Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays

Whole genome tiling arrays provide a high resolution platform for profiling of genetic, epigenetic, and gene expression polymorphisms. In this study we surveyed natural genomic variation in cytosine methylation among Arabidopsis thaliana wild accessions Columbia (Col) and Vancouver (Van) by comparing hybridization intensity difference between genomic DNA digested with either methylation-sensitive (HpaII) or -insensitive (MspI) restriction enzyme. Single Feature Polymorphisms (SFPs) were assayed on a full set of 1,683,620 unique features of Arabidopsis Tiling Array 1.0F (Affymetrix), while constitutive and polymorphic CG methylation were assayed on a subset of 54,519 features, which contain a 5'CCGG3' restriction site. 138,552 SFPs (1% FDR) were identified across enzyme treatments, which preferentially accumulated in pericentromeric regions. Our study also demonstrates that at least 8% of all analyzed CCGG sites were constitutively methylated across the two strains, while about 10% of all analyzed CCGG sites were differentially methylated between the two strains. Within euchromatin arms, both constitutive and polymorphic CG methylation accumulated in central regions of genes but under-represented toward the 5' and 3' ends of the coding sequences. Nevertheless, polymorphic methylation occurred much more frequently in gene ends than constitutive methylation. Inheritance of methylation polymorphisms in reciprocal F1 hybrids was predominantly additive, with F1 plants generally showing levels of methylation intermediate between the parents. By comparing gene expression profiles, using matched tissue samples, we found that magnitude of methylation polymorphism immediately upstream or downstream of the gene was inversely correlated with the degree of expression variation for that gene. In contrast, methylation polymorphism within genic region showed weak positive correlation with expression variation. Our results demonstrated extensive genetic and epigenetic polymorphisms between Arabidopsis accessions and suggested a possible relationship between natural CG methylation variation and gene expression variation.     

Global analysis of fluorescence fluctuation data

Over the last decade the number of applications of fluorescence correlation spectroscopy (FCS) has grown rapidly. Here we describe the development and application of a software package, FCS Data Processor, to analyse the acquired correlation curves. The algorithms combine strong analytical power with flexibility in use. It is possible to generate initial guesses, link and constrain fit parameters to improve the accuracy and speed of analysis. A global analysis approach, which is most effective in analysing autocorrelation curves determined from fluorescence fluctuations of complex biophysical systems, can also be implemented. The software contains a library of frequently used models that can be easily extended to include user-defined models. The use of the software is illustrated by analysis of different experimental fluorescence fluctuation data sets obtained with Rhodamine Green in aqueous solution and enhanced green fluorescent protein in vitro and in vivo.An erratum to this article can be found at Victor V. Skakun, Mark A. Hink and Anatoli V. Digris contributed equally to this work.     

Global analysis of an SAIS model

This paper is concerned with global analysis of an SAIS epidemiological model in a population of varying size introduced by Busenberg and van den Driessche. In this model the population is divided into three subgroups of susceptible, asymptomatic and infective individuals. It has been shown that this system has no periodic solutions and all its trajectories tend to the equilibria of the system. We use the Poincaré Index theorem to determine the number of the equilibria and their stability properties. We have shown that bistability occurs for suitable values of parameters and found a set of examples of all possible dynamics of the system.     

Global analysis of bird elevational diversity

Aim Elevational gradients distributed across the globe are a powerful test system for understanding biodiversity. Here I use a comprehensive set of bird elevational gradients to test the main drivers of diversity, including sampling, area, mid‐domain effect, temperature, temperature and water availability, and hypotheses of evolutionary history. Location Seventy‐eight elevational gradients of bird diversity from mountains in both hemispheres spanning 24.5° S to 48.2° N, including gradients from various climates, biogeographical regions and habitat types. Methods Data on bird elevational diversity were taken from the literature. Of the 150 datasets found or compiled, only those with a high, unbiased sampling effort were used in analyses. Datasets sampled all birds, all breeding birds or all forest birds; a few studies detailed seasonal, elevational shifts. Eighteen predictions of diversity theory were tested, including three sets of interactions. Results Birds display four distinct diversity patterns in nearly equal frequency on mountains: decreasing diversity, low‐elevation plateaus, low‐elevation plateaus with mid‐peaks, and unimodal mid‐elevational peaks. Bird elevational diversity strongly supports current climate as the main driver of diversity, particularly combined trends in temperature and water availability. Bird diversity on humid mountains is either decreasing or shows a low‐elevation plateau in diversity, while on dry mountains it is unimodal or a broad, low‐elevation plateau usually with a mid‐elevation maximum. The predictions of sampling, area and mid‐domain effect were not consistently supported globally. The only evolutionary hypothesis with preliminary support was niche conservatism. Main conclusions Both water and temperature variables are needed to comprehensively predict elevational diversity patterns for birds. This result is consistent for breeding and forest birds, for both hemispheres, and for local‐ or regional‐scale montane gradients. More analyses are needed to discern whether the mechanism underlying these relationships is ecological, based on direct physiological limitations or indirect food resource limitations, or historical, based on phylogenetic niche conservation or other evolutionary trends related to climate. The species–area and mid‐domain effects are not supported as primary drivers of elevational diversity in birds.     

Global conformation analysis of irradiated xyloglucans

Xyloglucan isolated and purified from tamarind seed was subjected to various degrees of γ-irradiation treatments, from 10 to 70 kGy, monitored for radiation damage and then studied using a new combined hydrodynamic approach with regards to conformation and flexibility. Radiation products were analysed with regard to molecular weight (weight average) M_w from size exclusion chromatography coupled to multi-angle laser light scattering (SEC–MALLs), intrinsic viscosity [η] and sedimentation coefficient s^o_20,w. Sedimentation coefficient distributions and elution profiles from SEC–MALLs confirmed the unimodal nature of the molecular weight distribution for each sample in solution. The chain flexibility was then investigated in terms of the persistence length, L_p of the equivalent worm-like chain model. The traditional Bushin–Bohdanecky (intrinsic viscosity) and Yamakawa–Fujii (sedimentation coefficient) relations were used separately then combined together by minimisation of a target function according to a recently published procedure [Ortega, A., & García de la Torre, J. (2007). Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility. Biomacromolecules, 8, 2464–2475 [see also Ortega, A. Metodologías computacionales para propiedades en disolución de macromoléculas rígidas y flexibles. Ph.D. Dissertation, Universidad de Murcia, 2005]] and yielded an estimate for L_p in the range 4–9 nm using floated and fixed mass per unit length analysis protocols and “point” global analysis: irradiated xyloglucans behave as flexible structures in common with pressure/heat treated materials.     

Global analysis of reptile elevational diversity

Aim Latitudinal‐ and regional‐scale studies of reptile diversity suggest a predominant temperature effect, unlike many other vertebrate richness patterns which tend to be highly correlated with both temperature and water variables. Here I examine montane gradients in reptile species richness with separate analyses of snakes and lizards from mountains around the world to assess a predominant temperature effect and three additional theories of diversity, including a temperature–water effect, the species–area effect and the mid‐domain effect (MDE). Location Twenty‐five elevational gradients of reptile diversity from temperate, tropical and desert mountains in both hemispheres, spanning 10.3° N to 46.1° N. Methods Elevational gradients in reptile diversity are based on data from the literature. Of the 63 data sets found or compiled, only those with a high, unbiased sampling effort were used in analyses. Twelve predictions and three interactions of diversity theory were tested using nonparametric statistics, linear regressions and multiple regression with the Akaike information criterion (AIC). Results Reptile richness and, individually, snake and lizard richness on mountains followed four distinct patterns: decreasing, low‐elevation plateaus, low‐elevation plateaus with mid‐elevation peaks, and mid‐elevation peaks. Elevational reptile richness was most strongly correlated with temperature. The temperature effect was mediated by precipitation; reptile richness was more strongly tied to temperature on wet gradients than on arid gradients. Area was a secondary factor of importance, whereas the MDE was not strongly associated with reptile diversity on mountains. Main conclusions Reptile diversity patterns on mountains did not follow the predicted temperature–water effect, as all diversity patterns were found on both wet and dry mountains. But the influence of precipitation on the temperature effect most likely reflects reptiles' use of radiant heat sources (sunning opportunities) that are more widespread on arid mountains than wet mountains due to lower humidity, sparser vegetation and less cloud cover across low and intermediate elevations.     

Global analysis of an SAIS model

This paper is concerned with global analysis of an SAIS epidemiological model in a population of varying size introduced by Busenberg and van den Driessche. In this model the population is divided into three subgroups of susceptible, asymptomatic and infective individuals. It has been shown that this system has no periodic solutions and all its trajectories tend to the equilibria of the system. We use the Poincaré Index theorem to determine the number of the equilibria and their stability properties. We have shown that bistability occurs for suitable values of parameters and found a set of examples of all possible dynamics of the system.     

Marker-aided genetic divergence analysis inBrassica

Genetic divergence was evaluated in 31 breeding lines from fourBrassica species using Mahalanobis'D ² . A new method of grouping usingD ² values was used to group the 31 lines, based on diagnostic morphological traits (called morphoqts). Isozyme variation of the individual enzymes esterase and glutamate oxaloacetate was quantified by five parameters (called isoqts) developed earlier. Grouping by the same method was also done based on the isoqts, and the grouping by isozymes was compared with that by morphoqts. Overall, there was an agreement of 73% suggesting that isoqts can be used in the choice of parents and also first stage selection of segregants in the laboratory. It was suggested that such an exercise would help to take care of season-bound and field-related problems of breeding. The new isozyme QTs, within lane variance of relative mobility and relative absorption, accounted for about 50% of the total divergence. The utility of the new method and isoqts in cost-effective breeding were highlighted.     

Semantics of genetic correlation analysis

A theory of genetic-correlation analysis has been put forward on the basis of notions concerning general and special codispersions . The complete set of genetic-correlation indexes is received and their genetic-statistical meaning revealed. The models for genetical component analysis of general and special codispersions of correlative connections are constructed.     

Software for genetic linkage analysis

Recent developments in human genetic linkage analysis have included the appearance of new software and collections of data and program resources, accessible by means of the Internet. Many of these new programs and collections are described, including their availability, literature background, and specific technical information.     

Combining microarrays and genetic analysis

Gene expression can be studied at a genome-wide scale with the aid of modern microarray technologies. Expression profiling of tens to hundreds of individuals in a genetic population can reveal the consequences of genetic variation. In this paper it is argued that the design and analysis of such a study is not a matter of simply applying the existing and more-or-less standard computational tools for microarrays to a new type of experimental data. It is shown how to fully exploit the power of genetics through optimal experimental design and analysis for two major microarray technologies, cDNA two-colour arrays and Affymetrix short oligonucleotide arrays.