A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

international linkages value added trade and firm productivity in latin america and the caribbean

This chapter addresses the following research questions: (i) Are firms characterized by international linkages more productive than other firms? (ii) Are those belonging to industries more involved in GVCs even more productive? To this end, we combine the World Bank Enterprise Survey dataset with the new OECD-WTO TiVA dataset and present three main empirical exercises: (1) an analysis of productivity premia associated with participation in international trade and presence of inward FDI; (2) a Cobb–Douglas output function expanded to firms' international linkages; (3) a further expanded version of the above relationship including the TiVA-based indicators of value added trade and industry participation and position in the global value chain. Our empirical outcomes confirm the presence of a positive causal relationship between participation in international activities and firm performance in the LAC region. Focusing on four big Latin American countries we show that the actual level of involvement into GVCs matters as well

Constraint-based genetic compilation

Synthetic biology aims at facilitating the design of new organisms via the standardization of biological parts and following engineering principles. We present atgc (Assistant To Genetic Compilation), a software tool that automatically builds a functional sequence of DNA from a minimal set of requirements. Through a simple language, the user provides in-house knowledge about their construct (e.g. relative placement of parts, number of restriction enzymes). atgc combines information from established biology, user knowledge and bioinformatics databases, and maps the problem to a constraint satisfaction setting. The solution is a functional DNA sequence ready to be assembled and transferred to a target organism