In situ surface topography measurement method of granite base in scanning wafer stage with laser interferometer

Topography of a granite surface has an effect on the vertical positioning of a wafer stage in a lithographic tool, when the wafer stage moves on the granite. The inaccurate measurement of the topography results in a bad leveling and focusing performance. In this paper, an in situ method to measure the topography of a granite surface with high accuracy is present. In this method, a high-order polynomial is set up to express the topography of the granite surface. Two double-frequency laser interferometers are used to measure the tilts of the wafer stage in the X- and Y-directions. From the sampling tilts information, the coefficients of the high-order polynomial can be obtained by a special algorithm. Experiment results shows that the measurement reproducibility of the method is better than 10 nm. (c) 2006 Elsevier GmbH. All rights reserved.

Theoretical investigation on the one- and two-photon absorption properties for a series of symmetrical charge transfer fluorene-phenylene and fluorene-thiophene derivatives

One- and two-photon absorption properties of a series of fluorene derivatives with symmetrical charge transfer D-IT-D and A-IT-A structural motifs have been theoretically investigated with ZINDO/S method. The optimized structures and the characterization of frontier molecular orbitals were obtained by using AMI calculations. Two-photon absorption properties of molecules have been studied using three-state model. The calculation results have shown that fluorene-thiophene derivatives exhibit larger two-photon absorption cross-section as compared with other studied molecules. To illustrate the results, the crucial effects of thiophene ring on fluorenethiophene derivatives and the net charge changes on the pi-conjugated bridges are analyzed theoretically. (c) 2006 Elsevier B.V. All rights reserved.

Three-photon absorption-induced fluorescence and optical limiting effects in a fluorene derivative

This paper reports on the steady-state fluorescence, three- photon absorption-induced fluorescence emission and subsequently induced optical limiting behaviour of a fluorene derivative with D-pi-D structural motifs. The lifetime of the steady-state fluorescence is 0.903 ns. Large optical limiting behaviour induced by 3PA has also been demonstrated, and the nonlinear absorption coefficient gamma derived from 3PA fitting curves is 5.92 x 10(-20) cm(3)/W-2 and the corresponding molecular 3PA cross-section sigma(3)' is 1.14 x 10(-76) cm(6) s(2).

Comparison of quantum chemistry calculation methods of nucleic acid base-quartets

Nine base-quartets were calculated by six semi-empirical methods and ab initio Hartree-Fork method using STO-3G basis set. The results showed that PM3 method can be use to calculate base quartets, the results of PM3 calculations are close to the ab initio

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

D77, one benzoic acid derivative, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular LEDGF/p75

Integration of viral-DNA into host chromosome mediated by the viral protein HIV-1 integrase (IN) is an essential step in the HIV-1 life cycle. In this process, Lens epithelium-derived growth factor (LEDGF/p75) is discovered to function as a cellular co-fa

Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water-K+-TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT. (C) 2002 Elsevier Science B.V. All rights reserved.

The comparative analysis of the energies of conjugated triple base triplets and their applications

We built 64 sets of 3D models of DNA triplex base triplets (TBT) and minimized their energies. The TBTs were divided into 32 pairs of conjugated ones on the basis of their sequence characteristic, and the energies of each pair of them were compared and analyzed, the results showed: (i) The duplex DNA of which any strand contains at least a couple of A or T, has a preference for selecting the oligodeoxyribonucleic acid (ODN) strand containing abundant T to form TBT. (ii) The duplex DNA of which any strand contains at least a couple of G or C has a preference for selecting ODN containing abundant G to form symmetric antiparallel TBT, but selecting ODN containing abundant C to form asymmetric parallel TBT. (iii) The duplex DNA of which any strand contains only one of A, T, G or C has a preference for selecting ODN containing abundant pyrimidines (T or C) to form antiparallel TBT. Additionally, two examples of TBTs applications, in designing ODN to form triplex with duplex were presented. The energy calculation result revealed that 15-TCG is the best ligand of the HIV PPT duplex. The comparative analysis of energies of the conjugated TBTs provides directive significance for designing ODN strand that is easy to form triplex in theory. (C) 2002 Elsevier Science B.V. All rights reserved.

Tentative study of the coding sequences without 3-base periodicity

Fourier spectra of 120 short coding sequences (<1 200 bp) show that not all coding sequences are characterized by 3-base periodicity. Statistical analysis suggests that whether a coding sequence has 3-base periodicity may be related to the composition and distribution of bases, the usage and the order of the amino acids of the encoded protein as well as the synonymous codon usage. Generally, the content of A+U is higher than that of G+C in non-period-3 sequences, inversely in period-3 sequences. In the three codon positions, the base distribution in the non-periodic-3 sequences is more uniform than in the periodic-3 sequences. The usage biases of the amino acids and the codons in non-period-3 sequences are weaker than that in period-3 sequences. All of these phenomena should be considered sufficiently in predicting the genes and exons of DNA sequences by Fourier analysis method.

PNA(T).DNA(AT) triplexes with Hoogsteen base pairing are more favorable

Peptide nucleic acids (PNAs) are nucleic acid analogs with the deoxyribose phosphate backbone replaced by pseudo-peptide polymers to which the nucleobases are linked. The achiral, uncharged and rather flexible properties of the peptide backbone permit peptide nucleic acids more potential than oligonucleotides in application to antisence and antigenic reagents. The process of PNA binding to DNA duplex and forming triplex is the first step of PNA interacting with PNA. But there are no PNA.2DNA triplex crystal data up to date and little has been reported on the structure features and the force of the PNA.2DNA triplex. In this work, PNA(T).DNA(AT) triplexes are successfully built and the structures and forces to stabilize the triplex after optimizations and molecule dynamics are systematically examined, which are expected to aid in the application of PNAs as anticense and antigene agents.

Moisture content in Dall's porpoise (Phocoenoides dalli) tissues: a reference base for conversion factors between dry and wet weight trace element concentrations in cetaceans

Concentration of trace elements measured by dry weight basis has become more commonly used in recent studies on cetaceans than wet weight basis, which was used more in earlier studies. Because few authors present moisture content data in their papers, it is difficult to compare the concentrations of trace elements between various studies. Therefore, we felt that it would be useful if a reference conversion factor (CF) for tissue types could be found to convert between wet weight and dry weight data on trace element concentrations. We determined the moisture contents of 14 tissues of Dall's porpoise (Phocoenoides dalli), and then, calculated the CF values for those tissues. Because the moisture content of each tissue differs from other tissues, it is necessary to use a specific CIF for each tissue rather than a general CF for several tissues. We have also found that CIF values for Dall's porpoise tissues are similar to the same tissues in other cetaceans. Therefore CF values from Dall's porpoise can be reliably used to convert between wet and dry weight concentrations for other cetacean tissues as reference data. (C) 2002 Elsevier Science Ltd. All rights reserved.