmonary angiotensin-converting enzyme kinetics with fluorine-18 fluorocaptopril and positron emission tomography (PET). The method is based on the application of a compartmental receptor model that represents the kinetics of two species of ligand, presumably the trans and cis conformers of captopril. The input function was characterized and includes corrections for the labeled metabolites of fluorocaptopril. Application of the procedure to lung time-activity data obtained with PET produced estimates of kinetic parameters demonstrating fast kinetics for one conformer and slower kinetics for the other. Simulation studies were performed to evaluate the sensitivity of the estimated parameters to errors in the model assumptions and in measured values for variables required for analysis of the PET data. Estimates for two of the kinetic parameters, the amount of perfused unbound functional enzyme normalized to regional lung volume and the association rate constant for the trans conformer, were relatively stable even with large errors in the input data, varying < 30% from true values for all perturbations. Thus, the procedure produces reliable estimates of the kinetics of the trans conformer of captopril as well as theoretical curves that are close to the observed data.

Animals↗
PubMed2005

Correlation function bootstrapping in quantum chaotic systems.

We discuss a general and efficient approach for "bootstrapping" short-time correlation data in chaotic or complex quantum systems to obtain information about long-time dynamics and stationary properties, such as the local density of states. When the short-time data are sufficient to identify an individual quantum system, we obtain a systematic approximation for the spectrum and wave functions. Otherwise, we obtain statistical properties, including wave function intensity distributions, for an ensemble of all quantum systems sharing the given short-time correlations. The results are valid for open or closed systems, and are stable under perturbation of the short-time input data. Numerical examples include quantum maps and two-dimensional anharmonic oscillators.

Journal Article↗
PubMed2005

Frontotemporal alterations in pediatric bipolar disorder: results of a voxel-based morphometry study.

CONTEXT: While numerous magnetic resonance imaging (MRI) studies have evaluated adults with bipolar disorder (BPD), few have examined MRI changes in children with BPD. OBJECTIVE: To determine volume alterations in children with BPD using voxel-based morphometry, an automated MRI analysis method with reduced susceptibility to various biases. A priori regions of interest included amygdala, accumbens, hippocampus, dorsolateral prefrontal cortex (DLPFC), and orbitofrontal cortex. DESIGN: Ongoing study of the pathophysiology of pediatric BPD. SETTING: Intramural National Institute of Mental Health; approved by the institutional review board. Patients Pediatric subjects with BPD (n = 20) with at least 1 manic or hypomanic episode meeting strict DSM-IV criteria for duration and elevated, expansive mood. Controls (n = 20) and their first-degree relatives lacked psychiatric disorders. Groups were matched for age and sex and did not differ in IQ. MAIN OUTCOME MEASURES: With a 1.5-T MRI machine, we collected 1.2-mm axial sections (124 per subject) with an axial 3-dimensional spoiled gradient recalled echo in the steady state sequence. Image analysis was by optimized voxel-based morphometry. RESULTS: Subjects with BPD had reduced gray matter volume in the left DLPFC. With a less conservative statistical threshold, additional gray matter reductions were found in the left accumbens and left amygdala. No difference was found in the hippocampus or orbitofrontal cortex. CONCLUSIONS: Our results are consistent with data implicating the prefrontal cortex in emotion regulation, a process that is perturbed in BPD. Reductions in amygdala and accumbens volumes are consistent with neuropsychological data on pediatric BPD. Further study is required to determine the relationship between these findings in children and adults with BPD.

Adolescent↗
PubMed1990

1H NMR assignment and melting temperature study of cis-syn and trans-syn thymine dimer containing duplexes of d(CGTATTATGC).d(GCATAATACG).

The preparation and spectroscopic characterization of duplex decamers containing site-specific cis-syn and trans-syn thymine dimers are described. Three duplex decamers, d(CGTATTATGC).d(GCATAATACG), d(CGTAT[c,s]TATGC).d(GCATAATACG), and d(CGTAT[t,s]TATGC).d(GCATAATACG), were prepared by solid-phase phosphoramidite synthesis utilizing cis-syn and trans-syn cyclobutane thymine dimer building blocks (Taylor et al., 1987; Taylor & Brockie, 1988). NMR spectra (500 MHz 2D 1H and 202 MHz 1D 31P) were obtained in "100%" D2O at 10 degrees C, and 1D exchangeable 1H spectra were obtained in 10% D2O at 10 degrees C. 1H NMR assignments for H5, H6, H8, CH3, H1', H2', and H2" were made on the basis of standard sequential NOE assignment strategies and verified in part by DQF COSY data. Comparison of the chemical shift data suggests that the helix structure is perturbed more to the 3'-side of the cis-syn dimer and more to the 5'-side of the trans-syn dimer. Thermodynamic parameters for the helix in equilibrium coil equilibrium were obtained by two-state, all or none, analysis of the melting behavior of the duplexes. Analysis of the temperature dependence of the T5CH3 1H NMR signal gave delta H = 44 +/- 4 kcal and delta S = 132 +/- 13 eu for the trans-syn duplex. Analysis of the concentration and temperature dependence of UV spectra gave delta H = 64 +/- 6 kcal and delta S = 178 +/- 18 eu for the parent duplex and delta H = 66 +/- 7 kcal and delta S = 189 +/- 19 eu for cis-syn duplex. It was concluded that photodimerization of the dTpdT unit to give the cis-syn product causes little perturbation of the DNA whereas dimerization to give the trans-syn product causes much greater perturbation, possibly in the form of a kink or dislocation at the 5'-side of the dimer.

Base Composition↗
PubMed1986

Erythrocyte membrane deformability and stability: two distinct membrane properties that are independently regulated by skeletal protein associations.

Skeletal proteins play an important role in determining erythrocyte membrane biophysical properties. To study whether membrane deformability and stability are regulated by the same or different skeletal protein interactions, we measured these two properties, by means of ektacytometry, in biochemically perturbed normal membranes and in membranes from individuals with known erythrocyte abnormalities. Treatment with 2,3-diphosphoglycerate resulted in membranes with decreased deformability and decreased stability, whereas treatment with diamide produced decreased deformability but increased stability. N-ethylmaleimide induced time-dependent changes in membrane stability. Over the first minute, the stability increased; but with continued incubation, the membranes became less stable than control. Meanwhile, the deformability of these membranes decreased with no time dependence. Biophysical measurements were also carried out on pathologic erythrocytes. Membranes from an individual with hereditary spherocytosis and a defined abnormality in spectrin-protein 4.1 association showed decreased stability but normal deformability. In a family with hereditary elliptocytosis and an abnormality in spectrin self-association, the membranes had decreased deformability and stability. Finally, membranes from several individuals with Malaysian ovalocytosis had decreased deformability but increased stability. Our data from both pathologic membranes and biochemically perturbed membranes show that deformability and stability change with no fixed relationship to one another. These findings imply that different skeletal protein interactions regulate membrane deformability and stability. In light of these data, we propose a model of the role of skeletal protein interactions in deformability and stability.

Cytoskeletal Proteins↗
PubMed1985

Dissociation of the receptor for immunoglobulin E in mild detergents.

We previously showed that, in the absence of phospholipids, exposure of the tetrameric receptor for immunoglobulin E to mild detergents dissociates the intact beta chain and two gamma chains from the alpha chains. Having developed a practical method for assaying the dissociation, we have now explored a variety of different detergents, detergent concentrations, temperatures, times, salts, pHs, and other factors that influence the detergent-induced dissociation. Our findings should be useful for optimizing the stability of the receptor and for future studies on recombination of the subunits. The data suggest the following: (1) The critical perturbant is micellar detergent. (2) Unlike solubilization of membranes, where a molar ratio of micellar detergent:lipid of 2 is adequate, dissociation of the receptor is incomplete even at molar ratios of micellar detergent:receptor of greater than 10(5) and may be limited by a reversible component. (3) Detergents that are best for solubilizing membranes are also best for dissociating the receptors. (4) The latter observation and other data implicate bound lipid as stabilizing the receptor. Our findings may be applicable to the study of interactions between membrane proteins in general.

Animals↗