A combined statistical model for multiple motifs search

Transcription factor binding sites (TFBS) play key roles in genebior 6.8 wavelet expression and regulation. They are short sequence segments with de¯nite structure and can be recognized by the corresponding transcription factors correctly. From the viewpoint of statistics, the candidates of TFBS should be quite di®erent from the segments that are randomly combined together by nucleotide. This paper proposes a combined statistical model for ¯nding over- represented short sequence segments in di®erent kinds of data set. While the over-represented short sequence segment is described by position weight matrix, the nucleotide distribution at most sites of the segment should be far from the background nucleotide distribution. The central idea of this approach is to search for such kind of signals. This algorithm is tested on 3 data sets, including binding sites data set of cyclic AMP receptor protein in E.coli, PlantProm DB which is a non-redundant collection of proximal promoter sequences from di®erent species, collection of the intergenic sequences of the whole genome of E.Coli. Even though the complexity of these three data sets is quite di®erent, the results show that this model is rather general and sensible.

Analysis of the characteristic sequence of intein and revision of its motifs

Since the first intein (Sce VMA) was found in Saccharomydes cerevisiae ATPases gene in 1990, more and more inteins were identified. It is necessary to analyze the new inteins to understand the sequence charateristics of inteins. By searching protein and n

Detection of potential positive regulatory motifs of transcription in yeast introns by comparative analysis of oligonucleotide frequencies

We conducted a comparative statistical analysis of tetra- through hexanucleotide frequencies in two sets of introns of yeast genes. The first set consisted of introns of genes that have transcription rates higher than 30 mRNAs/h while the second set contained introns of genes whose transcription rates were lower than or equal to 10 mRNAs/h. Some oligonucleotides whose occurrence frequencies in the first set of introns are significantly higher than those in the second set of introns were detected. The frequencies of occurrence of most of these detected oligonucleotides are also significantly higher than those in the exons flanking the introns of the first set. Interestingly some of these detected oligonucleotides are the same as well known "signature" sequences of transcriptional regulatory elements. This could imply the existence of potential positive regulatory motifs of transcription in yeast introns. (C) 2003 Elsevier Ltd. All rights reserved.

Crystal packing motifs of oligothiophenes end-capped with N-containing aryls

Oligothiophenes (OThs) end-capped with 3-quinolyl or pyridyl with nitrogen atom at meta-, ortho- or para-position were synthesized. The single-crystal structures of the resulting molecules, i.e., o-PyTh4, m-PyTh4, p-PyTh4, QuTh2, and QuTh3, were successfully determined by single-crystal X-ray analysis. Pyridyl end-capped OThs; o-PyTh4, m-PyTh4, and p-PyTh4, adopt the different herringbone packing arrangement in crystals depending on the position of the nitrogen atom because of the presence of weak C-H center dot center dot center dot N hydrogen bonds. The p-PyTh4 molecules are linked each other along the long axis of the molecules to form the extended chains by C-H center dot center dot center dot N dimer synthon. For m-PyTh4, the C-H center dot center dot center dot N interactions two-dimensionally extend through C-H center dot center dot center dot N trimer synthon.

Structural analysis of SNARE motifs from sea perch, Lateolabrax japonicus by computerized approaches

Three cDNA sequences encoding four SNARE (N-ethylmaleimide-sensitive fusion protein attachment protein receptors) motifs were cloned from sea perch, and the deduced peptide sequences were analyzed for structural prediction by using 14 different web servers and softwares. The "ionic layer" structure, the three dimensional extension and conformational characters of the SNARE 7S core complex by using bioinformatics approaches were compared respectively with those from mammalian X-ray crystallographic investigations. The result suggested that the formation and stabilization of fish SNARE core complex might be driven by hydrophobic association, hydrogen bond among R group of core amino acids and electrostatic attraction at molecular level. This revealed that the SNARE proteins interaction of the fish may share the same molecular mechanism with that of mammal, indicating the universality and solidity of SNARE core complex theory. This work is also an attempt to get the protein 3D structural information which appears to be similar to that obtained through X-ray crystallography, only by using computerized approaches. (C) 2007 Elsevier Ltd. All rights reserved.

Identification and analysis of the immune effects of CpG motifs that protect Japanese flounder (Paralichthys olivaceus) against bacterial infection

CpG-containing oligodeoxynucleotides (ODNs) are known to be immunostimulatory in vertebrate systems and can activate both innate and adaptive immune responses. In this report, we described the selection, identification, and analysis of CpG motifs with immunoprotective effects in Japanese flounder. Sixteen CpG ODNs were synthesized and examined for the ability to inhibit bacterial dissemination in Japanese flounder blood. Four ODNs with the strongest inhibitory effects were selected and mixed to form ODNs 4M. In addition, a plasmid, pCN6, was constructed that contains the sequences of the four selected ODNs. When administered into Japanese flounder via intraperitoneal injection, both ODNs 4M and pCN6 could, in dose and time dependent manners, afford short-term protection against the infections of two different bacterial pathogens. Immunological analyses showed that ODNs 4M and, especially, pCN6 activated head kidney macrophages and enhanced serum bactericidal activity via probably the alternative pathway of complement activation. When used as a DNA vaccine to immunize Japanese flounder, pCN6 conferred apparent protections (42.9% and 52.6%, respectively, in terms of relative percent survival) against the challenges of two different fish pathogens at 4-week post-vaccination. Transcriptional analysis showed that vaccination with pCN6 upregulated the expression of the genes encoding NKEF, MHC II alpha, IL-1 beta, Mx, and MHC I alpha. These results demonstrate that ODNs 4M and pCN6 are immunostimulatory in Japanese flounder and can induce short- and long-term nonspecific protections against bacterial infections. (C) 2010 Elsevier Ltd. All rights reserved.

Time-Frequency Analysis of Nonlinear Systems: The Skeleton Linear Model and the Skeleton Curves

The joint time-frequency analysis method is adopted to study the nonlinear behavior varying with the instantaneous response for a class of S.D.O.F nonlinear system. A time-frequency masking operator, together with the conception of effective time-frequency region of the asymptotic signal are defined here. Based on these mathematical foundations, a so-called skeleton linear model (SLM) is constructed which has similar nonlinear characteristics with the nonlinear system. Two skeleton curves are deduced which can indicate the stiffness and damping in the nonlinear system. The relationship between the SLM and the nonlinear system, both parameters and solutions, is clarified. Based on this work a new identification technique of nonlinear systems using the nonstationary vibration data will be proposed through time-frequency filtering technique and wavelet transform in the following paper.

A new method and instrument for accurately measuring interval between ultrashort pulses

Using second-order autocorrelation conception, a novel method and instrument for accurately measuring interval between two linearly polarized ultrashort pulses with real time were presented. The experiment demonstrated that the measuring method and instrument were simple and accurate (the measurement error <5 fs). During measuring, there was no moving element resulting in dynamic measurement error.

Large three-photon absorption and intramolecular charge transfer of the bis-donor fluorene-based molecules

Three-photon absorption (3PA) of two fluorene-based molecules with D-pi-D structural motifs (abbreviated as BPAF and BCZF) has been determined by using a Q-switched Nd: YAG laser pumped with 38 ps pulses at 1064 nm in DMF. The measured 3PA cross-sections are 222 and 140 x 10(-78) cm(6) s(2) for BPAF and BCZF, respectively. AM1 calculations show that attaching different donors changes the charge density distribution of the fluorene skeleton, and it is observed that the 3PA cross-section can be enhanced with increasing intramolecular charge transfer character, measured by the parameter Delta p(1)/Delta p(2)/Delta p(1)'. (c) 2005 Elsevier B.V. All fights 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).