Identifying and retargeting transcriptional hot spots in the human genome

Mammalian cell line development requires streamlined methodologies that will reduce both the cost and time to identify candidate cell lines. Improvements in site‐specific genomic editing techniques can result in flexible, predictable, and robust cell line engineering. However, an outstanding question in the field is the specific site of integration. Here, we seek to identify productive loci within the human genome that will result in stable, high expression of heterologous DNA. Using an unbiased, random integration approach and a green fluorescent reporter construct, we identify ten single‐integrant, recombinant human cell lines that exhibit stable, high‐level expression. From these cell lines, eight unique corresponding integration loci were identified. These loci are concentrated in non‐protein coding regions or intronic regions of protein coding genes. Expression mapping of the surrounding genes reveals minimal disruption of endogenous gene expression. Finally, we demonstrate that targeted de novo integration at one of the identified loci, the 12^th exon‐intron region of the GRIK1 gene on chromosome 21, results in superior expression and stability compared to the standard, illegitimate integration approach at levels approaching 4‐fold. The information identified here along with recent advances in site‐specific genomic editing techniques can lead to expedited cell line development.     

A method for in situ monitoring of the isotope composition of tree xylem water using laser spectroscopy

Field studies analyzing the stable isotope composition of xylem water are providing important information on ecosystem water relations. However, the capacity of stable isotopes to characterize the functioning of plants in their environment has not been fully explored because of methodological constraints on the extent and resolution at which samples could be collected and analysed. Here, we introduce an in situ method offering the potential to continuously monitor the stable isotope composition of tree xylem water via its vapour phase using a commercial laser‐based isotope analyser and compact microporous probes installed into the xylem. Our technique enables efficient high‐frequency measurement with intervals of only a few minutes per sample while eliminating the need for costly and cumbersome destructive collection of plant material and laboratory‐based processing. We present field observations of xylem water hydrogen and oxygen isotope compositions obtained over several days including a labelled irrigation event and compare them against results from concurrent destructive sampling with cryogenic distillation and mass spectrometric analysis. The data demonstrate that temporal changes as well as spatial patterns of integration in xylem water isotope composition can be resolved through direct measurement. The new technique can therefore present a valuable tool to study the hydraulic architecture and water utilization of trees.     

Just like the USA? Critical notes on Alba and Foner’s cross-Atlantic research agenda

ABSTRACT

A critical review of Alba and Foner's Strangers No More (2015 Foner, Nancy. 2015. “Is Islam in Western Europe Like Race in the United States?” Sociological Forum 30 (4): 885–899. [Google Scholar]) which focuses on questioning their comparative assimilation of European cases of immigrant integration to the North American, specifically U.S., experience. While this may work in terms of how national immigrant integration has mitigated over time racial discrimination for older, post-colonial migrants, it misrepresents the complex differentiations involved in the super-diversity of recent ‘new’ migrations within and to Europe. In particular, the variety of types and origins of recent migration is lost in their understanding of the U.K. case, with problems linked to their interpretation of data about minorities and foreigners in the country.     

Civic integration policies from below: accounting for processes of convergence and divergence in four European cities

The introduction of integration tests on a pre-entry or post-arrival basis has drawn attention to changing national integration policies. Yet, at the local level, language and civic culture courses have often been implemented before the development of national programmes. The way these policies came into place and the extent to which they responded to similar challenges has often been overlooked. This article explores the development of these measures in four cities – Stuttgart, Vienna, Barcelona and Turin – to find out which mechanisms account for convergence in policymaking. Integration courses present traits of similarity in their contents and target groups; however, this does not imply a consistent process towards convergence. Local introduction initiatives are the product of local policy arenas, which display different policy frames of migrant integration. On the other hand, new legislation and changes in the available financial resources for integration appear to be crucial factors that trigger divergence.     

Discovering phenotypic causal structure from nonexperimental data

The evolutionary potential of organisms depends on how their parts are structured into a cohesive whole. A major obstacle for empirical studies of phenotypic organization is that observed associations among characters usually confound different causal pathways such as pleiotropic modules, interphenotypic causal relationships and environmental effects. The present article proposes causal search algorithms as a new tool to distinguish these different modes of phenotypic integration. Without assuming an a priori structure, the algorithms seek a class of causal hypotheses consistent with independence relationships holding in observational data. The technique can be applied to discover causal relationships among a set of measured traits and to distinguish genuine selection from spurious correlations. The former application is illustrated with a biological data set of rat morphological measurements previously analysed by Cheverud et al. (Evolution 1983, 37, 895).     

异质性水分环境中克隆整合对活血丹生物量分配及叶片结构特征的影响

喀斯特石漠化环境有着高度的生境异质性,异质性生境中土被不连续,土壤瘠薄,岩溶漏斗上的土壤保水性差,严重制约着喀斯特植被的生长及分布。为探究克隆植物在喀斯特地区的适应策略,本研究以喀斯特黄色石灰土为基质,选用克隆植物活血丹（Glechoma longituba）,以一个节间连接的两个分株为材料,保持节间连接或切断,种植于相邻花盆中,并施以不同浇水量,以明确不同水分可用性水平下克隆整合对活血丹生物量积累、生物量分配、叶片气孔及叶片组织特征的影响。结果显示,克隆整合显著促进活血丹生物量的积累及对根、叶的生物量分配;增加了活血丹叶气孔导度,降低了气孔指数;叶海绵组织受克隆整合影响较小,但栅栏组织及栅海比（栅栏组织/海绵组织）表现为非整合分株高于整合分株。本研究表明,克隆整合可增加活血丹胁迫分株对根、叶的投资,并以更佳的叶气孔、组织适应策略提高其在喀斯特生境中的生存与适应。     

High efficiency Agrobacterium‐mediated site‐specific gene integration in maize utilizing the FLP‐FRT recombination system

An efficient Agrobacterium‐mediated site‐specific integration (SSI) technology using the flipase/flipase recognition target (FLP/FRT) system in elite maize inbred lines is described. The system allows precise integration of a single copy of a donor DNA flanked by heterologous FRT sites into a predefined recombinant target line (RTL) containing the corresponding heterologous FRT sites. A promoter‐trap system consisting of a pre‐integrated promoter followed by an FRT site enables efficient selection of events. The efficiency of this system is dependent on several factors including Agrobacterium tumefaciens strain, expression of morphogenic genes Babyboom (Bbm) and Wuschel2 (Wus2) and choice of heterologous FRT pairs. Of the Agrobacterium strains tested, strain AGL1 resulted in higher transformation frequency than strain LBA4404 THY‐ (0.27% vs. 0.05%; per cent of infected embryos producing events). The addition of morphogenic genes increased transformation frequency (2.65% in AGL1; 0.65% in LBA4404 THY‐). Following further optimization, including the choice of FRT pairs, a method was developed that achieved 19%–22.5% transformation frequency. Importantly, >50% of T0 transformants contain the desired full‐length site‐specific insertion. The frequencies reported here establish a new benchmark for generating targeted quality events compatible with commercial product development.