Distribution of simple repetitive (TG/CA)n and (CT/AG)n sequences in human and rodent genomes

Sixteen million nucleotide sequence of genome of various organisms have been analysed to detect and study the extent of occurrence of simple repetitive sequences. Two sequence motifs (TG/CA)n and (CT/AG)n capable of adopting unusual DNA structures, left handed Z-conformation and triple-helical conformation respectively, are found to be abundant in rodent and human genomes, but almost completely absent in bacterial genome. (TG/CA)n and (CT/AG)n sequences are present mostly in the intron or 5'/3' flanking regions of the genes. The presence of such repeat motifs in genomic sequence of higher eukaryotes has been correlated with their possible functional significance in nucleosome organization, recombination and gene expression.

Crystal Chemistry of the Noncentrosymmetric Eulytites: A(3)Bi(XO4)(3) (X = V, A = Pb; X = P, A = Ca, Cd, Sr, Pb)

Eulytite compounds, A(3)Bi(XO4)(3) (X = P, A = Ca, Cd, Sr, Pb), belong to the noncentrosymmetric space group l (4) over bar 3d (No. 220) as determined by single-crystal X-ray diffraction studies. The crystals were grown from the melt-cool technique with considerable difficulty as the compounds melt incongruently at their melting temperature, except for the compound Pb3Bi(PO4)(3). The unit cell parameter a is 9.984(5), 9.8611(3), 10.2035(3), and 10.3722(2) angstrom for Ca3Bi(PO4)(3), Cd3Bi(PO4)(3), Sr3Bi(PO4)(3), and Pb3Bi(PO4)(3) respectively, and there are four formula units in the unit cell. The structure of Pb3Bi(VO4)(3), a unique eulytite with vanadium substitution, is compared with all these phosphorus substituted eulytites. The A(2+) and Bi3+ cations occupy the special position (16c) while the O anions occupy the general Wyckoff position (48e) in the crystal structure. Only one O position has been identified for Pb3Bi(PO4)(3) and Pb3Bi(VO4)(3), whereas two O atom sites were identified for Ca3Bi(PO4)(3), Cd3Bi(PO4)(3), and Sr3Bi(PO4)(3). The UV-vis diffuse reflectance spectra indicate large band gaps for all the phosphate eulytites while a lower band gap is observed for the vanadate eulytite. The feasibility of the use of these compounds in optoelectronic devices has been tested by measuring the second-harmonic generation (SHG) values which have been found to be of a magnitude equivalent to the commercially used KDP (KH2PO4).

Cloning, expression, purification and preliminary X-ray crystallographic studies of 2-methylisocitrate lyase from Salmonella typhimurium. Acta Crystallogr

In Salmonella typhimurium, propionate is oxidized to pyruvate via the 2-methylcitric acid cycle. The last step of this cycle, the cleavage of 2-methylisocitrate to succinate and pyruvate, is catalysed by 2-methylisocitrate lyase (EC 4.1.3.30). Methylisocitrate lyase (molecular weight 32 kDa) with a C-terminal polyhistidine affinity tag has been cloned and overexpressed in Escherichia coli and purified and crystallized under different conditions using the hanging-drop vapour-diffusion technique. Crystals belong to the orthogonal space group P2(1)2(1)2(1), with unit-cell parameters a = 63.600, b = 100.670, c = 204.745 Angstrom. A complete data set to 2.5 Angstrom resolution has been collected using an image-plate detector system mounted on a rotating-anode X-ray generator.

Magnetic properties of pure, Sr- and Ca-Doped La2NiO4+δ ceramics: Onset of high-Tc superconductivity

We present the results for the temperature and field dependence of the magnetic for ceramic materials of the composition La2−xMxNiO4, with M=Sr or Ca and 0≤x≤0.4. The onset of a strong diamagnetism has been observed at temperatures between 8 and 70 K, depending on sample composition, annealing conditions. and thermal cycling procedures. The results are similar to those obtained earlier for monocrystalline samples and are likewise interpreted as due to the onset of superconductivity in a minority phase. A comparison with the results for superconducting La1.8Sr0.2Cu0.9Ni0.1O4 ceramics is also made; this illustrates some unique features of the nickelate systems, such as the high values of the critical fields Hc1 and Hc2. The differences between monocrystalline and ceramic systems are also discussed.

Combustion synthesis of rare earth cuprates

Rare earth cuprates, La2CuO4 Nd2CuO4, La1.8M0.2CuO4 (M=Ca.Sr) and Nd1.85Ce0.15CuO4 have been prepared by the combustion of redox mixtures containing corresponding metal nitrates and maleic hydrazide, C4H4N2O2, at 350°C. The solid combustion products are submicron size amorphous powders which on heat treatment (700°C, 30 minutes) yield crystalline single phase cuprates. Strontium doped lanthanum cuprate, La1.8Sr0.2CuO4, shows an onset of superconductivity at 36K.

Eu2+ luminescence in MAl3BO7 aluminoborates (M=Ca, Sr, Ba)

Three new aluminoborates having the composition MAl3BO7, where M = Ca,Sr or Ba, have been prepared. X-ray diffraction data indicate that all the phases are monoclinic, with close structural similarity to the meta stable aluminate, SrAl4O7. These aluminoborates are good host lattices for Eu2+ luminescence. The emission spectra show multiple bands in the blue region, corresponding to two inequivalent sites in each case, with one of them having quantum efficiency greater-than or equivalent to 75%. In the case of SrAl3BO7:Eu2+, the d–f band emission dominates at 300 K whereas at 77 K both d–f band and f–f line emissions are observed. Efficient Eu2+→Mn2+ energy transfer is observed in MAl3BO7 leading to strong green emission of Mn2+in the tetrahedral sites.aluminoborates; europium

CA/TG sequence at the 5' end of oligo(A)-tracts strongly modulates DNA curvature

An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5' end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5' and 3' ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing of the sequences with AC/GT and CA/TG doublet junctions gives a similar cutting pattern in the A-tracts, which is quite different from that in the C-tracts, indicating that the oligo(A)-tracts have similar structures in the two oligomers. KMnO4 probing shows that the oligomer with a CA/TG doublet junction forms a kink that is responsible for its inherent curvature and unusual electrophoretic mobility. UV melting shows a reduced thermal stability of the duplex with CA/TG doublet junction, and circular dichroism (CD) studies indicate that a premelting transition occurs in the oligomer with CA/TG doublet step before global melting but not in the oligomer with AC/GT doublet step, which may correspond to thermally induced unbending of the oligomer. These observations indicate that the CA/TG doublet junction at the 5' end of the oligo(A)-tract has a crucial role in modulating the overall curvature in DNA.

A reexamination of the permeability index of clays

The permeability index Ck, similar to the compression index, is the slope of the void ratio – coefficient of permeability relationship. Literature shows that, in general, for sensitive clays it can be related to initial void ratio by Ck = 0.5e0. The possibility of obtaining such a relationship for Cochin marine clays in terms of liquid limit void ratio is indicated in this paper. Analysis of permeability behaviour of Cochin marine clays and the test results available in published literature using generalized state parameter approach show that, in principle, these forms of equations for the permeability index are tenable, even though they were obtained based on experimental observation alone.

Effect of Substitution of Ca on Thermal Expansion of Cordierite (Mg2Al4Si5O18)

The effect of substitution of calcium on the anisotropic axial thermal expansion of cordierite was investigated by using a high-temperature X-ray diffraction technique. The compositions were prepared by the sol–gel route. In the Mg2-xCax-Al4Si5O18 system, single-phase cordierite can be prepared for x up to 0.5. Thermal expansion anisotropy (αa–αc) of cordierites reduces progressively by the substitution of increasing amounts of Ca for Mg.

Influence of Starch Polysaccharide on the Remolded Properties of 2 Indian clay Samples

The reported presence in marine clays and the recognized role of polysaccharide as a bonding agent provided the motivation to examine the role of starch polysaccharide in the remoulded properties of nonswelling (kaolinite) and swelling (bentonite) groups of clays. The starch polysaccharide belongs to a group of naturally occurring, large-sized organic molecules (termed polymers) and is built up by extensive repetition of simple chemical units called repeat units. The results of the study indicate that the impact of the starch polysaccharide on the remoulded properties of clays is dependent on the mineralogy of the clays. On addition to bentonite clay, the immensely large number of segments (repeat units) of the starch polysaccharide create several polymer segment - clay surface bonds that cause extensive aggregation of the bentonite units layers. The aggregation of the bentonite unit layers greatly curtails the available surface area of the clay mineral for diffuse ion layer formation. The reduction in diffuse ion layer thickness markedly lowers the consistency limits and vane shear strength of the bentonite clay. On addition to kaolinite, the numerous polymer segment - clay surface bonds enhance the tendency of the kaolinite particles to flocculate. The enhanced particle flocculation is responsible apparently for a small to moderate increase in the liquid limit and remoulded undrained strength of the nonswelling clay.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis x Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

CA\TG Sequence at the 5'end of Oligo(A)-tracts Strongly Modulates DNA Curvature

An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5' end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5' and 3' ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing of the sequences with AC/GT and CA/TG doublet junctions gives a similar cutting pattern in the A-tracts, which is quite different from that in the C-tracts, indicating that the oligo(A)-tracts have similar structures in the two oligomers. KMnO4 probing shows that the oligomer with a CA/TG doublet junction forms a kink that is responsible for its inherent curvature and unusual electrophoretic mobility. UV melting shows a reduced thermal stability of the duplex with CA/TG doublet junction, and circular dichroism (CD) studies indicate that a premelting transition occurs in the oligomer with CA/TG doublet step before global melting but not in the oligomer with AC/GT doublet step, which may correspond to thermally induced unbending of the oligomer. These observations indicate that the CA/TG doublet junction at the 5' end of the oligo(A)-tract has a crucial role in modulating the overall curvature in DNA.

Dependence of magnetism on GdFeO3 distortion in the t(2g) system ARuO(3) (A = Sr, Ca)

We have examined the stability of the ferromagnetic (FM) state in CaRuO3 and SrRuO3 as a function of the GdFeO3 distortion. Model calculations predict the dependence of the FM transition temperature (T-c) on the rotation angle theta to vary as cos(2)(2 theta) for e(g)-electron systems. However, here, we find an initial increase and then the expected decrease. Furthermore, a much faster decrease is found than predicted for e(g)-electron systems. Considering the specific case of CaRuO3, a larger deviation of the Ru-O-Ru angle from 180 degrees in CaRuO3 as compared to SrRuO3 should result in a more reduced bandwidth, thereby making the former more correlated. The absence of long-range magnetic order in the more correlated CaRuO3 is traced to the strong collapse of various exchange interaction strengths that arises primarily from the volume reduction and increased distortion of the RuO6 octahedra network that accompanies the presence of a smaller ion at the A site.

Influence of Substrate Temperature and Deposition Rate on Structural and Mechanical Properties of Shape Memory NiTi Films

NiTi thin films deposited by DC magnetron sputtering of an alloy (Ni/Ti:45/55) target at different deposition rates and substrate temperatures were analyzed for their structure and mechanical properties. The crystalline structure, phase-transformation and mechanical response were characterized by X-ray diffraction (XRD), Differential Scanning Calorimetry (DSC) and Nano-indentation techniques, respectively. The films were deposited on silicon substrates maintained at temperatures in the range 300 to 500 degrees C and post-annealed at 600 degrees C for four hours to ensure film crystallinity. Films deposited at 300 degrees C and annealed for 600 degrees C have exhibited crystalline behavior with Austenite phase as the prominent phase. Deposition onto substrates held at higher deposition temperatures (400 and 500 degrees C) resulted in the co-existence of Austenite phase along with Martensite phase. The increase in deposition rates corresponding to increase in cathode current from 250 to 350 mA has also resulted in the appearance of Martensite phase as well as improvement in crystallinity. XRD analysis revealed that the crystalline film structure is strongly influenced by process parameters such as substrate temperature and deposition rate. DSC results indicate that the film deposited at 300 degrees C had its crystallization temperature at 445 degrees C in the first thermal cycle, which is further confirmed by stress temperature response. In the second thermal cycle the Austenite and Martensite transitions were observed at 75 and 60 degrees C respectively. However, the films deposited at 500 degrees C had the Austenite and Martensite transitions at 73 and 58 degrees C, respectively. Elastic modulus and hardness values increased from 93 to 145 GPa and 7.2 to 12.6 GPa, respectively, with increase in deposition rates. These results are explained on the basis of change in film composition and crystallization. (C) 2010 Published by Elsevier Ltd