Distinguish Coding And Noncoding Sequences In A Complete Genome Using Fourier Transform

A Fourier transform method is proposed to distinguish coding and non-coding sequences in a complete genome based on a number sequence representation of the DNA sequence proposed in our previous paper (Zhou et al., J. Theor. Biol. 2005) and the imperfect periodicity of 3 in protein coding sequences. The three parameters P_x(S) (1), P_x(S) (1/3) and P_x(S) (1/36) in the Fourier transform of the number sequence representation of DNA sequences are selected to form a three-dimensional parameter space. Each DNA sequence is then represented by a point in this space. The points corresponding to coding and non-coding sequences in the complete genome of prokaryotes are seen to be divided into different regions. If the point (P_x(�ar S) (1), Px(�ar S) (1/3), P_x(�ar S) (1/36)) for a DNA sequence is situated in the region corresponding to coding sequences, the sequence is distinguished as a coding sequence; otherwise, the sequence is classified as a noncoding one. Fisher's discriminant algorithm is used to study the discriminant accuracy. The average discriminant accuracies pc, pnc, qc and qnc of all 51 prokaryotes obtained by the present method reach 81.02%, 92.27%, 80.77% and 92.24% respectively

A Mutual Information Based Sequence Distance For Vertebrate Phylogeny Using Complete Mitochondrial Genomes

Traditional sequence distances require alignment. A new mutual information based sequence distance without alignment is defined in this paper. This distance is based on compositional vectors of DNA sequences or protein sequences from complete genomes. First we establish the mathematical foundation of this distance. Then this distance is applied to analyze the phylogenetic relationship of 64 vertebrates using complete mitochondrial genomes. The phylogenetic tree shows that the mitochondrial genomes are separated into three major groups. One group corresponds to mammals; one group corresponds to fish; and the last one is Archosauria (including birds and reptiles). The structure of the tree based on our new distance is roughly in agreement in topology with the current known phylogenies of vertebrates

Finite Difference and Sinc-Collocation Approximations to a Class of Fractional Diffusion-Wave Equations

We propose an efficient numerical method for a class of fractional diffusion-wave equations with the Caputo fractional derivative of order α. This approach is based on the finite difference in time and the global sinc collocation in space. By utilizing the collocation technique and some properties of the sinc functions, the problem is reduced to the solution of a system of linear algebraic equations at each time step. Stability and convergence of the proposed method are rigorously analyzed. The numerical solution is of 3-α order accuracy in time and exponential rate of convergence in space. Numerical experiments demonstrate the validity of the obtained method and support the obtained theoretical results

The amino acid variation within the binding pocket 7 and 9 of HLA-DRB1 molecules are associated with primary Sjögren's syndrome

在这篇论文当中，郑俊峰博士领导的课题小组发现在人白细胞抗原二类基因（HLA-II）中，HLA-DRB1*0803是中国南方原发干燥综合征易感基因。进一步通过结构生物信息学模拟DRB1*0803 分子结构并分析，发现HLA的抗原肽结合槽口袋9的表面电势的不同，可能是疾病易感性差异的分子基础。自身免疫病是由遗传因素和环境因素共同导致的疾病，在遗传因素里，HLA位点是很多自身免疫病的主要易感基因。但是，尽管HLA和自身免疫病的相关性非常明确，这种相关背后的机理还不清楚。这项关于HLA和干燥综合征相关性的研究在这一问题上做出了探索性的发现，对HLA和干燥综合征的相关的机制提出了新的观点。该成果也是自身免疫学实验室在干燥综合征方向上陆续发表的第4篇学术论文。Primary Sjögren's syndrome (pSS) is associated with HLA-DRB1 loci, but the association of amino acid variations in the hypervariable region of the HLA-DR β1 chain with pSS is largely unknown. In this study, we aimed to identify the amino acid variations within the hypervariable region of HLA-DRB1 molecule which are associated with the susceptibility to pSS. We sequenced the 2nd exon of the HLA-DRB1 locus in 52 pSS patients and 179 controls. The HLA-DRB1*0803 is the allele that shows the strongest association with pSS in Chinese population (OR = 3.0, P = 2.4 × 10 −4 ). Furthermore, amino acid variations within the binding pocket P7 and P9 are associated with the susceptibility to pSS. An interaction between two residues within P7, β47 and β67, is associated with pSS. Structural modeling studies demonstrated that the electrostatics of peptide binding pocket 9 are opposite in pSS-susceptible and -protective HLA-DRB1 alleles. In conclusion, our results suggest that structural heterogeneity of the HLA-DRB1 peptide binding pocket P7 and P9 might play a role in the pathogenesis of pSS

Hyperlipidemia induces meibomian gland dysfunction

Abstract(#br)Purpose(#br)To investigate the pathological changes of the meibomian gland (MG) and ocular surface in Apolipoprotein E knockout ( ApoE −/− ) mice and to investigate the association of meibomian gland dysfunction (MGD) with hyperlipidemia.(#br)Methods(#br)Total plasma cholesterol was measured in different ages of ApoE −/− and wild type (WT) mice, whilst the ocular surfaces were observed by slit-lamp biomicroscopy. MG sections were subjected to H&E staining, Oil Red O staining, TUNEL assay and immunostaining. Quantitate RT-PCR and Western blot analyses were performed to detect the relative gene expression in MGs. The 5-month-old ApoE −/− mice were administered with rosiglitazone or GW9662 + rosiglitazone via oral gavage for 2 months to determine their effect on MG pathological change.(#br)Results(#br)We found eyelid abnormality, MG dropout, abnormal MG acinar morphology, dilated MG duct and plugging of the MG orifice in ApoE −/− mice. MG acini in ApoE −/− mice showed exaggerated lipid accumulation. Abnormal keratinization increased in MG duct, accompanied with decreased proliferation and increased apoptosis in ApoE −/− mice. Inflammatory cells infiltrated into the surrounding microenvironment of MG acini, and the NF-κB signaling pathway was activated in MG acinar cells. Oxidative stress was evident in MG acinar cells of ApoE −/− mice. Further investigation showed downregulation of PPAR-γ in MG acinar cells of ApoE −/− mice. PPAR-γ agonist rosiglitazone treatment reduced the morbidity of eyelid, as well as corneal pathological changes and MG inflammation in ApoE −/− mice.(#br)Conclusion(#br)MGD and hyperlipidemia are closely associated in ApoE −/− mice, which represent a new model to study the pathophysiology of MGD related to dyslipidemia

Cluster Protein Structures using Recurrence Quantification Analysis on Coordinates of Alpha-Carbon Atoms of Proteins

The 3-dimensional coordinates of alpha-carbon atoms of proteins are used to distinguish the protein structural classes based on recurrence quantification analysis (RQA). We consider two independent variables from RQA of coordinates of alpha-carbon atoms, %determ1 and %determ2, which were defined by Webber et al. [C.L. Webber Jr., A. Giuliani, J.P. Zbilut, A. Colosimo, Proteins Struct. Funct. Genet. 44 (2001) 292]. The variable %determ2 is used to define two new variables, %determ21 and %determ22. Then three variables %determ1, %determ21 and %determ22 are used to construct a 3-dimensional variable space. Each protein is represented by a point in this variable space. The points corresponding to proteins from the α, β, α+β and α/β structural classes position into different areas in this variable space. In order to give a quantitative assessment of our clustering on the selected proteins, Fisher's discriminant algorithm is used. Numerical results indicate that the discriminant accuracies are very high and satisfactory

Analysis of Global Geomagnetic Variability

The orthogonal field components from global INTERMAGNET magnetometer stations are studied via multifractal detrended fluctuation analysis to determine whether there are clear and consistent regional patterns in the behavior of the fluctuations. There are three distinct scaling regimes in the qth-order fluctuation function for each of the 24 stations studied covering Southwest North America, Northeast North America, Central Europe, Northern Europe, Australasia and Asia. There is a consistent break point at time scale around 23 h for all stations. The scaling exponents of the second-order fluctuation functions reflect the regional character of the stations, and can be used for station classification, and for possible regional models

Numerical Sequence Representation of DNA Sequences and Methods To Distinguish Coding And Non-Coding Sequences in a Complete Genome

In this presentation we introduce two methods to distinguish coding and non-coding sequences in a complete genome. A numerical sequence representation of DNA sequences is introduced first. There exists a one-to-one correspondence between a DNA sequence and its numerical sequence representation. In the first method, three exponents from a multifractal analysis are selected to construct the parameter space. In the second method, which is based on a Fourier transform approach, three parameters from the power spectrum of the numerical sequence representation are selected to construct the parameter space. Each DNA may be represented by a point in these three-dimensional spaces. We found that the points corresponding to coding and non-coding sequences in the complete genomes of prokaryotes are divided into different regions in both parameter spaces. If the point for a DNA sequence is situated in the region corresponding to coding sequences, the sequence is recognized as a coding sequence; otherwise, the sequence is classified as a non-coding one. The average accuracies using Fisher's discriminant algorithm for coding and non-coding sequences are satisfactory

Origin and Phylogeny of Chloroplasts Revealed by a Simple Correlation Analysis of Complete Genomes

The complete sequenced genomes of chloroplast have provided much information on the origin and evolution of this organelle. In this paper we attempt to use these sequences to test a novel approach for phylogenetic analysis of complete genomes based on correlation analysis of compositional vectors. All protein sequences from 21 complete chloroplast genomes are analyzed in comparison with selected archaea, eubacteria, and eukaryotes. The distance-based analysis shows that the chloroplast genomes are most closely related to cyanobacteria, consistent with the endosymbiotic origin of chloroplasts. The chloroplast genomes are separated to two major clades corresponding to chlorophytes (green plants) s.l. and rhodophytes (red algae) s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution. For instance, the analysis places the chloroplasts of two chromophytes (Guillardia and Odontella) within the rhodophyte lineage, supporting secondary endosymbiosis as the source of these chloroplasts. The relationships among the green algae and land plants in our tree also agree with results from traditional phylogenetic analyses. Thus, this study establishes the value of our simple correlation analysis in elucidating the evolutionary relationships among genomes. It is hoped that this approach will provide insights on comparative genome analysis