A novel Gateway®-compatible binary vector allows direct selection of recombinant clones in Agrobacterium tumefaciens

Background

In vivo detection of protein-bound genomic regions can be achieved by combining chromatin-immunoprecipitation with next-generation sequencing technology (ChIP-seq). The large amount of sequence data produced by this method needs to be analyzed in a statistically proper and computationally efficient manner. The generation of high copy numbers of DNA fragments as an artifact of the PCR step in ChIP-seq is an important source of bias of this methodology.

Results

We present here an R package for the statistical analysis of ChIP-seq experiments. Taking the average size of DNA fragments subjected to sequencing into account, the software calculates single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the ratio test or the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutations. Computational efficiency is achieved by implementing the most time-consuming functions in C++ and integrating these in the R package. An analysis of simulated and experimental ChIP-seq data is presented to demonstrate the robustness of our method against PCR-artefacts and its adequate control of the error rate.

Conclusions

The software ChIP-seq Analysis in R (CSAR) enables fast and accurate detection of protein-bound genomic regions through the analysis of ChIP-seq experiments. Compared to existing methods, we found that our package shows greater robustness against PCR-artefacts and better control of the error rate.     

Temporal variation of characteristic scales in urban landscapes: an insight into the evolving internal structures of China’s two largest cities

Urbanization has induced profound landscape changes. While the spatiotemporal patterns of urban landscapes have been extensively studied, the manner by which the internal structures of already urbanized areas change remains little understood. Characteristic scales are an important measure of landscape structure, and they represent the typical spatial extents of landscape elements in hierarchies. In this study, we quantified temporal variations of the characteristic scales in the central urban landscapes of Beijing and Shanghai over an 18?year period. Using transect data from Landsat images, characteristic scales were identified through wavelet analysis and then classified into several discrete domains using the k-means clustering method. These characteristic scale domains appeared to correspond with the typical extents of the blocks and block clusters in the study areas. Results showed that the number of the characteristic scale domains changed within a small range of 3?C5 while the mean values of the characteristic scales within the domains showed substantial temporal variation. Larger characteristic scales were more variable than smaller ones in both cities. Distinguishing relative change rates of building forms, land use and street layout of urban landscapes allowed us to interpret these differences. The street layout of urban landscapes usually reacts slowly to the force of change, acting as the skeleton of the urban landscape. As a result, block sizes can remain relatively stable and corresponding characteristic scales present inheritance features. Land use and building forms are more susceptible to changes. Block clusters with flexible extents could result in significant variation of characteristic scales.     

Policy impacts on regulating ecosystem services: looking at the implications of 60 years of landscape change on soil erosion prevention in a Mediterranean silvo-pastoral system

Context

Policy decisions form a major driver of land use change, with important implications for socially and environmentally susceptible regions. It is well known that there can be major unintended consequences, especially where policies are not tailored to regionally specific contexts.

Objectives

In this paper we assess the implications of 60 years of agricultural policies on soil erosion prevention (SEP) by vegetation, an essential regulating ecosystem service in Mediterranean Europe.

Methods

To assess these implications we produced and analysed a time series of land cover/use and environmental conditions datasets (from 1951 to 2012) in relation to changing agricultural policies for a specific region in the southern Portugal. A set of indicators related to SEP allowed us to identify that land use intensification as increased soil erosion in the last 60 years.

Results

Particularly in the last 35 years, as a consequence of headage payments for cattle, the agricultural policy had a significant effect in the density and renewal of the tree cover, resulting in drastic effects for the provision of the SEP service. These are more significant after 1986, coinciding with the implementation of several Common Agricultural Policy instruments focused on increasing the modernization and productivity capacity of farm systems.

Conclusions

The results show some unintended effects of agricultural policy mechanisms on ecosystem service provision and highlight the need for context-based policies, tailored to the environmental constrains and potentials of each region.