No abstract

Expression of genes in eukaryotic genomes is known to cluster, but cluster size is generally loosely defined and highly variable. We have here taken a very strict definition of cluster as sets of physically adjacent genes that are highly coexpressed and form so-called local coexpression domains. The Arabidopsis (Arabidopsis thaliana) genome was analyzed for the presence of such local coexpression domains to elucidate its functional characteristics. We used expression data sets that cover different experimental conditions, organs, tissues, and cells from the Massively Parallel Signature Sequencing repository and microarray data (Affymetrix) from a detailed root analysis. With these expression data, we identified 689 and 1,481 local coexpression domains, respectively, consisting of two to four genes with a pairwise Pearson's correlation coefficient larger than 0.7. This number is approximately 1-to 5-fold higher than the numbers expected by chance. A small (5%-10%) yet significant fraction of genes in the Arabidopsis genome is therefore organized into local coexpression domains. These local coexpression domains were distributed over the genome. Genes in such local domains were for the major part not categorized in the same functional category (GOslim). Neither tandemly duplicated genes nor shared promoter sequence nor gene distance explained the occurrence of coexpression of genes in such chromosomal domains. This indicates that other parameters in genes or gene positions are important to establish coexpression in local domains of Arabidopsis chromosomes.

The Mizoroki-Heck reaction generally refers to Pd-catalyzed C À C bond formation between organic (pseudo)halides and olefins. Today, it has become a powerful tool to prepare substituted olefins. [1] A key issue in intermolecular Heck reactions is the control of the site where aryl groups insert into olefins. High regioselectivity can be easily achieved for olefins carrying substituents with a significant electronic difference at the two olefinic sites, [2] such as acrylates [3] and vinyl ethers. [4] Aliphatic olefins, however, generally lack intrinsic electronic differentiation between two olefinic positions and it has been challenging to achieve good regiocontrol [Eq. (1), Scheme 1]. [5,6] To induce terminal insertion, coordinating groups are often present on olefins to serve as chelates. [7] The chelation strategy was also used in oxidative [8] and decarboxylative [9] Heck reactions to achieve regioselectivity. Recently, Sigman and Werner reported high terminal selectivity even for olefins without chelating groups. [10] For aliphatic olefins, high internal selectivity also proved very difficult to achieve, except a few special cases. [11] For example, Cabri et al. reported that olefin insertion into cationic aryl-Pd intermediates can be biased toward the internal position, but the selectivity was too low to be synthetically useful. [12] As a special case, allylic alcohol gave excellent internal selectivity, because owing to the inductive effect of its hydroxy group the electronic density on the internal carbon atom is decreased [Eq.(2), Scheme 1]. The inductive effect quickly diminishes over several bonds. Thus, for homoallylic alcohol the selectivity dropped drastically [Eq. (3), Scheme 1]. Herein, we report a general method for Heck reactions of aliphatic olefins in high internal selectivity, by using a set of ferrocene-based bisphosphine ligands [Eq. (4), Scheme 1].The Heck products, a-alkylstyrenes can be readily converted to various chiral building blocks by asymmetric catalytic processes. [13] They are also intermediates in the synthesis of bioactive natural products [14] and drug candidates. [15] The a-alkylstyrenes used to be prepared by crosscouplings of 2-alkenyl electrophiles or 2-alkenyl metallic reagents. Our new method directly uses simple olefins and does not require preactivation of olefin substrates.Initially, we used a model reaction of 1-naphthyl triflate and 1-octene and dppf as supporting ligand for the palladium catalyst (Figure 1). To our surprise, a dramatic effect of bases was observed (Figure 1). In particular, when trialkylamines, such as triethylamine and Hünigs base, were used, significant reduction of aryl triflate was observed, and the corresponding reduction product was obtained in up to 50 % yield. [16] In contrast, when urotropine was used, no reduction byproduct was detected and Heck products were formed in almost quantitative yield. The ratio of the desired isomer, 2-aryl-1octene versus all other isomers was 13:1, determined by GC. [17] It is worth pointing out that this rat...

Abstract-An ongoing area of study in synthetic biology has been the design and construction of synthetic circuits that maintain homeostasis at the population level. Here, we are interested in designing a synthetic control circuit that regulates the total cell population and the relative ratio between cell strains in a culture containing two different cell strains. We have developed a dual feedback control strategy that uses two separate control loops to achieve the two functions respectively. By combining both of these control loops, we have created a population regulation circuit where both the total population size and relative cell type ratio can be set by reference signals. The dynamics of the regulation circuit show robustness and adaptation to perturbations in cell growth rate and changes in cell numbers. The control architecture is general and could apply to any organism for which synthetic biology tools for quorum sensing, comparison between outputs, and growth control are available.