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PubMed2006

Femtosecond study on the isomerization dynamics of NK88. I. Ground-state dynamics after photoexcitation.

Recently, optimal control of a photoisomerization reaction in the liquid phase was demonstrated for the first time on the system 3,3(')-diethyl-2,2(')-thiacyanine (NK88). Additionally, the class of cyanines to which the molecule NK88 belongs draws a lot of attention in different recent theoretical publications. Therefore, a better understanding of the molecular dynamics of this molecular system is of special interest. Experiments using the femtosecond pump-supercontinuum probe technique with an excitation wavelength of 400 nm and a spectral range from 370 to 620 nm for the probe beam have been performed. In order to analyze the dynamics properly the time window has been chosen to comprise the characteristic times of the contributing processes, additionally we have employed two solvents, methanol and ethylene glycol, and have conducted anisotropy measurements. The spectroscopic data have been assigned to different molecular states with the help of density functional theory and second-order Moller-Plesset perturbation theory calculations. The analysis of the data has revealed in the most likely model that three different isomers exist with different lifetimes. On the basis of experimental and theoretical data, a conclusive scheme of the isomerization reaction is presented.

Anisotropy↗
PubMed2001

Psychopathy and developmental instability.

Psychopaths are manipulative, impulsive, and callous individuals with long histories of antisocial behavior. Two models have guided the study of psychopathy. One suggests that psychopathy is a psychopathology, i.e., the outcome of defective or perturbed development. A second suggests that psychopathy is a life-history strategy of social defection and aggression that was reproductively viable in the environment of evolutionary adaptedness (EEA). These two models make different predictions with regard to the presence of signs of perturbations or instability in the development of psychopaths. In Study 1, we obtained data on prenatal, perinatal, and neonatal signs of developmental perturbations from the clinical files of 643 nonpsychopathic and 157 psychopathic male offenders. In Study 2, we measured fluctuating asymmetry (FA, a concurrent sign of past developmental perturbations) in 15 psychopathic male offenders, 25 nonpsychopathic male offenders, and 31 male nonoffenders. Psychopathic offenders scored lower than nonpsychopathic offenders on obstetrical problems and FA; both psychopathic and nonpsychopathic offenders scored higher than nonoffenders on FA. The five offenders from Study 2 meeting the most stringent criteria for psychopathy were similar to nonoffenders with regard to FA and had the lowest asymmetry scores among offenders. These results provide no support for psychopathological models of psychopathy and partial support for life-history strategy models.

Journal Article↗
PubMed2003

Gait perturbation response in chronic anterior cruciate ligament deficiency and repair.

OBJECTIVE: To determine how chronic anterior cruciate ligament deficient and surgically repaired subjects react to unexpected forward perturbations during gait as compared to healthy controls. DESIGN: Gait testing of 10 chronic anterior cruciate ligament deficient subjects prior to and three months following reconstructive surgery, and 10 uninjured controls. BACKGROUND: The ability of an anterior cruciate ligament injured individual to react and maintain equilibrium during gait perturbations is critical for the prevention of reinjury. No studies have investigated how these individuals respond to unexpected perturbations during normal gait. METHODS: An unexpected forward perturbation was induced upon heel strike using a force plate capable of translational movement. RESULTS: Prior to surgery, the anterior cruciate ligament subjects exhibited a greater knee extensor moment in response to the perturbation compared to healthy controls. Following surgery, the anterior cruciate ligament injured subjects exhibited a static knee position and a sustained knee extensor moment throughout stance in response to the perturbation as compared to controls. CONCLUSIONS: These data suggest that chronic anterior cruciate ligament deficient subjects rely heavily on knee extensor musculature to prevent collapse in response to an unexpected perturbation. This same reactive response was more pronounced 3 months following surgery. RELEVANCE: The results suggest that, prior to and following surgery, chronic anterior cruciate ligament injured subjects respond differently than healthy controls to an unexpected perturbation during gait. Anterior cruciate ligament injured or repaired subjects do not reduce or avoid vigorous contraction of the quadriceps muscles when responding to gait perturbations.

Adult↗
PubMed2003

Recombination or mutation rate heterogeneity? Implications for Mitochondrial Eve.

The study of mitochondrial DNA (mtDNA) has helped to demonstrate the African origin of our species and the relationship between living humans and the Neanderthals. mtDNA data have also been used to establish the time and route of major events in human history, such as the expansion of Neolithic farmers into Europe, and the settlement of the Pacific and the New World. However, it is becoming apparent that mtDNA evolution is more complex than previously believed. Anomalous mutation patterns perturb phylogenetic assumptions based on mtDNA data. Although they are frequently dismissed as sequencing errors or mutation hotspots, some of the anomalies have no satisfactory explanation. The mechanisms behind apparent mutation rate heterogeneity, or even possible mtDNA recombination, remain unknown. These issues need to be addressed, as they have profound consequences for the interpretation of mtDNA data.

Base Sequence↗
PubMed2003

Geometric scaling in inclusive eA reactions and nonlinear perturbative QCD.

We report on geometric scaling in inclusive eA scattering data from the NMC and E665 experiments. This scaling and nuclear shadowing follows the pattern expected from nonlinear perturbative QCD for zero impact parameter at sufficiently small x(bj) and is compatible with geometric scaling in ep.

Journal Article↗
PubMed2006

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo.

We present a method (the Inferelator) for deriving genome-wide transcriptional regulatory interactions, and apply the method to predict a large portion of the regulatory network of the archaeon Halobacterium NRC-1. The Inferelator uses regression and variable selection to identify transcriptional influences on genes based on the integration of genome annotation and expression data. The learned network successfully predicted Halobacterium's global expression under novel perturbations with predictive power similar to that seen over training data. Several specific regulatory predictions were experimentally tested and verified.

Adenosine Triphosphatases↗
PubMed2007

The influence of pharmacogenetics on fatty liver disease in the wistar and kyoto rats: a combined transcriptomic and metabonomic study.

Although fatty liver disease is caused by a number of toxicological insults and the metabolic syndrome, the exact mechanisms by which many of these pathophysiological stimulii induce fatty liver are unknown. The rapid and profound steatosis caused by orotic acid, resulting from an impairment in the production of ApoB, has been investigated in the Wistar strain rat using a combined transcriptomic and metabonomic/metabolomic approach. Analysis of liver tissue from rats exposed to orotic acid for 1, 3, and 14 days was performed by DNA microarrays and high resolution 1H NMR spectroscopy based metabonomics of both tissue extracts and intact tissue (n = 3). Data were analyzed using a combination of ANOVA and principal components analysis, used as a data reduction tool to visualize the most perturbed transcripts and metabolites. Orotic acid produced a profound 8-fold increase in total lipids, and in particular increases in resonances associated with polyunsaturated fats (CH=CH and CH2CH=CH groups). This was accompanied by increases in the concentrations of trimethylamine-oxide (TMAO), betaine, choline, and phosphocholine, as well as a relative decrease in glucose and glycogen. At the transcriptional level, perturbations were detected in both oxidative stress and osmoregulation/pH homeostasis. However, this contrasts with a previous transcriptomic/metabolic study of fatty liver disease in a combined data set of Wistar (out-bred) and Kyoto (in-bred) strains of rats, with only 4 transcripts being found to be in common between the two analyses. This emphasizes the need to understand how strain background interacts with a given toxic lesion or genetic modification.

Animals↗
PubMed2005

Using large-scale perturbations in gene network reconstruction.

BACKGROUND: Recent analysis of the yeast gene network shows that most genes have few inputs, indicating that enumerative gene reconstruction methods are both useful and computationally feasible. A simple enumerative reconstruction method based on a discrete dynamical system model is used to study how microarray experiments involving modulated global perturbations can be designed to obtain reasonably accurate reconstructions. The method is tested on artificial gene networks with biologically realistic in/out degree characteristics. RESULTS: It was found that a relatively small number of perturbations significantly improve inference accuracy, particularly for low-order inputs of one or two genes. The perturbations themselves should alter the expression level of approximately 50-60% of the genes in the network. CONCLUSIONS: Time-series obtained from perturbations are a common form of expression data. This study illustrates how gene networks can be significantly reconstructed from such time-series while requiring only a relatively small number of calibrated perturbations, even for large networks, thus reducing experimental costs.

Algorithms↗
PubMed2005

An integrative genomics approach to infer causal associations between gene expression and disease.

A key goal of biomedical research is to elucidate the complex network of gene interactions underlying complex traits such as common human diseases. Here we detail a multistep procedure for identifying potential key drivers of complex traits that integrates DNA-variation and gene-expression data with other complex trait data in segregating mouse populations. Ordering gene expression traits relative to one another and relative to other complex traits is achieved by systematically testing whether variations in DNA that lead to variations in relative transcript abundances statistically support an independent, causative or reactive function relative to the complex traits under consideration. We show that this approach can predict transcriptional responses to single gene-perturbation experiments using gene-expression data in the context of a segregating mouse population. We also demonstrate the utility of this approach by identifying and experimentally validating the involvement of three new genes in susceptibility to obesity.

11-beta-Hydroxysteroid Dehydrogenase Type 1↗
PubMed1995

Muscle-joint models incorporating activation dynamics, moment-angle, and moment-velocity properties.

Muscle input/output models incorporating activation dynamics, moment-angle, and moment-velocity factors are commonly used to predict the moment produced by muscle during nonisometric contractions; the three factors are generally assumed to be independent. We examined the ability of models with independent factors, as well as models with coupled factors, to fit input/output data measured during simultaneous modulation of the fraction of muscle stimulated (recruitment) and joint angle inputs. The models were evaluated in stimulated cat soleus muscles producing ankle extension moment, with regard to their potential applications in neuroprostheses with either fixed parameters or parameter adaptation. Both uncoupled and coupled models predicted the output moment well for random angle perturbation sizes ranging from 10 degrees to 30 degrees. For the uncoupled model, the best parameter values depended on the range of perturbations and the mean angle. Introducing coupling between activation and velocity in the model reduced this parameter sensitivity; one set of model parameter values fit the data for all perturbation sizes and also fit the data under isometric or constant stimulation conditions. Thus, the coupled model would be the most appropriate for applications requiring fixed parameter values. In contrast, with continuous parameter adaptation, errors due to changing test conditions decreased more quickly for the uncoupled model, suggesting that it would perform well in adaptive control of neuroprostheses.

Animals↗
PubMed1994

Application of flow cytometry to determine the cytotoxicity of urethane dimethacrylate in human cells.

The effects of an oligomer, urethane dimethacrylate (UDMA), on two human cell lines were studied using flow cytometry (FCM). Untreated and treated cultures of propidium iodine-stained KB (epidermal oral carcinoma cells) and human foreskin fibroblast (HFF) cells were analyzed for cellular DNA content. Concentrations of 10 and 25 microM of UDMA slightly perturbed the KB cell cycle progression at 24 and 48 h of incubation. However, the effect of 50 microM was more pronounced at the latter incubation time period. In cell growth experiments, the sublethal concentrations (10 and 25 microM) produced inhibition of KB cell growth rate at a moderate level, which resulted in the prolongation of cell population doubling time. Significant inhibition of cell growth occurred when 50 microM (lethal concentration) was used. Data obtained from the cell cycle perturbation analysis, evidenced by FCM, correlated with the extent of inhibition in KB cell growth rates. The effects of sublethal concentrations were reversible during a 24 h period of oligomer withdrawal from culture medium. In contrast, the effects of 50 microM were not reversible. In HFF cells the depletion of S phase in the cell cycle was the major effect of 50 microM of UDMA. It was concluded that FCM technology is an ideal and practical approach for studying the cytotoxicity of components of dental composites.

Carcinoma↗
PubMed2003

Synchrotron SAXS studies on the structural stability of Carcinus aestuarii hemocyanin in solution.

The effect of GuHCl and of NaCl on the structural properties of the hemocyanin (Hc) from Carcinus aestuarii has been studied by small angle x-ray scattering (SAXS) using synchrotron radiation. SAXS data collected as a function of perturbant concentration have been used to analyze conformational states of hexameric holo and apoHc as well as the holo and apoforms of the monomeric subunit CaeSS2. In the case of the holoprotein in GuHCl, two concentration domains were identified: at lower concentration, the perturbant induces aggregation of Hc molecules, whereas at higher concentration the aggregates dissociate with concomitant denaturation of the protein. In contrast, with apoHc the denaturation occurs at rather low GuHCl, pointing to an important effect of the active site bound copper for the stabilization of Hc tertiary structure. The effects of NaCl are similar to those of GuHCl as far as CaeSS2 is concerned, namely oligomerization precedes denaturation, whereas in the case of the hexameric form no aggregation occurs. To improve data analysis, on the basis of the current models for Hc monomers and oligomers, the fraction of each aggregation state and/or unfolded protein has been determined by fitting experimental SAXS curves with form factors calculated from Monte Carlo methods. In addition, a global analysis has been carried out on the basis of a thermodynamic model involving an equilibrium between a monomer in a nativelike and denatured form as well as a class of equilibria among the monomer and other aggregates.

Algorithms↗
PubMed2004

Dynamics of water probed with vibrational echo correlation spectroscopy.

Vibrational echo correlation spectroscopy experiments on the OD stretch of dilute HOD in H(2)O are used to probe the structural dynamics of water. A method is demonstrated for combining correlation spectra taken with different infrared pulse bandwidths (pulse durations), making it possible to use data collected from many experiments in which the laser pulse properties are not identical. Accurate measurements of the OD stretch anharmonicity (162 cm(-1)) are presented and used in the data analysis. In addition, the recent accurate determination of the OD vibrational lifetime (1.45 ps) and the time scale for the production of vibrational relaxation induced broken hydrogen bond "photoproducts" ( approximately 2 ps) aid in the data analysis. The data are analyzed using time dependent diagrammatic perturbation theory to obtain the frequency time correlation function (FTCF). The results are an improved FTCF compared to that obtained previously with vibrational echo correlation spectroscopy. The experimental data and the experimentally determined FTCF are compared to calculations that employ a polarizable water model (SPC-FQ) to calculate the FTCF. The SPC-FQ derived FTCF is much closer to the experimental results than previously tested nonpolarizable water models which are also presented for comparison.

Deuterium↗
PubMedDate not supplied

Changes in oxidative balance in rat pericytes exposed to diabetic conditions.

Recent data indicate that the oxidative stress plays an important role in the pathogenesis of diabetes and its complications such as retinopathy, nephropathy and accelerated atherosclerosis. In diabetic retinopathy, it was demonstrated a selective loss of pericytes accompanied by capillary basement membrane thickening, increased permeability and neovascularization. This study was designed to investigate the role of diabetic conditions such as high glucose, AGE-Lysine, and angiotensin II in the modulation of antioxidant enzymes activities, glutathione level and reactive oxygen species (ROS) production in pericytes. The activity of antioxidant enzymes: superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and total glutathione (GSH) was measured spectrophotometrically. The production of ROS was detected by spectrofluorimetry and fluorescence microscopy after loading the cells with 2'-7' dichlorofluoresceine diacetate; as positive control H2O2 was used. Intracellular calcium was determined using Fura 2 AM assay. The results showed that the cells cultured in high glucose alone, do not exhibit major changes in the antioxidant enzyme activities. The presence of AGE-Lys or Ang II induced the increase of SOD activity. Their combination decreased significantly GPx activity and GSH level. A three times increase in ROS production and a significant impairment of intracellular calcium homeostasis was detected in cells cultured in the presence of the three pro-diabetic agents used. In conclusion, our data indicate that diabetic conditions induce in pericytes: (i) an increase of ROS and SOD activity, (ii) a decrease in GPx activity and GSH level, (iii) a major perturbation of the intracellular calcium homeostasis. The data may explain the structural and functional abnormalities of pericytes characteristic for diabetic retinopathy.

Angiotensin II↗
PubMed2002

The gene encoding the transcriptional regulator Yin Yang 1 (YY1) is a myeloid transforming gene interfering with neutrophilic differentiation.

The genetic defects underlying the pathogenesis of acute myeloid leukemia (AML) are still largely unknown. Retroviral insertion mutagenesis in mice has become a powerful tool to identify candidate genes involved in the development of leukemia and lymphoma. We have used this strategy with the 1.4 strain of Graffi murine leukemia virus (MuLV), which predominantly causes myeloid leukemias. Here, we report that Graffi-1.4-induced AML frequently harbors virus integrations in the gene encoding the transcription factor Yin Yang 1 (YY1). These integrations occurred in both orientations, and all were located in the 5' promoter region of the gene, 0.5 to 1.5 kb upstream of the major transcriptional start site. Luciferase reporter assays showed that virus integration in this region increases promoter activity and renders it independent of a functional binding site for Sp1, a major transcriptional regulator of YY1. We used the murine 32D model to study the consequence of perturbed YY1 expression for myelopoiesis. YY1 protein levels were high in 32D parental cells maintained in interleukin-3-containing medium, but they dropped when the cells were induced to differentiate by granulocyte-colony-stimulating factor (G-CSF). Strikingly, G-CSF-induced neutrophilic differentiation was reduced in 32D cell transfectants ectopically expressing YY1. In similar experiments on primary bone marrow cells, enforced YY1 expression blocked the outgrowth of CFU-GM colonies. Increased YY1 expression was seen in some cases of human AML. Collectively, these data imply a possible role of perturbed expression of YY1 in the development of AML through interference with the myeloid differentiation program in the leukemic progenitor cells.

Animals↗
PubMed2006

An empirical method for the determination of wall perturbation factors for parallel-plate chambers in high-energy electron beams.

The calibration of ion chambers in high-energy electron beams in terms of absorbed dose to water at the National Physical Laboratory requires knowledge of the ratio of perturbation factors in graphite and water phantoms. During a review of data required for the NPL calibration procedure an empirical model was developed to calculate the perturbation due to the rear wall, pwall, of a well-guarded ion chamber in a high-energy electron beam. The overall uncertainty in this method is estimated to be 0.4%, which is the lowest value reported to date. The model reproduces measured data at the 0.1% level or better and indicates that the NACP ion chamber has a nonzero perturbation factor in electron beams due to backscatter from the rear wall. The effect is small (<0.5%) at high energies (R50>4 cm, E0>10 MeV) but becomes large at low energies-up to 1.4% at E0=4 MeV (R50=1.2 cm). The model indicates that there is a nonzero correction for the NACP chamber in both a graphite and water phantom and that material adjacent to the air cavity has a significant effect on the measured ionization. These values are consistent with previous measurements and recent Monte Carlo calculations. The model could be used in the design of ion chambers and in the estimation of corrections for non-homogeneous systems, especially in the absence of accurate Monte Carlo simulations.

Calibration↗
PubMed1986

Conformational transitions in N-linked oligosaccharides.

An assignment strategy involving 1H-1H correlated spectroscopy (COSY), relayed correlation spectroscopy (RECSY), nuclear Overhauser effect spectroscopy (NOESY), and triple quantum filtered correlated spectroscopy (TQCOSY) is described for six related N-linked oligosaccharides. These are of three "types", i.e., complex, bisected complex, and oligomannose. Using spin-spin coupling constant data derived from these assignments, together with semiempirical quantum mechanical energy calculations, we have examined the rotamer distributions at the Man alpha 1-6Man beta-linkage in each structure, and additionally at the Man alpha 1-6Man alpha-linkage in oligomannose oligosaccharides. We show that while several primary sequence differences are "passive", certain key residues modulate the orientation of the alpha 1-6 arms. These residues may be proximal or distal to the site of the conformational change. There is no direct correlation between these perturbations and the oligosaccharide type. These data are discussed in terms of the proposed recognition function of oligosaccharides in biological systems.

Animals↗
PubMed1996

Fusogenic properties of the C-terminal domain of the Alzheimer beta-amyloid peptide.

A series of natural peptides and mutants, derived from the Alzheimer beta-amyloid peptide, was synthesized, and the potential of these peptides to induce fusion of unilamellar lipid vesicles was investigated. These peptide domains were identified by computer modeling and correspond to respectively the C-terminal (e.g. residues 29-40 and 29-42) and a central domain (13-28) of the beta-amyloid peptide. The C-terminal peptides are predicted to insert in an oblique way into a lipid membrane through their N-terminal end, while the mutants are either parallel or perpendicular to the lipid bilayer. Peptide-induced vesicle fusion was demonstrated by several techniques, including lipid-mixing and core-mixing assays using pyrene-labeled vesicles. The effect of peptide elongation toward the N-terminal end of the entire beta-amyloid peptide was also investigated. Peptides corresponding to residues 22-42 and 12-42 were tested using the same techniques. Both the 29-40 and 29-42 beta-amyloid peptides were able to induce fusion of unilamellar lipid vesicles and calcein leakage, and the amyloid 29-42 peptide was the most potent fusogenic peptide. Neither the two mutants or the 13-28 beta-amyloid peptide had any fusogenic activity. Circular dichroism measurements showed an increase of the alpha-helical content of the two C-terminal peptides at increasing concentrations of trifluoroethanol, which was accompanied by an increase of the fusogenic potential of the peptides. Our data suggest that the alpha-helical content and the angle of insertion of the peptide into a lipid bilayer are critical for the fusogenic activity of the C-terminal domain of the amyloid peptide. The differences observed between the fusogenic capacity of the amyloid 29-40 and 29-42 peptides might result from differences in the degree of penetration of the peptides into the membrane and the resulting membrane destabilization. The longer peptides, residues 22-42 and 12-42, had decreased, but significant, fusogenic properties associated with perturbation of the membrane permeability. These data suggest that the fusogenic properties of the C-terminal domain of the beta-amyloid peptide might contribute to the cytotoxicity of the peptide by destabilizing the cell membrane.

Alzheimer Disease↗