Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum)

Physical clustering of genes has been shown in plants; however, little is known about gene clusters that have different functions, particularly those expressed in the tomato fruit. A class I 17.6 small heat shock protein (Sl17.6 shsp) gene was cloned and used as a probe to screen a tomato (Solanum lycopersicum) genomic library. An 8.3-kb genomic fragment was isolated and its DNA sequence determined. Analysis of the genomic fragment identified intronless open reading frames of three class I shsp genes (Sl17.6, Sl20.0, and Sl20.1), the Sl17.6 gene flanked by Sl20.1 and Sl20.0, with complete 5' and 3' UTRs. Upstream of the Sl20.0 shsp, and within the shsp gene cluster, resides a box C/D snoRNA cluster made of SlsnoR12.1 and SlU24a. Characteristic C and D, and C' and D', boxes are conserved in SlsnoR12.1 and SlU24a while the upstream flanking region of SlsnoR12.1 carries TATA box 1, homol-E and homol-D box-like cis sequences, TM6 promoter, and an uncharacterized tomato EST. Molecular phylogenetic analysis revealed that this particular arrangement of shsps is conserved in tomato genome but is distinct from other species. The intronless genomic sequence is decorated with cis elements previously shown to be responsive to cues from plant hormones, dehydration, cold, heat, and MYC/MYB and WRKY71 transcription factors. Chromosomal mapping localized the tomato genomic sequence on the short arm of chromosome 6 in the introgression line (IL) 6-3. Quantitative polymerase chain reaction analysis of gene cluster members revealed differential expression during ripening of tomato fruit, and relatively different abundances in other plant parts.

Effect of charge asymmetry and charge screening on structure of superlattices formed by oppositely charged colloidal particles

Colloidal suspensions made up of oppositely charged particles have been shown to self-assemble into substitutionally ordered superlattices. For a given colloidal suspension, the structure of the superlattice formed from self-assembly depends on its composition, charges on the particles, and charge screening. In this study we have computed the pressure-composition phase diagrams of colloidal suspensions made up of binary mixtures of equal sized and oppositely charged particles interacting via hard core Yukawa potential for varying values of charge screening and charge asymmetry. The systems are studied under conditions where the thermal energy is equal or greater in magnitude to the contact energy of the particles and the Debye screening length is smaller than the size of the particles. Our studies show that charge asymmetry has a significant effect on the ability of colloidal suspensions to form substitutionally ordered superlattices. Slight deviations of the charges from the stoichiometric ratio are found to drastically reduce the thermodynamic stability of substitutionally ordered superlattices. These studies also show that for equal-sized particles, there is an optimum amount of charge screening that favors the formation of substitutionally ordered superlattices. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.3700226]

Valence band offset at GaN/beta-Si3N4 and beta-Si3N4/Si(111) heterojunctions formed by plasma-assisted molecular beam epitaxy

Ultra thin films of pure beta-Si3N4 (0001) were grown on Si (111) surface by exposing the surface to radio- frequency nitrogen plasma with a high content of nitrogen atoms. Using beta-Si3N4 layer as a buffer layer, GaN epilayers were grown on Si (111) substrate by plasma-assisted molecular beam epitaxy. The valence band offset (VBO) of GaN/beta-Si3N4/ Si heterojunctions is determined by X-ray photoemission spectroscopy. The VBO at the beta-Si3N4 /Si interface was determined by valence-band photoelectron spectra to be 1.84 eV. The valence band of GaN is found to be 0.41 +/- 0.05 eV below that of beta-Si3N4 and a type-II heterojunction. The conduction band offset was deduced to be similar to 2.36 eV, and a change of the interface dipole of 1.29 eV was observed for GaN/ beta-Si3N4 interface formation. (c) 2011 Elsevier B.V. All rights reserved.

Synthesis and Characterization of a Fluorescent Analogue of Cyclic di-GMP

Cyclic di-GMP (c-di-GMP), a ubiquitous bacterial second messenger, has emerged as a key controller of several biological processes. Numbers of reports that deal with the mechanistic aspects of this second messenger have appeared in the literature. However, the lack of a reporter tag attached to the c-di-GMP at times limits the understanding of further details. In this study, we have chemically coupled N-methylisatoic anhydride (MANT) with c-di-GMP, giving rise to Mant-(c-di-GMP) or MANT-CDG. We have characterized the chemical and physical properties and spectral behavior of MANT-CDG. The fluorescence of MANT-CDG is sensitive to changes in the microenvironment, which helped us study its interaction with three different c-di-GMP binding proteins (a diguanylate cyclase, a phosphodiesterase, and a PilZ domain-containing protein). In addition, we have shown here that MANT-CDG can inhibit diguanylate cyclase activity; however, it is hydrolyzed by c-di-GMP specific phosphodiesterase. Taken together, our data suggest that MANT-CDG behaves like native c-di-GMP, and this study raises the possibility that MANT-CDG will be a valuable research tool for the in vitro characterization of c-di-GMP signaling factors.

A full-length bifunctional protein involved in c-di-GMP turnover is required for long-term survival under nutrient starvation in Mycobacterium smegmatis

The bacterial second messenger cyclic diguanosine monophosphate (c-di-GMP) plays an important role in a variety of cellular functions, including biofilm formation, alterations in the cell surface, host colonization and regulation of bacterial flagellar motility, which enable bacteria to survive changing environmental conditions. The cellular level of c-di-GMP is regulated by a balance between opposing activities of diguanylate cyclases (DGCs) and cognate phosphodiesterases (PDE-As). Here, we report the presence and importance of a protein, MSDGC-1 (an orthologue of Rv1354c in Mycobacterium tuberculosis), involved in c-di-GMP turnover in Mycobacterium smegmatis. MSDGC-1 is a multidomain protein, having GAF, GGDEF and EAL domains arranged in tandem, and exhibits both c-di-GMP synthesis and degradation activities. Most other proteins containing GGDEF and EAL domains have been demonstrated to have either DGC or PDE-A activity. Unlike other bacteria, which harbour several copies of the protein involved in c-di-GMP turnover, M. smegmatis has a single genomic copy, deletion of which severely affects long-term survival under conditions of nutrient starvation. Overexpression of MSDGC-1 alters the colony morphology and growth profile of M. smegmatis. In order to gain insights into the regulation of the c-di-GMP level, we cloned individual domains and tested their activities. We observed a loss of activity in the separated domains, indicating the importance of full-length MSDGC-1 for controlling bifunctionality.

Strongly magnetized cold degenerate electron gas: Mass-radius relation of the magnetized white dwarf

We consider a relativistic, degenerate electron gas at zero temperature under the influence of a strong, uniform, static magnetic field, neglecting any form of interactions. Since the density of states for the electrons changes due to the presence of the magnetic field (which gives rise to Landau quantization), the corresponding equation of state also gets modified. In order to investigate the effect of very strong magnetic field, we focus only on systems in which a maximum of either one, two, or three Landau level(s) is/are occupied. This is important since, if a very large number of Landau levels are filled, it implies a very low magnetic field strength which yields back Chandrasekhar's celebrated nonmagnetic results. The maximum number of occupied Landau levels is fixed by the correct choice of two parameters, namely, the magnetic field strength and the maximum Fermi energy of the system. We study the equations of state of these one-level, two-level, and three-level systems and compare them by taking three different maximum Fermi energies. We also find the effect of the strong magnetic field on the mass-radius relation of the underlying star composed of the gas stated above. We obtain an exciting result that it is possible to have an electron-degenerate static star, namely, magnetized white dwarfs, with a mass significantly greater than the Chandrasekhar limit in the range 2.3-2.6M(circle dot), provided it has an appropriate magnetic field strength and central density. In fact, recent observations of peculiar type Ia supernovae-SN 2006gz, SN 2007if, SN 2009dc, SN 2003fg-seem to suggest super-Chandrasekhar-mass white dwarfs with masses up to 2.4-2.8M(circle dot) as their most likely progenitors. Interestingly, our results seem to lie within these observational limits.

Texture and microstructure evolution during cold rolling of Cu-Fe laminates prepared by accumulative roll bonding

Multi-layered materials have been made from Cu-Fe with approximately equal volume fractions using the Accumulated Roll Bonding (ARB) technique with less than 1 μm thickness of the individual layers. The so-obtained multi-layers have been subjected to deformation by cold rolling to 25, 50, 75, 87 and 93% reduction in thickness. A detailed characterization has been carried out using X-ray diffraction (line profile analysis and texture measurement) and electron (scanning and transmission) microscopy. It has been found that Fe layers are disintegrated whereas Cu retains its continuity within a layer. Microstructural Characterization from X-Ray Line profile Analysis (XRDLPA) through Variance Method reveals that large amount of strain is initially carried by Cu layers during deformation. In the Cu-Fe layer, the texture is comparatively weaker in Cu layer and strong in Fe layers. Brass Component increases up to 75% reduction and then decreases, while the ratio of Cu/S and Bs/S remains almost constant through out the deformation. After 50% reduction, dynamic recovery is predominant as indicated by the increase in the amount of low angle grain boundaries and decrease in dislocation density. The presence of R component indicates continuous dynamic recovery and recrystallization (CDRR) at the advanced stage of deformation.

High-temperature, high-pressure granulites (retrogressed eclogites) in the central region of the Lewisian, NW Scotland: Crustal-scale subduction in the Neoarchaean

Eclogites and associated high-pressure (HP) rocks in collisional and accretionary orogenic belts preserve a record of subduction and exhumation, and provide a key constraint on the tectonic evolution of the continents. Most eclogites that formed at high pressures but low temperatures at > 10-11 kbar and 450-650 degrees C can be interpreted as a result of subduction of cold oceanic lithosphere. A new class of high-temperature (HT) eclogites that formed above 900 degrees C and at 14 to 30 kbar occurs in the deep continental crust, but their geodynamic significance and processes of formation are poorly understood. Here we show that Neoarchaean mafic-ultramafic complexes in the central granulite facies region of the Lewisian in NW Scotland contain HP/HT garnet-bearing granulites (retrogressed eclogites), gabbros, Iherzolites, and websterites, and that the HP granulites have garnets that contain inclusions of omphacite. From thermodynamic modeling and compositional isopleths we calculate that peak eclogite-facies metamorphism took place at 24-22 kbar and 1060-1040 degrees C. The geochemical signature of one (G-21) of the samples shows a strong depletion of Eu indicating magma fractionation at a crustal level. The Sm-Nd isochron ages of HP phases record different cooling ages of ca. 2480 and 2330 Ma. We suggest that the layered mafic-ultramafic complexes, which may have formed in an oceanic environment, were subducted to eclogite depths, and exhumed as HP garnet-bearing orogenic peridotites. The layered complexes were engulfed by widespread orthogneisses of tonalite-trondhjemite-granodiorite (TTG) composition with granulite facies assemblages. We propose two possible tectonic models: (1) the fact that the relicts of eclogitic complexes are so widespread in the Scourian can be taken as evidence that a >90 km x 40 km-size slab of continental crust containing mafic-ultramafic complexes was subducted to at least 70 km depth in the late Archaean. During exhumation the gneiss protoliths were retrogressed to granulite facies assemblages, but the mafic-ultramafic rocks resisted retrogression. (2) The layered complexes of mafic and ultramafic rocks were subducted to eclogite-facies depths and during exhumation under crustal conditions they were intruded by the orthogneiss protoliths (TTG) that were metamorphosed in the granulite facies. Apart from poorly defined UHP metamorphic rocks in Norway, the retrogressed eclogites in the central granulite/retrogressed eclogite facies Lewisian region, NW Scotland have the highest crustal pressures so far reported for Archaean rocks, and demonstrate that lithospheric subduction was transporting crustal rocks to HP depths in the Neoarchaean. (C) 2012 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

Continuous beam of laser-cooled Yb atoms

We demonstrate the launching of laser-cooled Yb atoms in a continuous atomic beam. The continuous cold beam has significant advantages over the more-common pulsed fountain, which was also demonstrated by us recently. The cold beam is formed in the following steps: i) atoms from a thermal beam are first Zeeman-slowed to a small final velocity; ii) the slowed atoms are captured in a two-dimensional magneto-optic trap (2D-MOT); and iii) atoms are launched continuously in the vertical direction using two sets of moving-molasses beams, inclined at +/- 15 degrees to the vertical. The cooling transition used is the strongly allowed S-1(0) -> P-1(1) transition at 399 nm. We capture about 7x10(6) atoms in the 2D-MOT, and then launch them with a vertical velocity of 13m/s at a longitudinal temperature of 125(6) mK. Copyright (C) EPLA, 2013

Synthesis and evaluation of 2,5-di(4-aryloylaryloxymethyl)-1,3,4-oxadiazoles as anti-cancer agents

A series of 2,5-di(4-aryloylaryloxymethyl)-1,3,4-oxadiazoles 9a-j were obtained via multistep synthesis from hydroxybenzophenones 4a-e. The cytotoxicity of compounds 9a-j was evaluated against human leukemia cell lilies (K562 and CEM). The compounds exhibited moderate to good anti-cancer activity with compounds 9b and 9i having a chloro group exhibiting the best activity (IC50 = 10 mu M). Compound 9i exhibited activity against both the cell lines and 9b only exhibited activity against CEM. Further, a lactate dehydrogenase (LDH) assay and DNA fragmentation studies of the compounds 9a-j were also performed. (C) 2013 Elsevier Masson SAS. All rights reserved.

Identification and characterization of starvation induced msdgc-1 promoter involved in the c-di-GMP turnover

C-di-GMP Bis-(3'-5')-cyclic-dimeric-guanosine monophosphate], a second messenger is involved in intracellular communication in the bacterial species. As a result several multi-cellular behaviors in both Gram-positive and Gram-negative bacteria are directly linked to the intracellular level of c-di-GMP. The cellular concentration of c-di-GMP is maintained by two opposing activities, diguanylate cyclase (DGC) and phosphodiesterase (PDE-A). In Mycobacterium smegmatis, a single bifunctional protein MSDGC-1 is responsible for the cellular concentration of c-di-GMP. A better understanding of the regulation of c-di-GMP at the genetic level is necessary to control the function of above two activities. In this work, we have characterized the promoter element present in msdgc-1 along with the + 1 transcription start site and identified the sigma factors that regulate the transcription of msdgc-1. Interestingly, msdgc-1 utilizes SigA during the initial phase of growth, whereas near the stationary phase SigB containing RNA polymerase takes over the expression of msdgc-1. We report here that the promoter activity of msdgc-1 increases during starvation or depletion of carbon source like glucose or glycerol. When msdgc-1 is deleted, the numbers of viable cells are similar to 10 times higher in the stationary phase in comparison to that of the wild type. We propose here that msdgc-1 is involved in the regulation of cell population density. (C) 2013 Elsevier B.V. All rights reserved.

G-Quadruplex Structures Formed at the HOX11 Breakpoint Region Contribute to Its Fragility during t(10;14) Translocation in T-Cell Leukemia

The t(10;14) translocation involving the HOX11 gene is found in several T-cell leukemia patients. Previous efforts to determine the causes of HOX11 fragility were not successful. The role of non-B DNA structures is increasingly becoming an important cause of genomic instability. In the present study, bioinformatics analysis revealed two G-quadruplex-forming motifs at the HOX11 breakpoint cluster. Gel shift assays showed formation of both intra- and intermolecular G-quadruplexes, the latter being more predominant. The structure formation was dependent on four stretches of guanines, as revealed by mutagenesis. Circular dichroism analysis identified parallel conformations for both quadruplexes. The non-B DNA structure could block polymerization during replication on a plasmid, resulting in consistent K K+-dependent pause sites, which were abolished upon mutation of G-motifs, thereby demonstrating the role of the stretches of guanines even on double-stranded DNA. Extrachromosomal assays showed that the G-quadruplex motifs could block transcription, leading to reduced expression of green fluorescent protein (GFP) within cells. More importantly, sodium bisulfite modification assay showed the single-stranded character at regions I and II of HOX11 in the genome. Thus, our findings suggest the occurrence of G-quadruplex structures at the HOX11 breakpoint region, which could explain its fragility during the t(10;14) translocation.

Effects of a Delocalizable Cation on the Headgroup of Gemini Lipids on the Lipoplex-Type Nanoaggregates Directly Formed from Plasmid DNA

Lipoplex-type nanoaggregates prepared from pEGFP-C3 plasmid DNA (pDNA) and mixed liposomes, with a gemini cationic lipid (CL) 1,2-bis(hexadecyl imidazolium) alkanes], referred as (C(16)Im)(2)C-n (where C-n is the alkane spacer length, n = 2, 3, 5, or 12, between the imidazolium heads) and DOPE zwitterionic lipid, have been analyzed by zeta potential, gel electrophoresis, SAXS, cryo-TEM, fluorescence anisotropy, transfection efficiency, fluorescence confocal microscopy, and cell viability/cytotoxicity experiments to establish a structure-biological activity relationship. The study, carried out at several mixed liposome compositions, alpha, and effective charge ratios, rho(eff), of the lipoplex, demonstrates that the transfection of pDNA using CLs initially requires the determination of the effective charge of both. The electrochemical study confirms that CLs with a delocalizable positive charge in their headgroups yield an effective positive charge that is 90% of their expected nominal one, while pDNA is compacted yielding an effective negative charge which is only 10-25% than that of the linear DNA. SAXS diffractograms show that lipoplexes formed by CLs with shorter spacer (n = 2, 3, or 5) present three lamellar structures, two of them in coexistence, while those formed by CL with longest spacer (n = 12) present two additional inverted hexagonal structures. Cryo-TEM micrographs show nanoaggregates with two multilamellar structures, a cluster-type (at low alpha value) and a fingerprint-type, that coexist with the cluster-type at moderate alpha composition. The optimized transfection efficiency (TE) of pDNA, in HEK293T, HeLa, and H1299 cells was higher using lipoplexes containing gemini CLs with shorter spacers at low a value. Each lipid formulation did not show any significant levels of toxicity, the reported lipoplexes being adequate DNA vectors for gene therapy and considerably better than both Lipofectamine 2000 and CLs of the 1,2-bis(hexadecyl ammnoniun) alkane series, recently reported.