Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals.

A base-pair resolution method for determining nucleosome position in vitro has been developed to com- plement existing, less accurate methods. Cysteaminyl EDTA was tethered to a recombinant histone octamer via a mutant histone H4 with serine 47 replaced by cysteine. When assembled into nucleosome core particles, the DNA could be cut site specifically by hydroxyl radical-catalyzed chain scission by using the Fenton reaction. Strand cleavage occurs mainly at a single nucleotide close to the dyad axis of the core particle, and assignment of this location via the symmetry of the nucleosome allows base-pair resolution mapping of the histone octamer position on the DNA. The positions of the histone octamer and H3H4 tetramer were mapped on a 146-bp Lytechinus variegatus 5S rRNA sequence and a twofold-symmetric derivative. The weakness of translational determinants of nucleosome positioning relative to the overall affinity of the histone proteins for this DNA is clearly demonstrated. The predominant location of both histone octamer and H3H4 tetramer assembled on the 5S rDNA is off center. Shifting the nucleosome core particle position along DNA within a conserved rotational phase could be induced under physiologically relevant conditions. Since nucleosome shifting has important consequences for chromatin structure and gene regulation, an approach to the thermodynamic characterization of this movement is proposed. This mapping method is potentially adaptable for determining nucleosome position in chromatin in vivo.

A small bispecific antibody construct expressed as a functional single-chain molecule with high tumor cell cytotoxicity.

Construction of a bispecific single-chain antibody derivative is described that consists of two different single-chain Fv fragments joined through a Gly-Ser linker. One specificity of the two Fv fragments is directed against the CD3 antigen of human T cells and the other is directed against the epithelial 17-1A antigen; the latter had been found in a clinical trial to be a suitable target for antibody therapy of minimal residual colorectal cancer. The construct could be expressed in CHO cells as a fully functional protein, while its periplasmic expression in Escherichia coli resulted in a nonfunctional protein only. The antigen-binding properties of the bispecific single-chain antibody are indistinguishable from those of the corresponding univalent single-chain Fv fragments. By redirecting human peripheral T lymphocytes against 17-1A-positive tumor cells, the bispecific antibody proved to be highly cytotoxic at nanomolar concentrations as demonstrated by 51Cr release assay on various cell lines. The described bispecific construct has a molecular mass of 60 kDa and can be easily purified by its C-terminal histidine tail on a Ni-NTA chromatography column. As bispecific antibodies have already been shown to be effective in vivo in experimental tumor systems as well as in phase-one clinical trials, the small CD3/17-1A-bispecific antibody may be more efficacious than intact antibodies against minimal residual cancer cells.

An activity gel assay detects a single, catalytically active histone acetyltransferase subunit in Tetrahymena macronuclei.

Macronuclei of the ciliated protozoan Tetrahymena thermophila possess a histone acetyltransferase activity closely associated with transcription-related histone acetylation. Nothing definitive is known concerning the polypeptide composition of this activity in Tetrahymena or any comparable activity from any cellular source. An acetyltransferase activity gel assay was developed which identifies a catalytically active subunit of this enzyme in Tetrahymena. This activity gel assay detects a single polypeptide of 55 kDa (p55) in crude macronuclear extracts, as well as in column-purified fractions, which incorporates [3H]acetate from [3H]acetyl-CoA into core histone substrates polymerized directly into SDS polyacrylamide gels. p55 copurifies precisely with acetyltransferase activity through all chromatographic steps examined, including reverse-phase HPLC. Gel-filtration chromatography of this activity indicates a molecular mass of 220 kDa, suggesting that the native enzyme may consist of four identical subunits of 55 kDa. Furthermore, p55 is tightly associated with di- and greater polynucleosomes and therefore may be defined as a component of histone acetyltransferase type A--i.e., chromatin associated.

Optical and ultraviolet observations of a strong flare in the young, single K2 dwarf LQ Hya

We present high-resolution optical echelle spectra and IUE observations during a strong flare on 1993 December 22 in the very active, young, rapidly rotating, single K2 dwarf LQ Hya. The initial impulsive phase of the flare, which started sometime between 2:42 ut and 4:07 ut, was characterized by strong optical continuum enhancement and blueshifted emission lines with broad wings. The optical chromospheric lines reached their maximum intensity at ≈ 5:31 ut, by which time the blueshift vanished and the optical continuum enhancement had sharply decreased. Thereafter, the line emission slowly decreased and the lines redshift in a gradual phase that lasted at least two more hours. The Mg II lines behaved similarly. Quiescent C IV flux levels were not recovered until 21 h later, though a data gap and a possible second flare make the interpretation uncertain. In addition to the typically flare-enhanced emission lines (e.g., H α and H β), we observe He I D_3 going into emission, plus excess emission (after subtraction of the quiescent spectrum) in other He I and several strong neutral metal lines (e.g., Mg I b). Flare enhancement of the far-ultraviolet continuum generally agrees with an Si I recombination model. We estimate the total flare energy, and discuss the broad components, asymmetries and Doppler shifts seen in some of the emission lines.

Phase Transitions in Disordered Systems: The Example of the Random-Field Ising Model in Four Dimensions

By performing a high-statistics simulation of the D = 4 random-field Ising model at zero temperature for different shapes of the random-field distribution, we show that the model is ruled by a single universality class. We compute to a high accuracy the complete set of critical exponents for this class, including the correction-to-scaling exponent. Our results indicate that in four dimensions (i) dimensional reduction as predicted by the perturbative renormalization group does not hold and (ii) three independent critical exponents are needed to describe the transition.

Characterization of the interfaces between Au(hkl) single crystal basal plane electrodes and [Emmim][Tf2N] ionic liquid

The interface between Au(hkl) basal planes and the ionic liquid 1-Ethyl-2,3-dimethyl imidazolium bis(trifluoromethyl)sulfonil imide was investigated by using both cyclic voltammetry and laser-induced temperature jump. Cyclic voltammetry showed characteristic features, revealing surface sensitive processes at the interfaces Au(hkl)/[Emmim][Tf2N]. From laser-induced heating the potential of maximum entropy (pme) is determined. Pme is close to the potential of zero charge (pzc) and, therefore, the technique provides relevant interfacial information. The following order for the pme values has been found: Au(111) > Au(100) > Au(110). This order correlates well with work function data and values of pzc in aqueous solutions.

Mécanismes de transfert de proton d’une réaction acido-basique en phase aqueuse : une étude ab-initio

Les réactions de transfert de proton se retrouvent abondamment dans la nature et sont des processus cruciaux dans plusieurs réactions chimiques et biologiques, qui se produisent souvent en milieu aqueux. Les mécanismes régissant ces échanges de protons sont complexes et encore mal compris, suscitant un intérêt des chercheurs en vue d’une meilleure compréhension fondamentale du processus de transfert. Le présent manuscrit présente une étude mécanistique portant sur une réaction de transfert de proton entre un acide (phénol fonctionnalisé) et une base (ion carboxylate) en phase aqueuse. Les résultats obtenus sont basés sur un grand nombre de simulations de dynamique moléculaire ab-initio réalisées pour des systèmes de type « donneur-pont-accepteur », où le pont se trouve à être une unique molécule d’eau, permettant ainsi l’élaboration d’un modèle cinétique détaillé pour le système étudié. La voie de transfert principalement observée est un processus ultra-rapide (moins d’une picoseconde) passant par la formation d’une structure de type « Eigen » (H9O4+) pour la molécule d’eau pontante, menant directement à la formation des produits. Une seconde structure de la molécule d’eau pontante est également observée, soit une configuration de type « Zündel » (H5O2+) impliquant l’accepteur de proton (l’ion carboxylate) qui semble agir comme un cul-de-sac pour la réaction de transfert de proton.

Mécanismes de transfert de proton d’une réaction acido-basique en phase aqueuse : une étude ab-initio

Les réactions de transfert de proton se retrouvent abondamment dans la nature et sont des processus cruciaux dans plusieurs réactions chimiques et biologiques, qui se produisent souvent en milieu aqueux. Les mécanismes régissant ces échanges de protons sont complexes et encore mal compris, suscitant un intérêt des chercheurs en vue d’une meilleure compréhension fondamentale du processus de transfert. Le présent manuscrit présente une étude mécanistique portant sur une réaction de transfert de proton entre un acide (phénol fonctionnalisé) et une base (ion carboxylate) en phase aqueuse. Les résultats obtenus sont basés sur un grand nombre de simulations de dynamique moléculaire ab-initio réalisées pour des systèmes de type « donneur-pont-accepteur », où le pont se trouve à être une unique molécule d’eau, permettant ainsi l’élaboration d’un modèle cinétique détaillé pour le système étudié. La voie de transfert principalement observée est un processus ultra-rapide (moins d’une picoseconde) passant par la formation d’une structure de type « Eigen » (H9O4+) pour la molécule d’eau pontante, menant directement à la formation des produits. Une seconde structure de la molécule d’eau pontante est également observée, soit une configuration de type « Zündel » (H5O2+) impliquant l’accepteur de proton (l’ion carboxylate) qui semble agir comme un cul-de-sac pour la réaction de transfert de proton.

Dissolved organic carbon concentrations, amino sugar concentrations and highly significantly correlating FT-ICR mass peak magnitudes obtained from solid phase extracted marine dissolved organic matter during POLARSTERN cruise ANT-XXV/1

Dissolved organic matter (DOM) was extracted with solid phase extraction (SPE) from 137 water samples from different climate zones and different depths along an Eastern Atlantic Ocean transect. The extracts were analyzed with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with electrospray ionization (ESI). D14C analyses were performed on subsamples of the SPE-DOM. In addition, the amount of dissolved organic carbon was determined for all water and SPE-DOM samples as well as the yield of amino sugars for selected samples. Linear correlations were observed between the magnitudes of 43% of the FT-ICR mass peaks and the extract D14C values. Decreasing SPE-DOM D14C values went along with a shift in the molecular composition to higher average masses (m/z) and lower hydrogen/carbon (H/C) ratios. The correlation was used to model the SPE-DOM D14C distribution for all 137 samples. Based on single mass peaks a degradation index was developed to compare the degradation state of marine SPE-DOM samples analyzed with FT-ICR MS. A correlation between D14C, degradation index, DOC values and amino sugar yield supports that SPE-DOM analyzed with FT-ICR MS reflects trends of bulk DOM. A relative mass peak magnitude ratio was used to compare aged SPE-DOM and fresh SPE-DOM regarding single mass peaks. The magnitude ratios show a continuum of different reactivities for the single compounds. Only few of the compounds present in the FT-ICR mass spectra are expected to be highly degraded in the oldest water masses of the Pacific Ocean. All other compounds should persist partly thermohaline circulation. Prokaryotic (bacterial) production, transformation and accumulation of this very stable DOM occurs probably primarily in the upper ocean. This DOM is an important contribution to very old DOM, showing that production and degradation are dynamic processes.

Demand-responsive decentralized urban traffic control : part 1, single-intersection policies /

"February 1982."

Multilevel coherence effects in a two-level atom driven by a trichromatic field

We study the absorption and dispersion properties of a weak probe field monitoring a two-level atom driven by a trichromatic field. We calculate the steady-state linear susceptibility and find that the system can produce a number of multilevel coherence effects predicted for atoms composed of three and more energy levels. Although the atom has only one transition channel, the multilevel effects are possible because there are multichannel transitions between dressed states induced by the driving field. In particular, we show that the system can exhibit multiple electromagnetically induced transparency and can also produce a strong amplification at the central frequency which is not attributed to population inversion in both the atomic bare states and in the dressed atomic states. Moreover, we show that the absorption and dispersion of the probe field is sensitive to the initial relative phase of the components of the driving field. In addition, we show that the group velocity of the probe field can be controlled by changing the initial relative phases or frequencies of the driving fields and can also be varied from subluminal to superluminal. (C) 2003 Elsevier Science B.V. All rights reserved.

Does interhemispheric competition mediate motion-induced blindness? A transcranial magnetic stimulation study

Motion-induced blindness (MIB) is a phenomenon, perhaps related to perceptual rivalry, where stationary targets disappear and reappear in a cyclic mode when viewed against a background (mask) of coherent, apparent 3-D motion. Since MIB has recently been shown to share similar temporal properties with binocular rivalry, we probed the appearance-disappearance cycle of MIB using unilateral, single-pulse transcranial magnetic stimulation (TMS)-a manipulation that has previously been shown to influence binocular rivalry. Effects were seen for both hemispheres when the timing of TMS was determined prospectively on the basis of a given subject's appearance-disappearance cycle, so that it occurred on average around 300 ms before the time of perceptual switch. Magnetic stimulation of either hemisphere shortened the time to switch from appearance to disappearance and vice versa. However, TMS of left posterior parietal cortex more selectively shortened the disappearance time of the targets if delivered in phase with the disappearance cycle, but lengthened it if TMS was delivered in the appearance phase after the perceptual switch. Opposite effects were seen in the right hemisphere, although less marked than the left-hemisphere effects. As well as sharing temporal characteristics with binocular rivalry, MIB therefore seems to share a similar underlying mechanism of interhemispheric modulation. Interhemispheric switching may thus provide a common temporal framework for uniting the diverse, multilevel phenomena of perceptual rivalry.

Doxorubicin pharmacokinetics following a single-dose infusion to sulphur-crested cockatoos (Cacatua galerita)

Objective To determine the pharmacokinetics of doxorubicin in sulphur-crested cockatoos, so that its use in clinical studies in birds can be considered. Design A pharmacokinetic study of doxorubicin, following a single intravenous (IV) infusion over 20 min, was performed in four healthy sulphur-crested cockatoos (Cacatua galerita). Procedure Birds were anaesthetised and both jugular veins were cannulated, one for doxorubicin infusion and the other for blood collection. Doxorubicin hydrochloride (2 mg/kg) in normal saline was infused IV over 20 min at a constant rate. Serial blood samples were collected for 96 h after initiation of the infusion. Plasma doxorubicin concentrations were assayed using an HPLC method involving ethyl acetate extraction, reverse-phase chromatography and fluorescence detection. The limit of quantification was 20 ng/mL. Established non-parametric methods were used for the analysis of plasma doxorubicin data. Results During the infusion the mean +/- SD for the C-max of doxorubicin was 4037 +/- 2577 ng/mL. Plasma concentrations declined biexponentially immediately after the infusion was ceased. There was considerable intersubject variability in all pharmacokinetic variables. The terminal (beta-phase) half-life was 41.4 +/- 18.5 min, the systemic clearance (Cl) was 45.7 +/- 18.0 mL/min/kg, the mean residence time (MRT) was 4.8 +/- 1.4 min, and the volume of distribution at steady state (V-SS) was 238 131 mL/kg. The extrapolated area under the curve (AUC(0-infinity)) was 950 +/- 677 ng/mL.h. The reduced metabolite, doxorubicinol, was detected in the plasma of all four parrots but could be quantified in only one bird with the profile suggesting formation rate-limited pharmacokinetics of doxorubicinol. Conclusions and clinical relevance Doxorubicin infusion in sulphur-crested cockatoos produced mild, transient inappetence. The volume of distribution per kilogram and terminal half-life were considerably smaller, but the clearance per kilogram was similar to or larger than reported in the dog, rat and humans. Traces of doxorubicinol, a metabolite of doxorubicin, were detected in the plasma.

Miscibility and phase separation in blends of phenolphthalein poly(aryl ether ketone) and poly(ethylene oxide): a differential scanning calorimetric study

Miscibility and phase separation in the blends of phenolphthalein poly(aryl ether ketone) (PPAEK) and poly(ethylene oxide) (PEO) were investigated by means of differential scanning calorimetry (DSC). The PPAEK/PEO blends prepared by solution casting from N,N-dimethylformamide (DMF) displayed single composition-dependent glass transition temperatures (T-g), intermediate between those of the pure components, suggesting that the blend system is miscible in the amorphous state at all compositions. All the blends underwent phase separation at higher temperatures and the system exhibited a lower critical solution temperature (LCST) behavior. A step-heating thermal analysis was designed to determine the phase boundaries with DSC. The significant changes in the thermal properties of blends were utilized to judge the mixing status for the blends and the phase diagram was thus established. (C) 2004 Elsevier B.V. All rights reserved.

Thermosetting Blends of Polybenzoxazine and Poly(ε-caprolactone): Phase Behavior and Intermolecular Specific Interactions

Polybenzoxazine (PBA-a)/poly(epsilon-caprolactone) (PCL) blends were prepared by an in situ curing reaction of benzoxazine (BA-a) in the presence of PCL. Before curing, the benzoxazine (BA-a)/PCL blends are miscible, which was evidenced by the behaviors of single and composition-dependant glass transition temperature and equilibrium melting point depression. However, the phase separation induced by polymerization was observed after curing at elevated temperature. It was expected that after curing, the PBA-a/PCL blends would be miscible since the phenolic hydroxyls in the PBA-a molecular backbone have the potential to form inter- molecular hydrogen-bonding interactions with the carbonyls of PCL and thus would fulfil the miscibility of the blends. The resulting morphology of the blends prompted an investigation of the status of association between PBA-a and PCL under the curing conditions. Although Fourier-transform infrared spectroscopy (FT-IR) showed that there were intermolecular hydrogen-bonding interactions between PBA-a and PCL at room temperature, especially for the PCL-rich blends, the results of variable temperature FT-IR spectroscopy by the model compound indicate that the phenolic hydroxyl groups could not form efficient intermolecular hydrogen-bonding interactions at elevated temperatures, i.e., the phenolic hydroxyl groups existed mainly in the non-associated form in the system during curing. The results are valuable to understand the effect of curing temperature on the resulting morphology of the thermosetting blends. SEM micrograph of the dichloromethane-etched fracture surface of a 90:10 PBA-a PCL blend showing a heterogeneous morphology.