Classification and comparative analysis of Curcuma longa L. expressed sequences tags (ESTs) encoding glycine-rich proteins (GRPs)

Glycine-rich proteins (GRPs) are a group of proteins characterized by their high content of glycine residues often occurring in repetitive blocs. The diverse expression pattern and sub cellular localization of various GRPs suggest their implication in different physiological processes. Several GRPs has been isolated and characterized from different monocots and dicots. However, little or no information is available about the structure and function of GRPs in asexually reproducing plants. In this study, in-silico analysis of expressed sequence tag database resulted in the isolation of fifty-one GRPs from Curcuma longa L., an asexually reproducible plant of great medicinal and economic significance. Phylogenetic analysis grouped the GRPs into four distinct classes based on conserved motifs and nature of glycine-rich repeats. Majority of the isolated GRPs exhibited high homology with known GRPs from other plants that are expressed in response to various stresses. The presence of high structural diversity and signal peptide in some GRPs suggest their diverse physiological role and tissue specific localization. The isolated sequences can be used as a framework for cloning, characterization and expressional analysis of GRPs in response to various biotic and abiotic stresses in Curcuma longa as well as other asexually reproducing plants.     

Models for circular-linear and circular-circular data constructed from circular distributions based on nonnegative trigonometric sums

Johnson and Wehrly (1978, Journal of the American Statistical Association 73, 602-606) and Wehrly and Johnson (1980, Biometrika 67, 255-256) show one way to construct the joint distribution of a circular and a linear random variable, or the joint distribution of a pair of circular random variables from their marginal distributions and the density of a circular random variable, which in this article is referred to as joining circular density. To construct flexible models, it is necessary that the joining circular density be able to present multimodality and/or skewness in order to model different dependence patterns. Fernández-Durán (2004, Biometrics 60, 499-503) constructed circular distributions based on nonnegative trigonometric sums that can present multimodality and/or skewness. Furthermore, they can be conveniently used as a model for circular-linear or circular-circular joint distributions. In the current work, joint distributions for circular-linear and circular-circular data constructed from circular distributions based on nonnegative trigonometric sums are presented and applied to two data sets, one for circular-linear data related to the air pollution patterns in Mexico City and the other for circular-circular data related to the pair of dihedral angles between consecutive amino acids in a protein.     

Functional equivalence of industrial metal cleaning processes comparison of metal cleaning processes within LCA

In an LCA case study, the three most frequent industrial metal cleaning technologies were assessed: Cleaning based on aqueous cleaning agents, non-halogenated hydrocarbon solvents and halogenated hydrocarbon solvents. Beside optimisation analysis, the comparison of the cleaning processes was a main goal of the study. The function of metal cleaning processes can be described with a set of parameters called functional parameters. In order to compare different cleaning processes within LCA, it is a precondition that all relevant functional parameters be equivalent. However, metal cleaning processes from different companies normally differ in most of the functional parameters and, thus, are not functionally equivalent. Therefore, it is necessary to calculate the material and energy flows of the processes corresponding to a reference function as a basis for comparison. This can be achieved by simulating the processes according to the functional parameters with the help of a process model. For a general comparison of the technologies, it is also necessary to consider the assessed machines having the same level of optimisation and the same scale.     

Brefeldin A, thapsigargin, and AIF4- stimulate the accumulation of GRP78 mRNA in a cycloheximide dependent manner, whilst induction by hypoxia is independent of protein synthesis.

The glucose regulated proteins (GRPs) are major structural components of the endoplasmic reticulum (ER) and are involved in the import, folding, and processing of ER proteins. Expression of the glucose regulated proteins (GRP78 and GRP94) is greatly increased after cells are exposed to stress agents (including A23187 and tunicamycin) which inhibit ER function. Here, we demonstrate that three novel inhibitors of ER function, thapsigargin (which inhibits the ER Ca(2+)-ATPase), brefeldin A (an inhibitor of vesicle transport between the ER and Golgi) and AIF4-, (which inhibits trimeric G-proteins), can increase the expression of both GRP78 and 94. The common characteristic shared by activators of GRP expression is that they disrupt some function of the ER. The increased levels of GRPs may be a response to the accumulation of aberrant proteins in the ER or they may be increased in response to structural/functional damage to the ER. The increased accumulation of GRP78 mRNA after exposure of cells to either thapsigargin, brefeldin A, AIF4-, A23187, or tunicamycin can be blocked by pre-incubation in cycloheximide. In contrast, accumulation of GRPs after exposure to hypoxia was independent of cycloheximide. In addition, the protein kinase inhibitor genistein blocked the thapsigargin induced accumulation of GRP78 mRNA, whereas the protein phosphatase inhibitor okadaic acid caused increased accumulation of GRP78 mRNA. The data indicates that there are at least 2 mechanisms for induced expression of GRPs, one of which involves a phosphorylation step and requires new protein synthesis (e.g., thapsigargin, A23187) and one which is independent of both these steps (hypoxia).     

Structural determinants crucial to the RNA chaperone activity of glycine-rich RNA-binding proteins 4 and 7 in Arabidopsis thaliana during the cold adaptation process

Although glycine-rich RNA-binding proteins (GRPs) have been determined to function as RNA chaperones during the cold adaptation process, the structural features relevant to this RNA chaperone activity remain largely unknown. To uncover which structural determinants are necessary for RNA chaperone activity of GRPs, the importance of the N-terminal RNA recognition motif (RRM) and the C-terminal glycine-rich domains of two Arabidopsis thaliana GRPs (AtGRP4 harbouring no RNA chaperone activity and AtGRP7 harbouring RNA chaperone activity) was assessed via domain swapping and mutation analyses. The results of domain swapping and deletion experiments showed that the domain sequences encompassing the N-terminal RRM of GRPs were found to be crucial to the ability to complement cold-sensitive Escherichia coli mutant cells under cold stress, RNA melting ability, and freezing tolerance ability in the grp7 loss-of-function Arabidopsis mutant. In particular, the N-terminal 24 amino acid extension of AtGRP4 impedes the RNA chaperone activity. Collectively, these results reveal that domain sequences and overall folding of GRPs governed by a specific modular arrangement of RRM and glycine-rich sequences are critical to the RNA chaperone activity of GRPs during the cold adaptation process in cells.     

基于生态效率的辽宁省循环经济分析

生态效率与循环经济相辅相成。基于区域生态效率评价是考量区域循环经济的重要内容,又基于目前对于循环经济与生态效率结合的实证研究相对较少,因此,以生态效率理论为基础,对我国最早开展循环经济的试点省份——辽宁省的循环经济发展作以综合衡量。通过生态效率度量模型与循环经济度量模型,以辽宁省1990～2008年数据为基础,运用基于熵权的TOPSIS方法,分别计算了19a间辽宁省各年的资源效率、环境效率、生态效率,进而综合评价了辽宁省循环经济发展轨迹。研究表明：在19a间,辽宁省生态效率总体呈现波动上升态势,经历了传统经济发展模式——末端治理模式——循环经济模式的转变;19a间,辽宁省循环经济发展状态总体上处于循环性不断增强的状态,即经济发展的同时,环境压力不断减小。研究证明了辽宁省2002年实行循环经济以来取得了明显成效,对全国尤其是东北地区发展循环经济,走新型工业化道路具有重要的示范意义。     

Parameter estimation and model selection for Neyman-Scott point processes

This paper proposes an approximative method for maximum likelihood estimation of parameters of Neyman-Scott and similar point processes. It is based on the point pattern resulting from forming all difference points of pairs of points in the window of observation. The intensity function of this constructed point process can be expressed in terms of second-order characteristics of the original process. This opens the way to parameter estimation, if the difference pattern is treated as a non-homogeneous Poisson process. The computational feasibility and accuracy of this approach is examined by means of simulated data. Furthermore, the method is applied to two biological data sets. For these data, various cluster process models are considered and compared with respect to their goodness-of-fit.     

Genetic regulation of the processes of neurogenesis

Neurons proved to be a convenient experimental model for studies of regulatory properties of the genetic apparatus during development. Formation of neuronal ensembles is controlled by multiple modifier-genes at different levels. The following gene groups can be distinguished: 1) Genes that function in differentiating neurons; 2) Genes that function in other neurons; 3) Genes that function in glial cells; 4) Genes that function in surrounding tissues; 5) Genes that function at the organism level.     

The spatiotemporal transfer function of the Limulus lateral eye

The dynamics of the Limulus retina may be well described by the spatiotemporal transfer function, which measures the response of the eye to moving sinusoidal gratings. We consider a model for this system, which incorporates an excitatory generator potential, and self- and lateral inhibitory processes. Procedures are described which allow estimation of parameters for the model consistent with the empirical transfer function data. Transfer functions calculated from the model show good agreement with laboratory measurements, and may be used to predict accurately the response of the eye to arbitrary moving stimuli. The model allows convenient interpretation of the transfer function measurements in terms of physiological processes which underly the response of the Limulus retina.     

Interrogation of multimeric DNA amplification products by competitive primer extension using bst DNA polymerase (large fragment).

Linear dsDNA composed of tandem repeats may be exponentially amplified by the strongly strand-displacing Bst DNA polymerase (large fragment) and two primers specific for opposite strands. When the repetitive DNA is derivedfrom rolling circle replication of a circular template, the reaction is termed cascade rolling circle amplification (CRCA). We have developed a variant of CRCA in which one primer is attached to the surface of a microwell and the other is labeled, thus enabling detection of amplified material using an ELISA-like protocol. The circular template is derived by annealing and ligation of a padlock on target DNA. It was found that there was good correlation between the synthesis of amplified material and signal. The specificity of the reaction with respect to single-nucleotide polymorphisms was investigated, and it was found that Bst DNA polymerase is prone to extension from primers with mismatched 3' ends. Reliable single nucleotide specificity was only obtained when pre-synthesized amplified material was interrogated by competitive primer extension.     

A Note on Circular Nonparametrical Classification

Following the linear approach by Stoller a circular discriminant analytical method is described. Marginally, following Ling, a simple method is mentioned to find clusters on a circle. Both methods are distribution-free and invariant under rotation.     

NMR relaxation processes of 31P in macromolecules

³¹P-Nmr relaxation parameters (spin-lattice relaxation time, linewidth, and nuclear Overhauser effect) were obtained at three different frequencies for poly(U) and a well-defined (145 ± 3 base-pair) fragment of DNA in solution. Data sets for the two samples were analyzed by theories which included relaxation by the mechanisms of ³¹P chemical shift anisotropy as well as by ¹H-³¹P dipole–dipole interaction. Neither data set could be satisfactorily described by a single correlation time. A model of a rigid rotor most nearly fits the data for the DNA molecule. Parameters obtained from the least-square fit indicate (1) that the DNA undergoes anisotropic reorientation with a correlation time τ₀ = 6.5 × 10^?7 sec for the end-to-end motion, (2) the ratio of diffusion constants D_∥/D_⊥ is 91, and (3) that the linewidth is due to chemical shift dispersion to the extent of 0.5 ppm. Some deviations of the calculated from the observed values suggested that significant torsional and bending motions may also take place for this DNA. Another model which contains isotropic motion but with a broad distribution of correlation times was required to fit the data for poly(U). A log ? χ² distribution function of correlation times [Scheafer, J. (1973) Macromolecules 6 , 881–888] described well the motion of poly(U) with the average correlation time τ = 3.3 × 10^?9 sec and a distribution parameter p = 14.     

Non-circular geometry and radiogrammetry of the second metacarpal

Traditional radiogrammetry of the second metacarpal mid-shaft reconstructs cortical cross-sectional geometry from mediolateral (ML) linear dimensions based on a circular model. However, comparison of antero-posterior (AP) versus mediolateral radiographic dimensions in a sample of paired metacarpals shows that AP total and medullary widths typically exceed ML widths by 5% to 10%. As well, in 13% of males and 25% of females, the two metacarpals are dissimilarly shaped, i.e., the AP/ML ratio is >1.0 for one side and <1.0 for the other. This situation exaggerates the differences in geometric properties between sides and constitutes a potentially significant source of bias for analyses of bilateral asymmetry. These results suggest that the circular model is inappropriate for estimation of cross-sectional geometry at this anatomical location. © 1995 Wiley-Liss, Inc.     

特定环状RNA表达与衰老的关系研究*

目的:研究小鼠不同组织器官中环状RNA的表达量在年老与年幼中的差异,揭示环状RNA与衰老的联系。方法:通过对不同组织器官的总RNA的提取,分别逆转录,并扩增circUSP34、circTCF4、circTCF20、circZFP64、circPWWP2A、circLIN54,通过凝胶电泳比较其在年轻小鼠与年老小鼠的组织器官中的表达情况,明确上述环状RNA与衰老的联系。结果:环状RNA在不同年龄小鼠的组织器官中存在广泛性的差异性表达,不同组织不同环状RNA有着不同的表达量的改变,其与衰老存在联系。在卵巢中除circTCF4,其余五种环状RNA表达量均与年龄负相关;在肾脏中,除circTCF4与circPWWP2A,其余与年龄呈负相关;在乳腺中只有circUSP3与衰老呈负相关;而在肠道与生长相关的只有上述后三种环状RNA,均呈正相关。其他样本与组织的发育阶段有不同的相关性,具体在结果体现。结论:环状RNA的表达量在组织中与年龄的增大有着显著相关性,环状RNA可能广泛地参与了不同的衰老通路,起到不同的生物学作用,其在衰老的产生中扮演重要角色。     

An estimating function approach to inference for inhomogeneous Neyman-Scott processes

This article is concerned with inference for a certain class of inhomogeneous Neyman-Scott point processes depending on spatial covariates. Regression parameter estimates obtained from a simple estimating function are shown to be asymptotically normal when the "mother" intensity for the Neyman-Scott process tends to infinity. Clustering parameter estimates are obtained using minimum contrast estimation based on the K-function. The approach is motivated and illustrated by applications to point pattern data from a tropical rain forest plot.     

Kinetics of the salt-induced B- to Z-DNA transition

The salt-induced B- to Z-DNA conformational transition is a cooperative- and time-dependent process. From a modified form of the logistic equation which describes an equilibrium between two states we have deduced a kinetic function to quantify the degree of the B to Z transition of a synthetic (dG-dC) ⋅ (dG-dC) polynucleotide. This function was obtained by introduction of time as a variable in the logistic function so that the equilibrium constant, K, is replaced by a new constant K _s , characteristic of the type of salt used. This constant is defined as the salt concentration needed to reach the B-Z transition-midpoint in the time unit. The equation fits the data obtained by circular dichroism (CD) for changes in molecular ellipticity of poly(dG-m⁵dC) ⋅ poly(dG-m⁵dC) and poly(dG-dC) ⋅ poly(dG-dC) incubated with various concentrations of mono-, di-, and trivalent salts at a constant temperature. The derived expression may be a very useful tool for studying the kinetics of the B- to Z-DNA transition. Received: 1 December 1997 / Revised version: 16 March 1998 / Accepted: 27 March 1998     

CIRCexplorer3:A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression

Sequences of circular RNAs(circ RNAs) produced from back-splicing of exon(s) completely overlap with those from cognate linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction(BSJ) sites.Therefore,examination of global circ RNA expression from RNA-seq datasets generally relies on the detection of RNA-seq fragments spanning BSJ sites,which is different from the quantification of linear RNA expression by normalized RNA-seq fragments mapped to whole gene bodies.Thus,direct comparison of circular and linear RNA expression from the same gene loci in a genome-wide manner has remained challenging.Here,we update the previously-reported CIRCexplorer pipeline to version 3 for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq(CIRCexplorer3-CLEAR).A new quantitation parameter,fragments per billion mapped bases(FPB),is applied to evaluate circular and linear RNA expression individually by fragments mapped to circ RNA-specific BSJ sites or to linear RNA-specific splicing junction(SJ) sites.Comparison of circular and linear RNA expression levels is directly achieved by dividing FPBcircby FPBlinearto generate a CIRCscore,which indicates the relative circ RNA expression level using linear RNA expression level as the background.Highlyexpressed circ RNAs with low cognate linear RNA expression background can be readily identified by CIRCexplorer3-CLEAR for further investigation.CIRCexplorer3-CLEAR is publically available at https://github.com/Yang Lab/CLEAR.     

Some properties of the point processes generated by integral density modulation of renewal processes

Integral density modulation of point processes is defined, and the properties of the modulated point processes are described. When a homogeneous renewal process is modulated by a step random signal, the mathematical expressions are derived of the probability density functions of the sums of r-successive inter point intervals, the intensity functions and the first order correlation coefficient of intervals. These quantities are calculated and illustrated for several parameter values. Modulated point sequences are generated by computer simulation method. The interval histograms and the serial correlation coefficients of counts and of intervals of the sequences are obtained. The results are compared with the theoretical results on the point processes modulated by the step random signal.Abbreviations IDM Integral density modulation - SRS Step random signal - PP Point process - PS Point sequence - PDF Probability density function - CPDF Conditional probability density function - JCPDF Joint conditional probability density function - SED Special Earlangian distribution - SCC Serial correlation coefficients - SIC Serial intensity coefficients     

Analyzing wearable device data using marked point processes

This paper introduces two sets of measures as exploratory tools to study physical activity patterns: active‐to‐sedentary/sedentary‐to‐active rate function (ASRF/SARF) and active/sedentary rate function (ARF/SRF). These two sets of measures are complementary to each other and can be effectively used together to understand physical activity patterns. The specific features are illustrated by an analysis of wearable device data from National Health and Nutrition Examination Survey (NHANES). A two‐level semiparametric regression model for ARF and the associated activity magnitude is developed under a unified framework using the marked point process formulation. The inactive and active states measured by accelerometers are treated as a 0‐1 point process, and the activity magnitude measured at each active state is defined as a marked variable. The commonly encountered missing data problem due to device nonwear is referred to as “window censoring,” which is handled by a proper estimation approach that adopts techniques from recurrent event data. Large sample properties of the estimator and comparison between two regression models as measurement frequency increases are studied. Simulation and NHANES data analysis results are presented. The statistical inference and analysis results suggest that ASRF/SARF and ARF/SRF provide useful analytical tools to practitioners for future research on wearable device data.