Interruptions of (CG)n sequences by GG, TG and CA need not prevent B to Z transition in solution

Oligonucleotides containing alternating purines-pyrimidines with AT base pairs have been shown to exist in the Z-form preferably in solid state. We report that oligodeoxyribonucleotides with GG, TG and CA interruptions in their alternating CG sequences can undergo B to Z transition in solution in the absence of any chemical modification or topological constraint. The sequences, d(CGCGCGGCGCGC) and d(CGTGCGCACG) have been synthesised and shown to adopt Z- conformation in presence of millimolar concentrations of Ni2+ under low water activity conditions. Significance of GG, TG and CA interruptions in the B to Z transition is discussed.

Cattle Teeth in Graves : Interpretations of animal bones found in Finnish inhumation graves (ca AD 550-1700)

The nature of a burial is always ritualistic. This is often forgotten when dealing with Finnish inhumation burials containing animal bones. Only the animal bones found close to the deceased have traditionally been thought to have a ritualistic purpose. The animal bones found in the filling of the grave, which is still part of the burial, has on the other hand, often been neglected in the previous research. In this Master s thesis I will discuss the function and interpretation of animal bones in graves. The base of this study is six sites, all of different nature, from Finland. Luistari in Eura is from the western coast and is dated to Late Iron Age (and possibly Medieval period), the Medieval hamlet of Finno is situated in Espoo which is situated on the southern coast. Two town burials, Turku and Porvoo, are also included in this study. The graves from Turku are dated to Late Medieval period and Early Renaissance, whereas the cemetery in Porvoo is from the 18th century. Visulahti in Mikkeli is from the Late Iron Age and represents Eastern Finnish burial tradition, the same as Suotniemi from Käkisalmi parish, which is nowadays part of Russia. While parts of the animal bones had already been analysed before, the author also analysed animal bones for the purpose of the present Master´s thesis. The bones were compared to the burial contexts, when possible. Based on the comparisons I have made interpretations which might explain the existence of animal bones in the graves. The interpretations are among others sacrifice, commemoration meals and animal burials. The site could also have been a settlement site prior to the graves, thus the bones in the graves would belong to the settlement phase. When comparing the date of the studied sites, the town burials are later and the animal bones are probably related to previous or contemporary use of the sites as graveyards. On top of this there does not seem to be much difference in burial tradition between Eastern and Western Finland, although at least from the hamlet burials of Finno there are aspects that could be linked to Eastern burials. In making the interpretations I have taken into consideration the aspects of belief during different time periods when they could be accounted as relevant. Also the problems with bone preservation were relevant and challenging for the study. Often only the hardest substance of the skeleton, namely teeth, has been preserved. For this reason the quality of the archaeological documentation was a key issue in this study. In producing quality interpretations of the animal bones in graves, the bones, contexts and their relationship to the surrounding site should be documented with care.

Superconductivity in the 100–120 K region in oxides of the Tl-Ca-Ba-Cu-O system

Oxides with different cation ratios 2122, 2212, 2213 and 2223 in the Ti-Ca-Ba-Cu-O system exhibit onset of superconductivity in the 110–125 K range with zero-resistance in the 95–105 K range. Electron microscopic studies show dislocations, layered morphology and other interesting features. These oxides absorb electromagnetic radiation (9.11 GHz) in the superconducting phase.

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).

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.

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.

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.

Molecular diagnosis of developmental disorders

ABSTRACT Idiopathic developmental disorders (DDs) affect ~1% of the population worldwide. This being a considerable amount, efforts are being made to elucidate the disease mechanisms. One or several genetic factors cause 30-40% of DDs, and only 10% are caused by environmental factors. The remaining 50% of DD patients go undiagnosed, mostly due to a lack of diagnostic techniques. The cause in most undiagnosed cases is though to be a genetic factor or a combination of genetic and environmental factors. Despite the surge of new technologies entering the market, their implementation into diagnostic laboratories is hampered by costs, lack of information about the expected diagnostic yield, and the wide range of selection. This study evaluates new microarray methods in diagnosing idiopathic DDs, providing information about their added diagnostic value. Study I analysed 150 patients by array comparative genomic hybridization (array CGH, 44K and 244K), with a subsequent 18% diagnostic yield. These results are supported by other studies, indicating an enourmous added diagnostic value of array CGH, compared with conventional cytogenetic analysis. Nevertheless, 80% of the patients remained undiagnosed in Study I. In an effort to diagnose more patients, in Study IV the resolution was increased from 8.9 Kb of the 244K CGH array to 0.7 Kb, by using a single-nucleotide polymorphism (SNP) array. However, no additional pathogenic changes were detected in the 35 patients assessed, and thus, for diagnostic purposes, an array platform with ca 9 Kb resolution appears adequate. The recent vast increase in reports of detected aberrations and associated phenotypes has enabled characterization of several new syndromes first based on a common aberration and thereafter by delineation of common clinical characteristics. In Study II, a familial deletion at 9q22.2q22.32 with variable penetrance was described. Despite several reports of aberrations in the adjacent area at 9q associated with Gorlin syndrome, the patients in this family had a unique phenotype and did not present with the syndrome. In Study III, a familial duplication of chromosome 6p22.2 was described. The duplication caused increased expression of an important enzyme of the γ-aminobutyric acid (GABA) degradation pathway, causing oxidative stress of the brain, and thus, very likely, the mild mental retardation of these patients. These two case studies attempted to pinpoint candidate genes and to resolve the pathogenic mechanism causing the clinical characteristics of the patients. Presenting rare genetic and clinical findings to the international science and medical community enables interpretation of similar findings in other patients. The added value of molecular karyotyping in patients with idiopathic DD is evident. As a first line of testing, arrays with a median resolution of at least 9 Kb should be considered and further characterization of detected aberrations undertaken when possible. Diagnostic whole-exome sequencing may be the best option for patients who remain undiagnosed after high-resolution array analysis.

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.