Some implications of an alternative structure for DNA

We have constructed a space-filling (Corey-Pauling-Koltun) model of an alternative structure for DNA. This structure is not a double helix, but consists of a pair of polynucleotide strands lying side by side and held together by Watson-Crick base pairing. Each of the two strands has alternating right- and left-handed helical segments approximately five base pairs in length. Sugar residues in alternating segments along a strand point in opposite directions. A structure slightly different from the present one proposed earlier by ourselves and another group and in which sugars in a strand all point in the same direction is ruled out. The present structure yields natural solutions to the problems of supercoiling of DNA and of strand separation during DNA replication. This model is energetically more favorable than the double helix.

Synthesis, structure and DNA cleavage studies of coumarin analogues of tetrahydroisoquinoline and protoberberine alkaloids

Novel molecular matrices have been derived from coumarin-4-acetic acids and beta-phenylethylamines using the Bischler-Napieralski protocol which has led to the synthesis of analogues of tetrahydropapaverine in which the dimethoxybenzene moiety has been replaced by substituted coumarins. One carbon homologation has led to cyclization at the C3 position of coumarin generating the protoberberine skeleton. Structures have been confirmed by diffraction studies. The results showed that compounds 6e, 6f, 7e and 7f were found to be very effective against DNA samples of Gram positive bacterium Staphylococcus aureus and fungus Aspergillus niger. (C) 2010 Elsevier Masson SAS. All rights reserved.

Plasmid DNA mediated transfer of the herpes simplex virus thymidine kinase gene to a new bromodeoxyuridine resistant variant of human primary lung carcinoma cells

A human primary lung carcinoma cell line (HPL-R1) established from the tumor biopsy of a lung cancer patient, lacking in cytochrome P1-450 [aryl hydrocarbon (benzo[a]pyrene) hydroxylase (AHH)], was cloned and used to obtain variants deficient in the expression of thymidine-kinase via treatment with 5-bromo-2'-deoxyuridine, and selection for drug resistance phenotype. The variant cell line, precharacterized for thymidine kinase negative phenotype, was transfected with the thymidine kinase gene bearing p R-tk and px1-tk plasmids. Transfections from both the plasmids, demonstrated a frequency of 5.5 X 10(-5). The transfectants showed a 76-100% retention of the transferred phenotype. These data suggest that transfection in variant human cells can approach significant levels of stability observed with rodent cell recipients.

Sequence specificity of Z-DNA formation in oligonucleotides

The sequence specific requirement for B----Z transition in solution was examined in d(CGTGCGCACG), d(CGTACGTACG), d(ACGTACGT) in presence of various Z-inducing factors. Conformational studies show that inspite of the alternating nature of purines and pyrimidines, the aforementioned sequences do not undergo B----Z transition under the influence of NaCl, hexamine cobalt chloride and ethanol. A comparison with the crystal structures of an assorted array of purine and pyrimidine sequences show that the sequence requirement for B----Z transition is much more stringent in solution as compared to the solid state. The disruptive influence of AT base pairs in B to Z transition is discussed.

Stability Analysis of Composite Skew Plates Using a Dynamic Method

Stability analysis is carried out considering free lateral vibrations of simply supported composite skew plates that are subjected to both direct and shear in-plane forces. An oblique stress component representation is used, consistent with the skew-geometry of the plate. A double series, expressed in Chebyshev polynomials, is used here as the assumed deflection surface and Ritz method of solution is employed. Numerical results for different combinations of side ratios, skew angle, and in-plane loadings that act individually or in combination are obtained. In this method, the in-plane load parameter is varied until the fundamental frequency goes to zero. The value of the in-plane load then corresponds to a critical buckling load. Plots of frequency parameter versus in-plane loading are given for a few typical cases. Details of crossings and quasi degeneracies of these curves are presented.

Static and dynamic properties of incommensurate smectic-AIC liquid crystals

We study the elasticity, topological defects, and hydrodynamics of the recently discovered incommensurate smectic (AIC) phase, characterized by two collinear mass density waves of incommensurate spatial frequency. The low-energy long-wavelength excitations of the system can be described by a displacement field u(x) and a ��phason�� field w(x) associated, respectively, with collective and relative motion of the two constituent density waves. We formulate the elastic free energy in terms of these two variables and find that when w=0, its functional dependence on u is identical to that of a conventional smectic liquid crystal, while when u=0, its functional dependence on w is the same as that for the angle variable in a slightly anisotropic XY model. An arbitrariness in the definition of u and w allows a choice that eliminates all relevant couplings between them in the long-wavelength elastic energy. The topological defects of the system are dislocations with nonzero u and w components. We introduce a two-dimensional Burgers lattice for these dislocations, and compute the interaction between them. This has two parts: one arising from the u field that is short ranged and identical to the interaction between dislocations in an ordinary smectic liquid crystal, and one arising from the w field that is long ranged and identical to the logarithmic interaction between vortices in an XY model. The hydrodynamic modes of the AIC include first- and second-sound modes whose direction-dependent velocities are identical to those in ordinary smectics. The sound attenuations have a different direction dependence, however. The breakdown of hydrodynamics found in conventional smectic liquid crystals, with three of the five viscosities diverging as 1/? at small frequencies ?, occurs in these systems as well and is identical in all its details. In addition, there is a diffusive phason mode, not found in ordinary smectic liquid crystals, that leads to anomalously slow mechanical response analogous to that predicted in quasicrystals, but on a far more experimentally accessible time scale.

Study Of The Hvdc-Torsional Interactions Through Digital Dynamic Simulation

This paper presents the detailed dynamic digital simulation for the study of phenomenon of torsional interaction between HVDC-Turbine generator shaft, dynamics using the novel converter model presented in [ 1 ] The system model includes detailed representation of the synchronous generator and the shaft dynamics, the ac and dc network transients. The results of a case study indicate the various factors that influence the torsional interaction.

Theoretical studies on alpha-helix--DNA interactions

The interaction energies between (Ala)10 and alpha-helix fragment and different nucleotide sequences in right-handed B-form have been optimized using semi-empirical potential energy functions. The energies are calculated for two different orientations of the alpha-helix, viz., when the alpha-helix axis taken in the N----C direction is (i) parallel and (ii) antiparallel to the 5'-3' ascending strand of DNA, proximal to it. When both the DNA molecule as well as the alpha-helix are treated as rigid molecules it is found that a polyalanine alpha-helix has slightly more favourable contacts when it is in the proximity of a four nucleotide sequence of 5'-(N-A-T-N)-3' type, where N is either a purine or a pyrimidine. However, when the two interacting molecules are allowed to undergo local structural variations then the interaction energy appears to be independent of the base sequence confirming the non-specific nature of these interactions.

Dynamic security assessment of power systems using structure-preserving energy functions

An application of direct methods to dynamic security assessment of power systems using structure-preserving energy functions (SPEF) is presented. The transient energy margin (TEM) is used as an index for checking the stability of the system as well as ranking the contigencies based on their severity. The computation of the TEM requires the evaluation of the critical energy and the energy at fault clearing. Usually this is done by simulating the faulted trajectory, which is time-consuming. In this paper, a new algorithm which eliminates the faulted trajectory estimation is presented to calculate the TEM. The system equations and the SPEF are developed using the centre-of-inertia (COI) formulation and the loads are modelled as arbitrary functions of the respective bus voltages. The critical energy is evaluated using the potential energy boundary surface (PEBS) method. The method is illustrated by considering two realistic power system examples.

Integration of miRNA and mRNA expression with DNA copy number of Ewing sarcoma cell lines

Ewing sarcoma is an aggressive and poorly differentiated malignancy of bone and soft tissue. It primarily affects children, adolescents, and young adults, with a slight male predominance. It is characterized by a translocation between chromosomes 11 and 22 resulting in the EWSR1-FLI1fusion transcription factor. The aim of this study is to identify putative Ewing sarcoma target genes through an integrative analysis of three microarray data sets. Array comparative genomic hybridization is used to measure changes in DNA copy number, and analyzed to detect common chromosomal aberrations. mRNA and miRNA microarrays are used to measure expression of protein-coding and miRNA genes, and these results integrated with the copy number data. Chromosomal aberrations typically contain also bystanders in addition to the driving tumor suppressor and oncogenes, and integration with expression helps to identify the true targets. Correlation between expression of miRNAs and their predicted target mRNAs is also evaluated to assess the results of post-transcriptional miRNA regulation on mRNA levels. The highest frequencies of copy number gains were identified in chromosome 8, 1q, and X. Losses were most frequent in 9p21.3, which also showed an enrichment of copy number breakpoints relative to the rest of the genome. Copy number losses in 9p21.3 were found have a statistically significant effect on the expression of MTAP, but not on CDKN2A, which is a known tumor-suppressor in the same locus. MTAP was also down-regulated in the Ewing sarcoma cell lines compared to mesenchymal stem cells. Genes exhibiting elevated expression in association with copy number gains and up-regulation compared to the reference samples included DCAF7, ENO2, MTCP1, andSTK40. Differentially expressed miRNAs were detected by comparing Ewing sarcoma cell lines against mesenchymal stem cells. 21 up-regulated and 32 down-regulated miRNAs were identified, includingmiR-145, which has been previously linked to Ewing sarcoma. The EWSR1-FLI1 fusion gene represses miR-145, which in turn targets FLI1 forming a mutually repressive feedback loop. In addition higher expression linked to copy number gains and compared to mesenchymal stem cells, STK40 was also found to be a target of four different miRNAs that were all down-regulated in Ewing sarcoma cell lines compared to the reference samples. SLCO5A1 was identified as the only up-regulated gene within a frequently gained region in chromosome 8. This region was gained in over 90 % of the cell lines, and also with a higher frequency than the neighboring regions. In addition, SLCO5A1 was found to be a target of three miRNAs that were down-regulated compared to the mesenchymal stem cells.

Dynamic Factor Models and Forecasting Finnish Macroeconomic Variables

In recent years, thanks to developments in information technology, large-dimensional datasets have been increasingly available. Researchers now have access to thousands of economic series and the information contained in them can be used to create accurate forecasts and to test economic theories. To exploit this large amount of information, researchers and policymakers need an appropriate econometric model.Usual time series models, vector autoregression for example, cannot incorporate more than a few variables. There are two ways to solve this problem: use variable selection procedures or gather the information contained in the series to create an index model. This thesis focuses on one of the most widespread index model, the dynamic factor model (the theory behind this model, based on previous literature, is the core of the first part of this study), and its use in forecasting Finnish macroeconomic indicators (which is the focus of the second part of the thesis). In particular, I forecast economic activity indicators (e.g. GDP) and price indicators (e.g. consumer price index), from 3 large Finnish datasets. The first dataset contains a large series of aggregated data obtained from the Statistics Finland database. The second dataset is composed by economic indicators from Bank of Finland. The last dataset is formed by disaggregated data from Statistic Finland, which I call micro dataset. The forecasts are computed following a two steps procedure: in the first step I estimate a set of common factors from the original dataset. The second step consists in formulating forecasting equations including the factors extracted previously. The predictions are evaluated using relative mean squared forecast error, where the benchmark model is a univariate autoregressive model. The results are dataset-dependent. The forecasts based on factor models are very accurate for the first dataset (the Statistics Finland one), while they are considerably worse for the Bank of Finland dataset. The forecasts derived from the micro dataset are still good, but less accurate than the ones obtained in the first case. This work leads to multiple research developments. The results here obtained can be replicated for longer datasets. The non-aggregated data can be represented in an even more disaggregated form (firm level). Finally, the use of the micro data, one of the major contributions of this thesis, can be useful in the imputation of missing values and the creation of flash estimates of macroeconomic indicator (nowcasting).

DNA photocleavage and anticancer activity of terpyridine copper(II) complexes having phenanthroline bases

Copper(II) complexes Cu(ph-tpy)(B)](ClO4) (1-3), where ph-tpy is (4'-phenyl)-2,2':6',2 `'-terpyridine and B is N,N-donor phenanthroline base, viz. 1,10-phenanthroline (phen, 1), dipyridoquinoxaline (dpq, 2), and dipyridophenazine (dppz, 3), were prepared and characterized from analytical and spectral data. Complex 1, characterized by X-ray crystallography, shows a distorted square-pyramidal (4 + 1) CuN5 coordination geometry having the tridentate ph-tpy ligand at the basal plane and bidentate phen bound to the axial-equatorial sites. The complexes display a d-d band near 650 nm in aqueous DMF. The complexes are avid binders to calf thymus DNA giving the binding order: 3 (dppz) > 2 (dpq) > 1 (phen). The dpq and dppz complexes show photo-induced DNA cleavage activity in red light via photo-redox pathway forming hydroxyl radicals. The cytotoxicity of the dppz complex 3 was studied by MTT assay in HeLa cancer cells. The IC50 values are 3.7 and 12.4 mu M in visible light of 400-700 nm and dark, respectively. (C) 2010 Elsevier Ltd. All rights reserved.

Effect of primary system damping on the optimum design of an untuned viscous dynamic vibration absorber

Explicit criteria for the optimum design of an untuned viscous dynamic vibration absorber are developed for the case of a viscously damped single degree of freedom springmass system. It is shown that for the particular case of an undamped main system, the results reduce to the classical ones obtained by using the concept of a fixed point on the response curve.