Microbial evolution in vivo and in silico: methods and applications
In this review we focus on the strengths and limitations of in vivo and in silico techniques for studying microbial evolution in the laboratory, and we discuss how these complementary approaches can be integrated in a unifying framework.
Light-responsive control of bacterial gene expression: precise triggering of the lac promoter activity using photocaged IPTG
An optogenetic tool was established allowing for precise, gradual and homogeneous light-triggering of lac-based gene expression in a non-invasive fashion.
Probing subcellular organic hydroperoxide formation via a genetically encoded ratiometric and reversible fluorescent indicator
A ratiometric fluorescent indicator for organic hydroperoxide (OHP) was developed and utilized for the study of endogenous OHP dynamics with subcellular precision.
ERG9 and COQ1 disruption reveals isoprenoids biosynthesis is closely related to mitochondrial function in Saccharomyces cerevisiae
Understanding in vivo regulation of isoprenoid biosynthesis is important for identifying strategies to improve carbon fluxes to desirable endproducts.
Physiological formation of fluorescent and conductive
protein microfibers in live fibroblasts upon spontaneous uptake of biocompatible fluorophores
Living fibroblasts spontaneously incorporate a synthetic semiconducting fluorophore and physiologically generate fluorescent conductive microfibers, secreted intracellularly and subsequently extruded.
Design principles for generating robust gene expression patterns in dynamic engineered tissues
This work experimentally and computationally evaluates the conditions necessary to establish robust gene expression patterns in engineered tissues in vitro.
Experiment and mathematical modeling of gene expression dynamics in a cell-free system
The authors investigate the expression dynamics in a cell-free expression system and establish a minimalistic rate equation model to concurrently fit multiple data sets of GFP synthesis.
A statistical feature of Hurst exponents of essential genes in bacterial genomes
A normal distribution exists for the Hurst exponent of the essential genes in most of the analyzed bacterial genomes.
Real-time optogenetic control of intracellular protein concentration in microbial cell cultures
We have developed a culturing apparatus and feedback control scheme which, in combination with an optogenetic system, allows us to generate defined perturbations in the intracellular concentration of a specific protein in microbial cell culture.
Development of siRNA-probes for studying intracellular trafficking of siRNA
This study describes the development of probes for studying the intracellular disassembly kinetics and trafficking of siRNA nanocarriers in a cancer cell line from two different viewpoints; siRNA release and nanoparticle disassembly.
Quantitative assessment of Ras over-expression via shotgun deployment of vectors utilizing synthetic promoters
Cells were transduced with Ras transgenes expressed from various synthetic promoters. High resolution dose-response curves relating expression and phenotype were achieved through analysis of cell heterogeneity.
About this collection
This collection of articles includes articles published between 2012 and 2014 in Integrative Biology under the theme of Synthetic Biology.