Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3'-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.

Friction-formed liquid droplets

The formation of nanoscale liquid droplets by friction of a solid is observed in real-time. This is achieved using a newly developed in situ transmission electron microscope (TEM) triboprobe capable of applying multiple reciprocating wear cycles to a nanoscale surface. Dynamical imaging of the nanoscale cyclic rubbing of a focused-ion-beam (FIB) processed Al alloy by diamond shows that the generation of nanoscale wear particles is followed by a phase separation to form liquid Ga nanodroplets and liquid bridges. The transformation of a two-body system to a four-body solid-liquid system within the reciprocating wear track significantly alters the local dynamical friction and wear processes. Moving liquid bridges are observed in situ to play a key role at the sliding nanocontact, interacting strongly with the highly mobile nanoparticle debris. In situ imaging demonstrates that both static and moving liquid droplets exhibit asymmetric menisci due to nanoscale surface roughness. Nanodroplet kinetics are furthermore dependent on local frictional temperature, with solid-like surface nanofilaments forming on cooling. TEM nanotribology opens up new avenues for the real-time quantification of cyclic friction, wear and dynamic solid-liquid nanomechanics, which will have widespread applications in many areas of nanoscience and nanotechnology.

Parallel Tempering Simulations of Liquid-Phase Adsorption of n-Alkane Mixtures in Zeolite LTA-5A

Adsorption of n-alkane mixtures in the zeolite LTA-5A under liquid-phase conditions has been studied using grand canonical Monte Carlo (GCMC) simulations combined with parallel tempering. Normal GCMC techniques fail for some of these systems due to the preference of linear molecules to coil within a single cage in the zeolite. The narrow zeolite windows severerly restrict interactions of the molecules, making it difficult to simulate cooperative rearrangements necessary to explore configuration space. Because of these reasons, normal GCMC simulations results show poor reproducibility in some cases. These problems were overcome with parallel tempering techniques. Even with parallel tempering, these are very challenging systems for molecular simulation. Similar problems may arise for other zeolites such as CHA, AFX, ERI, KFI, and RHO having cages connected by narrow windows. The simulations capture the complex selectivity behavior observed in experiments such as selectivity inversion and azeotrope formation.

Crystallography of solid-liquid interface and evolution of texture during directional solidification of Tb0.3Dy0.7Fe1.95 alloy

The effect of growth texture on the magnetostriction of ternary Tb0.3Dy0.7Fe1.95 was studied by conducting unidirectional solidification experiments using a zoning set-up. Detailed texture evolutions were studied using X-ray diffraction on samples obtained by varying growth rates from 18 to 72 cm/h, under a temperature gradient of 100 degrees C/cm. The estimated texture co-efficient and pole figures of the samples indicate that during the onset of the solidification, < 110 > and < 331 >/'rotated < 110 >' texture components nucleate and grow in all the samples. However, as the solidification progresses, < 112 > texture component becomes dominant at higher growth rate. This results in an improvement of magnetostriction from 1000 to 1300 microstrains for samples grown at growth rates of 18 and 72 cm/h respectively. The transition of preferred growth direction occurs through intermediate orientations < 123 >. An attempt has been made in this paper to explain the occurrence of different growth texture by considering the stability of growing interface, its planar packing fraction and atomic stacking sequence of several low index planes. (C) 2010 Elsevier Ltd. All rights reserved.

Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3'-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.

Liquid-Liquid Interphase (Biphasic) as the Reaction Medium in the Assembly of a Hierarchy of Structures of 4,4 `-Azodibenzoic Acid with Zinc and Cadmium

The compounds Zn(C12H8N2)](2)C12N2H8(COO)(2)](2)center dot(C6H12O)center dot(H2O), I, Zn(C12H8N2)]C12N2H8(COO)(2)], II, Cd(C12H8N2)(H2O)]C12N2H8(COO)(2)]center dot(H2O), III, Zn(C10N2H8)]C12N2H8(COO)(2)]center dot 0.5(C10N2H8), IV, Cd(C12N2H8(COO)(2)center dot H2O], V, and Zn-3(mu(2)-O)(mu(3)-O)(3)]C12N2H8(COO)(2)], VI, have been synthesized by using a biphasic approach (I, III, V, VI) or regular hydrothermal method (II, IV). The compounds exhibit one (I and II), two (In), and three dimensionally (IV, V, VI) extended structures. The flexible azodibenzoate ligand gives rise to a 3-fold interpenetration (IV) when the synthesis was carried out using normal hydrothermal methods. The biphasic approach forms structures without any interpenetrations, especially in the three-dimensional structures of V and VI. Formation of Cd2O2 dimers in V and extended M-O(H)-M two-dimensional layers in VI suggests the subtle structural control achieved by the biphasic method. Transformation studies indicate that it is possible to transform I to II. Lewis acid catalytic studies have been performed to evaluate the role of the coordination environment in such reactions. All the compounds have been characterized by a variety of techniques that includes powder X-ray diffraction, infrared, thermogravitric analysis, UV-vis, photoluminescence studies.

Conductance of Tomonaga-Luttinger liquid wires and junctions with resistances

We study the effect that resistive regions have on the conductance of a quantum wire with interacting electrons which is connected to Fermi liquid leads. Using the bosonization formalism and a Rayleigh dissipation function to model the power dissipation, we use both scattering theory and Green's function techniques to derive the DC conductance. The resistive regions are generally found to lead to incoherent transport. For a single wire, we find that the resistance adds in series to the contact resistance of h/e(2) for spinless electrons, and the total resistance is independent of the Luttinger parameter K-W of the wire. We numerically solve the bosonic equations to illustrate what happens when a charge density pulse is incident on the wire; the results depend on the parameters of the resistive and interacting regions in interesting ways. For a junction of Tomonaga-Luttinger liquid wires, we use a dissipationless current splitting matrix to model the junction. For a junction of three wires connected to Fermi liquid leads, there are two families of such matrices; we find that the conductance matrix generally depends on K-W for one family but is independent of K-W for the other family, regardless of the resistances present in the system. Copyright (c) EPLA, 2011

Heavy-metal removal using liquid membrane

Experiments have been conducted to obtain the optimum conditions of hydrogen ion concentration of feed and strip phases and concentration of the carrier ALAMINE 336, in the extraction of Cr(VI) and Hg(II) using two different types of liquid membranes-bulk liquid membrane and emulsion liquid membrane. Experiments have also been carried out to find the effect of metal loading and the effect of extraction time on metal flux.

Ionic and dipolar solvation dynamics in liquid water

The solvation time correlation function for solvation in liquid water was measured recently. The solvation was found to be very fast, with a time constant equal to 55 fs. In this article we present theoretical studies on solvation dynamics of ionic and dipolar solutes in liquid water, based on the molecular hydrodynamic approach developed earlier. The molecular hydrodynamic theory can successfully predict the ultrafast dynamics of solvation in liquid water as observed from recent experiments. The present study also reveals some interesting aspects of dipolar solvation dynamics, which differs significantly from that of ionic solvation.

Non-Fermi liquid behavior in a mean-field study of the t-J model: Role of zero-point spin fluctuations

We present analytic results to show that the Schwinger-boson hole-fermion mean-field state exhibits non-Fermi liquid behavior due to spin-charge separation. The physical electron Green's function consists of three additive components. (a) A Fermi-liquid component associated with the bose condensate. (b) A non-Fermi liquid component which has a logarithmic peak and a long tail that gives rise to a linear density of states that is symmetric about the Fermi level and a momentum distribution function with a logarithmic discontinuity at the Fermi surface. (c) A second non-Fermi liquid component associated with the thermal bosons which leads to a constant density of states. It is shown that zero-point fluctuations associated with the spin-degrees of freedom are responsible for the logarithmic instabilities and the restoration of particle-hole symmetry close to the Fermi surface.

Orientational Order of Liquid-Crystalline 4-Alkyl-N-(p-cyanophenyl)piperidines by 2H and 13C NMR Spectroscopies

The orientational order of nematic 4-alkyl-N-(4-cyanophenyl) piperidines (I) has been determined from H-2 and C-13 NMR spectra. Molecular-order parameters are derived from the carbon-13 chemical shift of the cyano carbon atom in the nematic and the isotropic phases; the sign of the diamagnetic anisotropy is positive. Deuterium quadrupolar splittings from the partially deuterated piperidine ring of I are then related to various C-D bonds.

Crossover dynamics at large metastability in gas-liquid nucleation

We have developed an alternate description of dynamics of nucleation in terms of an extended set of order parameters. The order parameters consist of an ordered set of kth largest clusters, ordered such that k = 1 is the largest cluster in the system, k = 2 is the second largest cluster, and so on. We have derived an analytic expression for the free energy for the kth largest cluster, which is in excellent agreement with the simulated results. At large supersaturation, the free energy barrier for the growth of the kth largest cluster disappears and the nucleation becomes barrierless. The major success of this extended theoretical formalism is that it can clearly explain the observed change in mechanism at large metastability P. Bhimalapuram et al., Phys. Rev. Lett. 98, 206104 (2007)] and the associated dynamical crossover. The classical nucleation theory cannot explain this crossover. The crossover from activated to barrierless nucleation is found to occur at a supersaturation where multiple clusters cross the critical size. We attribute the crossover as the onset of the kinetic spinodal. We have derived an expression for the rate of nucleation in the barrierless regime by modeling growth as diffusion on the free energy surface of the largest cluster. The model reproduces the slower increase in the rate of growth as a function of supersaturation, as observed in experiments.

Characterization of aerosol black carbon over a tropical semi-arid region of Anantapur, India

Black carbon (BC) aerosol mass concentrations measured using an aethalometer at Anantapur, a semi-arid tropical station in the southern part of peninsular India, from August 2006 to July 2007 are analyzed. Seasonal and diurnal variations of BC in relation to changes in the regional meteorological conditions have been studied along with the mass fraction of BC to the total aerosol mass concentration (M-t) and fine particle mass (FPM) concentration in different months. The data collected during the study period shows that the annual average BC mass concentration at Anantapur is 1.97 +/- 0.12 mu g m(-3). Seasonal variations of BC aerosol mass concentration showed high during the dry (winter and summer) seasons and low during the post-monsoon followed by the monsoon seasons. Diurnal variations of BC aerosols attain a gradual build up in BC concentration from morning and a sharp peak occurs between 07:00 and 09:00 h almost an hour after local sunrise and a broad nocturnal peak from 19:00 to 21:00 h with a minimum in noon hours. The ratio of BC to the fine particle mass concentration was high during the dry season and low during the monsoon season. The regression analysis between BC mass concentration and wind speed indicates that, with increase in wind speeds the BC mass concentrations would decrease and vice-versa. Aerosol BC mass concentration shows a significant positive correlation with total mass concentration (M-t) and aerosol optical depth (ACID, tau(p)) at 500 nm. (C) 2010 Elsevier B.V. All rights reserved.

A novel method for mapping assembled epitopes in batches: Identification of three epitopes at the receptor binding region of human chorionic gonadotropin

Identification of conformation-specific epitopes of hCG beta has been done using a simple batch method, Chemically or enzymatically-modified hCG beta has been prepared in a batch and the effect of modifications on the integrity of different epitope regions has been investigated in a quantitative manner using monoclonal antibodies (MAbs) immobilized on plastic tubes from culture supernatants. Based on the extent of damage done to different regions by different modifications, three conformation-specific epitopes of hCG beta have been identified. The method has been shown to have important advantages over the existing methods on many considerations, Using this approach, these epitopes have been shown to be at/near the receptor-binding region.

C-13 MAS NMR spectra of cis,cis-mucononitrile in liquid-crystalline media and in the solid state. Orientation of the carbon chemical-shift tensors

The spinning sidebands observed in the C-13 MAS NMR spectra of cis,cis-mucononitrile oriented in liquid-crystalline media and of the neat sample in the solid state are studied. There are differences in the sideband intensity patterns in the two cases. These differences arise because the order parameters which characterize the orientation of the solute in the liquid-crystalline media differ for different axes. It is shown that, in general, the relative intensities of the sidebands contain information on the sign and magnitude of an effective chemical-shift parameter which is a function of the sum of the products of the principal components of the chemical-shift tensor and the corresponding order parameters with respect to the director. A method for obtaining the orientation of the carbon chemical-shift tensor is proposed. The carbon chemical-shift tensors obtained from gauge-including atomic orbital calculations are also presented for comparison. (C) 1996 Academic Press, Inc.