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At least 991 records · Page 55Linked to original sources
PubMed2004

Crystallographic analysis of the interaction of nitric oxide with quaternary-T human hemoglobin.

In addition to interacting with hemoglobin as a heme ligand to form nitrosylhemoglobin, NO can react with cysteine sulfhydryl groups to form S-nitrosocysteine or cysteine oxides such as cysteinesulfenic acid. Both modes of interaction are very sensitive to the quaternary structure of hemoglobin. To directly view the interaction of NO with quaternary-T deoxyhemoglobin, crystallographic studies were carried out on crystals of deoxyhemoglobin that were exposed to gaseous NO under a variety of conditions. Consistent with previous spectroscopic studies in solution, these crystallographic studies show that the binding of NO to the heme groups of crystalline wild-type deoxyhemoglobin ruptures the Fe-proximal histidine bonds of the alpha-subunits but not the beta-subunits. This finding supports Perutz's theory that ligand binding induces tension in the alpha Fe-proximal histidine bond. To test Perutz's theory, deoxy crystals of the mutant hemoglobin betaW37E were exposed to NO. This experiment was carried out because previous studies have shown that this mutation greatly reduces the quaternary constraints that oppose the ligand-induced movement of the alpha-heme Fe atom into the plane of the porphyrin ring. As hypothesized, the Fe-proximal histidine bonds in both the beta- and the alpha-subunits remain intact in crystalline betaW37E after exposure to NO. With regard to S-nitrosocysteine or cysteine oxide formation, no evidence for the reaction of NO with any cysteine residues was detected under anaerobic conditions. However, when deoxyhemoglobin crystals are first exposed to air and then to NO, the appearance of additional electron density indicates that Cys93(F9)beta has been modified, most likely to cysteinesulfenic acid. This modification of Cys93(F9)beta disrupts the intrasubunit salt bridge between His146(HC3)beta and Asp94(FG1)beta, a key feature of the quaternary-T hemoglobin structure. Also presented is a reanalysis of our previous crystallographic studies [Chan, N.-L., et al. (1998) Biochemistry 37, 16459-16464] of the interaction of NO with liganded hemoglobin in the quaternary-R2 structure. These studies showed additional electron density at Cys93(F9)beta that was consistent with an NO adduct. However, for reasons discussed in this paper, we now believe that this adduct may be the Hb-S-N.-O-H radical intermediate and not Hb-S-N=O as previously suggested.

Anaerobiosis↗
PubMed2003

Substrate-induced conformational changes in Escherichia coli taurine/alpha-ketoglutarate dioxygenase and insight into the oligomeric structure.

The enzymes in the alpha-ketoglutarate (alphaKG) dependent dioxygenase superfamily represent the largest class of non-heme iron oxidases and have important medical, ecological, and biotechnological roles. One such enzyme, taurine/alpha-ketoglutarate dioxygenase (TauD), catalyzes the conversion of 2-aminoethanesulfonate (taurine) to sulfite and aminoacetaldehyde while decomposing alphaKG to succinate and CO(2). This alphaKG dependent dioxygenase is expressed in Escherichia coli under sulfur starvation conditions and allows the cell to utilize taurine, and other similar sulfonates in the environment, as an alternative sulfur source. In this work, we report the structures of the apo and holo forms of TauD to 1.9 A resolution (R(cryst) = 21.2%, R(free) = 24.9%) and 2.5 A resolution (R(cryst) = 22.5%, R(free) = 27.8%), respectively. The models reported herein provide significant new insight into the substrate orientations at the active site and the conformational changes that are induced upon taurine binding. Furthermore, analysis of our crystallographic data coupled with reanalysis of the crystallographic model (resolution = 3.0 A, R(cryst) = 28.1, R(free) = 32.0) presented by Elkins et al. (Biochemistry (2002) 41, 5185-5192) reveals an alternative oligomeric arrangement for the enzyme that is consistent with the conserved primary and secondary structure elements of other alphaKG dependent dioxygenases.

Apoenzymes↗
PubMed2004

An appraisal of multiple NADPH binding-site models proposed for cytochrome P450 reductase, NO synthase, and related diflavin reductase systems.

The diflavin reductases exemplified by mammalian cytochrome P450 reductase catalyze NADPH dehydrogenation and electron transfer to an associated monooxygenase. It has recently been proposed that double occupancy of the NADPH dehydrogenation site inhibits the NADPH to FAD hydride transfer step in this series of enzymes. This has important implications for the mechanism of enzyme turnover. However, the conclusions are drawn from a series of pre-steady-state stopped-flow experiments in which the data analysis and interpretation are flawed. Recent data published for P450-BM3 reductase show a decrease in the rate constant for pre-steady-state flavin oxidation with increasing NADP(+) concentration. This is interpreted as evidence of inhibition by multiple substrate binding. A detailed reanalysis shows that the data are in fact consistent with a simple single-binding-site model in which reversible hydride transfer causes the observed effect. Data for the related systems are also discussed.

Alanine↗
PubMed2002

Formation constants of copper(I)-olefin complexes in aqueous solution.

A simple kinetic method has been applied to measure the formation constants of aqueous copper(I) with fumaronitrile, dimethyl fumarate, and fumaric and maleic acids. At 0.14 M ionic strength, the values of beta(1) are (0.85 +/- 0.02) x 10(3), (6.1 +/- 0.1) x 10(3), (7.3 +/- 0.1) x 10(3), and (2.2 +/- 0.4) x 10(3) M(-1), respectively. The values for the last two olefins are compared to previous results. Values of beta(1) for hydrogen maleate and beta(2) for fumaronitrile also have been determined. A reanalysis of much earlier work has been done, and all the results are discussed in terms of the effect of substituents on the olefin on the beta(1) values. The structure of bis(fumaronitrile)copper(I) nitrate also is reported. The nitrile is N-coordinated to copper(I), which has a distorted tetrahedral geometry, while the overall structure consists of macrocyclic Cu(6)(fumaronitrile)(6) rings which extend in three dimensions.

Journal Article↗
PubMed2002

Kinetic study of the oxidation of catechol by aqueous copper(II).

The kinetics of the oxidation of catechol by aqueous copper(II) have been studied as a function of reactant concentrations at pH 6.4-7.2. To follow the reaction, a spectrophotometric method has been developed that circumvents the problem of precipitation of decomposition products of the initial o-quinone oxidation product. The rate law shows that the reactive species is the monocatecholate complex of Cu(II), and that this species undergoes rate-limiting intramolecular electron transfer with k = 1.9 x 10(-5) s(-1) (22 +/- 1 degrees C, mu = 0.125 M NaClO(4)). The results have allowed a reanalysis of previous work on the autoxidation in the aqueous Cu(II)-catechol-dioxygen system, and comparisons to mechanisms of copper(II) oxidases.

Journal Article↗
PubMed2004

Sensitive PCR analysis of animal tissue samples for fragments of endogenous and transgenic plant DNA.

An optimized DNA extraction protocol for animal tissues coupled with sensitive PCR methods was used to determine whether trace levels of feed-derived DNA fragments, plant and/or transgenic, are detectable in animal tissue samples including dairy milk and samples of muscle (meat) from chickens, swine, and beef steers. Assays were developed to detect DNA fragments of both the high copy number chloroplast-encoded maize rubisco gene (rbcL) and single copy nuclear-encoded transgenic elements (p35S and a MON 810-specific gene fragment). The specificities of the two rbcL PCR assays and two transgenic DNA PCR assays were established by testing against a range of conventional plant species and genetically modified maize crops. The sensitivities of the two rbcL PCR assays (resulting in 173 and 500 bp amplicons) were similar, detecting as little as 0.08 and 0.02 genomic equivalents, respectively. The sensitivities of the p35S and MON 810 PCR assays were approximately 5 and 10 genomic equivalents for 123 bp and 149 bp amplicons, respectively, which were considerably less than the sensitivity of the rbcL assays in terms of plant cell equivalents, but approximately similar when the higher numbers of copies of the chloroplast genome per cell are taken into account. The 173 bp rbcL assay detected the target plant chloroplast DNA fragment in 5%, 15%, and 53% of the muscle samples from beef steers, broiler chickens, and swine, respectively, and in 86% of the milk samples from dairy cows. Reanalysis of new aliquots of 31 of the pork samples that were positive in the 173 bp rbcL PCR showed that 58% of these samples were reproducibly positive in this same PCR assay. The 500 bp rbcL assay detected DNA fragments in 43% of the swine muscle samples and 79% of the milk samples. By comparison, no statistically significant detections of transgenic DNA fragments by the p35S PCR assay occurred with any of these animal tissue samples.

Animal Feed↗
PubMed2004

Intermolecular forces in spread phospholipid monolayers at oil/water interfaces.

The lateral intermolecular forces between phospholipids are of particular relevance to the behavior of biomembranes, and have been approached via studies of monolayer isotherms at aqueous interfaces, mostly restricted to air/water (A/W) systems. For thermodynamic properties, the oil/water (O/W) interface has major advantages but is experimentally more difficult and less studied. A comprehensive reanalysis of the available thermodynamic data on spread monolayers of phosphatidyl cholines (PC) and phosphatidyl ethanolamines (PE) at O/W interfaces is conducted to identify the secure key features that will underpin further development of molecular models. Relevant recourse is made to isotherms of single-chain molecules and of mixed monolayers to identify the contributions of chain-chain interactions and interionic forces. The emphasis is on the properties of the phase transitions for a range of oil phases. Apparent published discrepancies in thermodynamic properties are resolved and substantial agreement emerges on the main features of these phospholipid monolayer systems. In compression to low areas, the forces between the zwitterions of like phospholipids are repulsive. The molecular model for phospholipid headgroup interactions developed by Stigter et al. accounts well for the virial coefficients in expanded phospholipid O/W monolayers. Inclusion of the changes in configuration and orientation of the zwitterion headgroups on compression, which are indicated by the surface potentials in the phase transition region, and inclusion of the energy of chain demixing from the oil phase will be required for molecular modeling of the phase transitions.

Lipid Bilayers↗
PubMed1999

Cancer risk estimation of genotoxic chemicals based on target dose and a multiplicative model.

A mechanistic model and associated procedures are proposed for cancer risk assessment of genotoxic chemicals. As previously shown for ionizing radiation, a linear multiplicative model was found to be compatible with published experimental data for ethylene oxide, acrylamide, and butadiene. The validity of this model was anticipated in view of the multiplicative interaction of mutation with inherited and acquired growth-promoting conditions. Concurrent analysis led to rejection of an additive model (i.e. the model commonly applied for cancer risk assessment). A reanalysis of data for radiogenic cancer in mouse, dog and man shows that the relative risk coefficient is approximately the same (0.4 to 0.5 percent per rad) for tumours induced in the three species. Doses in vivo, defined as the time-integrated concentrations of ultimate mutagens, expressed in millimol x kg-1 x h (mMh) are, like radiation doses given in Gy or rad, proportional to frequencies of potentially mutagenic events. The radiation dose equivalents of chemical doses are, calculated by multiplying chemical doses (in mMh) with the relative genotoxic potencies (in rad x mMh-1) determined in vitro. In this way the relative cancer incidence increments in rats and mice exposed to ethylene oxide were shown to be about 0.4 percent per rad-equivalent, in agreement with the data for radiogenic cancer. Our analyses suggest that values of the relative risk coefficients for genotoxic chemicals are independent of species and that relative cancer risks determined in animal tests apply also to humans. If reliable animal test data are not available, cancer risks may be estimated by the relative potency. In both cases exposure dose/target dose relationships, the latter via macromolecule adducts, should be determined.

Acrylamide↗
PubMed1997

The pyloric pattern of the lobster (Panulirus interruptus) stomatogastric ganglion comprises two phase-maintaining subsets.

The pyloric pattern approximately maintains phase over a three- to fivefold frequency range when the pattern is defined by the pacemaker burst beginning. However, in this reference frame certain pattern elements maintain phase better than others, which suggests phase-maintaining subgroups might exist. Reanalysis of these data in reference frames defined by each element shows the pattern contains two groups of pattern elements within which phase is well maintained but between which maintenance is relatively poor. A third element shows intermediate maintenance with each group. If ventricular dilator neuron burst beginning (VDB) is chosen as pattern beginning, all members of one group occur early in the pattern, all members of the other occur late in the pattern, and the intermediate element occurs between the groups. Thus, at least for phase maintenance, VDB is a "natural" pyloric pattern beginning. These results suggest full description of complex patterns is best achieved by analysis in many reference frames.

Animals↗
PubMed1998

Epidermal iontophoresis: I. Development of the ionic mobility-pore model.

PURPOSE: An integrated ionic mobility-pore model for epidermal iontophoresis is developed from theoretical considerations using both the free volume and pore restriction forms of the model for a range of solute radii (rj) approaching the pore radii (rp) as well as approximation of the pore restriction form for rj/rp < 0.4. In this model, we defined the determinants for iontophoresis as solute size (defined by MV, MW or radius), solute mobility, solute shape, solute charge, the Debye layer thickness, total current applied solute concentration, fraction ionized, presence of extraneous ions (defined by solvent conductivity), epidermal permselectivity, partitioning rates to account for interaction of unionized and ionized lipophilic solutes with the wall of the pore and electroosmosis. METHODS: The ionic mobility-pore model was developed from theoretical considerations to include each of the determinants of iontophoretic transport. The model was then used to reexamine iontophoretic flux conductivity and iontophoretic flux-fraction ionized literature data on the determinants of iontophoretic flux. RESULTS: The ionic mobility-pore model was found to be consistent with existing experimental data and determinants defining iontophoretic transport. However, the predicted effects of solute size on iontophoresis are more consistent with the pore-restriction than free volume form of the model. A reanalysis of iontophoretic flux-conductivity data confirmed the model's prediction that, in the absence of significant electroosmosis, the reciprocal of flux is linearly related to either donor or receptor solution conductivity. Significant interaction with the pore walls, as described by the model, accounted for the reported pH dependence of the iontophoretic transport for a range of ionizable solutes. CONCLUSIONS: The ionic mobility-pore iontophoretic model developed enables a range of determinants of iontophoresis to be described in a single unifying equation which recognises a range of determinants of iontophoretic flux.

Biological Transport↗
PubMed2002

Investigating the effects of distance and number interference in processing subject-verb dependencies: an ERP study.

Event-related potentials (ERPs) were used to investigate whether the processing of subject-verb dependencies is influenced by (1) the linear distance between the subject and the verb and (2) the presence of an intervening noun phrase with interfering number features. Linear distance did not affect integration and diagnosis or revision processes at the verb, as indexed by early negative and P600 components. This is in accordance with hierarchy-based models of reanalysis, but is problematic for distance-based integration models. However, tracking of the subject features is affected by linear factors: more judgment errors were made in the long compared to the short condition. Furthermore, the presence of a plural object between the singular subject and the verb led to more judgment errors, and an enhanced positivity around 250 ms for the grammatical verbs. This suggests that linear factors affect feature tracking, but not integration processes following feature retrieval or repair processes following the detection of a mismatch.

Adolescent↗
PubMed2001

Genome wide oscillations in expression. Wavelet analysis of time series data from yeast expression arrays uncovers the dynamic architecture of phenotype.

A reanalysis of expression arrays in yeast cells synchronized by alpha factor blockade or through the use of temperature sensitive mutants uncovered a genome wide pattern of oscillations in mRNA concentrations. Using wavelet decomposition as a signal processing technique and enhancement strategies borrowed from image processing, noise and trends in the Stanford yeast cell cycle data were partitioned away from time series profiles to uncover genome-wide oscillations in expression. These oscillations which were typically of cell cycle or half cell cycle duration, 40 and 80 minutes in the Stanford data set suggest that there are large-scale temporal structures and high frequency oscillations in mRNA levels through the cell cycle. Wavelet decomposition, which acts like a band pass filter bank, was used to determine where most of the power appeared in the decomposition. The approximately 40-min oscillation is mirrored in continuous chemostat cultures. In these cultures, metabolic synchrony involving an unknown proportion of the transcriptome can be monitored by measurement of oxygen consumption and can be sustained for weeks. These 40-min oscillations are stable and precise with coefficients of variation less than 1% for both period and amplitude. The hypothesis that high and low amplitude oscillations are a ubiquitous property of the genetic regulatory circuitry was supported by the observation of period doubling bifurcations in the distribution of population doubling times in yeast.

Cell Cycle↗
PubMed1997

Correction of the NMR structure of the ETS1/DNA complex.

The ETS family of transcription factors consists of a group of proteins that share a highly conserved 85 amino acid DNA-binding domain (DBD). This family recognizes a consensus sequence rich in purine bases with a central GGAA motif. A comparison of the published three-dimensional structures of the DBD/DNA complexes of ETS1 by NMR [Werner et al. (1995) Cell, 83, 761-771] and the related Pu.1 by X-ray crystallography [Kodandapani et al. (1996) Nature, 380, 456-460] reveals an apparent discrepancy in which the protein domains bind with opposite polarity to their target sequences. This surprising and highly unlikely result prompted us to reexamine our NMR structure. Additional NMR experiments now reveal an error in the original interpretation of the spectra defining the orientation of the ETS1-DBD on DNA. It was originally reported that the ETS1-DBD bound to DNA with a bipartite motif involving major groove recognition via a helix-turn-helix element and minor groove recognition via protein side-chain intercalation. The presence of intercalation was deduced on the basis of numerous NOEs between several amino acids in the protein and a resonance at 12.33 ppm originally assigned to a DNA imino proton. New NMR experiments now conclusively demonstrate that this resonance, which is located within the DNA imino proton region of the spectrum, arises from the hydroxyl proton of Tyr86. Realization of this error necessitated reanalysis of the intermolecular NOEs. This revealed that the orientation of the ETS1-DBD in the complex is opposite to that originally reported and that a tryptophan residue does not intercalate into the DNA. The calculation of a new ensemble of structures based on the corrected data indicates that the structure of the ETS1-DBD/DNA complex is indeed similar to the X-ray structure of the Pu.1-DBD/DNA complex.

Amino Acid Sequence↗
PubMed1999

Advantages of day 4 embryo transfer in patients undergoing preimplantation genetic diagnosis of aneuploidy.

PURPOSE: Following preimplantation genetic diagnosis of aneuploidy, embryo transfer was executed on day 4, with the aim of providing more time for expanding from six to nine the number of diagnosed chromosomes per single cell (Group 2; 45 cycles). The results obtained were compared to those derived from conventional day 3 transfer (Group 1; 71 cycles). METHODS: For multicolor fluorescence in situ hybridization analysis, two panels of probes were used: the first, specific for chromosomes XY, 13, 16, 18, and 21, was tested in all patients (Groups 1 and 2); the second was implemented only in Group 2 patients for the detection of chromosomes 14, 15, and 22. RESULTS: A total of 406 embryos underwent fluorescence in situ hybridization analysis in Group 1, and 236 in Group 2. Comparable percentages of both chromosomal abnormalities (61% and 62%) and pregnancy and implantation rates (36% and 24.5% in Group 1, 41% and 23.6% in Group 2) resulted, regardless of the higher mean age in Group 2. CONCLUSIONS: The diagnosis of the nine chromosomes which are most frequently associated with aneuploidy in humans could have an immediate impact on the rate of spontaneous abortions. Additional advantages are represented by the more accurate morphological evaluation of euploid embryos; the advanced compaction, which means that embryos are less exposed to damage during the transfer procedure; and the possibility of performing a reanalysis in cases where a fluorescence in situ hybridization diagnosis is not obtained.

Adult↗
PubMed2003

Sex pheromone of the vine mealybug, Planococcus ficus in Israel: occurrence of a second component in a mass-reared population.

Two pheromonal components were detected in airborne collections from the vine mealybug Planococcus ficus (Signoret) (Hemiptera: Pseudococcidae) mass-reared on potato sprouts. The compounds were identified as (S)-lavandulyl senecioate (I) and (S)-lavandulyl isovalerate (II) by GC and GC-MS by comparison with synthetic standards. Chiral GC analysis on a cyclodextrin column established their chirality. Compound I was identified recently as the sex pheromone of P. ficus in California. The attraction of vine mealybug males to both components I and II was demonstrated in a Petri dish bioassay and in a flight assay in the rearing chamber. Indoors, both compounds displayed a similar level of attractiveness to the mass-reared males. However, trials in a vineyard indicated that feral males were attracted only to compound I. Reanalysis of the airborne pheromone indicated that laboratory first generation daughters of females that were collected in the vineyard produce only (S)-lavandulyl senecioate (I). The relative amount of (S)-lavandulyl isovalerate (II) increased gradually in each subsequent generation of P. ficus reared on potatoes. These findings indicate that feral P. ficus mealybugs produce and respond only to (S)-lavandulyl senecioate (I), whereas mealybugs that were reared in the laboratory on potato sprouts produce and respond to both (S)-lavandulyl senecioate (I) and (S)-lavandulyl isovalerate (II).

Alkenes↗
PubMed1997

A comparison of retained and appointed counsel in cases of capital murder.

We examined the role of counsel as a source of arbitrary and capricious sentencing in cases of capital murder. The method is a reanalysis of the data of Baldus, Woodworth, & Pulaski (1990) on 606 cases of capital murder in Georgia in the 1970s. Controlling for variables describing the character of the defendant and the circumstances of the crime, a death sentence was more likely when defense counsel was appointed rather than retained privately. This was a consequence primarily of the prosecutor's decision to seek a death sentence rather than jury bias in sentencing. Our data support the conclusion that sentencing under the Georgia statute was in the 1970s, and is today to some degree, arbitrary and capricious.

Bias↗
PubMed1997

Gender and hedging: from sex differences to situated practice.

In a reanalysis of women's language, Holmes (1995) has argued that women's use of hedges expresses interpersonal warmth and not, as many researchers have maintained, linguistic tentativeness. It is typically men, she suggests, who employ hedges to convey imprecision and incertitude. In this study, we investigated the use of the hedges sort of and you know in a sample of South African students. Holmes's method of analysis was applied to hedging behavior in 52 dyadic conversations. The study consisted of a 2 (Speaker Gender: Male/Female) x 2 (Audience Gender: Male/Female) x 2 (CONDITION: Competitive/Noncompetitive) between-subjects experimental design. The results showed that contextual influences eclipsed the effects of gender: in fact, no main effects were found for speaker gender. Fewer hedges were deployed in the competitive condition than in the noncompetitive condition. Moreover, perhaps reflecting differences in social status, both sexes used sort of to express tentativeness more frequently when talking to male addressees. When speaking to female addressees, on the other hand, men deployed facilitative you know hedges more readily than women.

Adolescent↗
PubMed2004

Spatiotemporal analysis of ERP during chinese idiom comprehension.

The objective of the present study was to elucidate the neural underpinning of Chinese idiom comprehension with spatiotemporal patterns of ERP. Thirteen subjects were required to decide whether the last character of each viewed Chinese four-character idiom was correct or not. Fuzzy c-means algorithm based on shape similarity was applied to segmenting spatiotemporal patterns of ERP. Statistical parametric map of t-statistic (SPM(t)) was performed after realignment according to the referential frame provided by fuzzy clustering in order to overcome temporal mismatch. Within 540 ms post-stimulus onset, the spatiotemporal patterns of ERP under both conditions could be segmented into 7 stages optimally and both share the first four microstates with variant membership functions and durations. SPM(t) presented significant differences in multiple regions in 3 stages: (1) during 120-150 ms, the early right hemispheric negativities (ERHN) inboth frontal and temporoparietal areas were likely to reflect both initial syntactic processing and visual word-form mismatch; (2) during 320-380 ms (the N400 stage), negative deflections in left frontal, left anterior temporal, centrofrontal regions might coordinate and integrate both syntactic and semantic analysis in extensive right hemisphere; (3) during 480-540 ms (the P600 stage), positive deflections in left temporoparietal and occipital regions seemed to reflect the reanalysis and the integration of word meanings to obtain the over all meaning of idioms. Our study has implicated the brain mechanism of language comprehension common to alphabetic language as well as that specialized in logographic language.

Adult↗