Cell-free gene expression dynamics in synthetic cell populations

The ability to build synthetic cellular populations from the bottom-up provides the groundwork to realize minimal living tissues comprising single cells which can communicate and bridge scales into multicellular systems. Engineered systems made of synthetic micron-sized compartments and integrated reaction networks coupled with mathematical modeling can facilitate the design and construction of complex and multiscale chemical systems from the bottom-up. Toward this goal, we generated populations of monodisperse liposomes encapsulating cell-free expression systems (CFESs) using double-emulsion microfluidics and quantified transcription and translation dynamics within individual synthetic cells of the population using a fluorescent Broccoli RNA aptamer and mCherry protein reporter. CFE dynamics in bulk reactions were used to test different coarse-grained resource-limited gene expression models using model selection to obtain transcription and translation rate parameters by likelihood-based parameter estimation. The selected model was then applied to quantify cell-free gene expression dynamics in populations of synthetic cells. In combination, our experimental and theoretical approaches provide a statistically robust analysis of CFE dynamics in bulk and monodisperse synthetic cell populations. We demonstrate that compartmentalization of CFESs leads to different transcription and translation rates compared to bulk CFE and show that this is due to the semipermeable lipid membrane that allows the exchange of materials between the synthetic cells and the external environment

Solar cell emitter design with PV-tailored implantation

A potentially cost-effective ion implanter for solar cells has become commercially available very recently. As the emitter dopant profiles differ from the standard diffusions, a combination of process simulation and device simulation is used to predict possible applications as front emitter. The simulations show that ion energies of 10 to 30 keV and doses in the range of 5×1014 to 7×1015 cm-2 are sufficient for reducing the phosphorus peak density and, hence, obtaining cell efficiency levels above 20%, if appropriate surface passivation and wafer materials are used. The simulations strongly indicate, however, that cell efficiency improves only marginally if the cell has a fully metallized rear Al-BSF and a boron-doped Cz base in the degraded state. Simulated cells with a local rear Al-BSF show an efficiency improvement of more than 0.3% absolute in the degraded state

Unsaturated fatty acids are inhibitors of bacterial conjugation

This report describes a high-throughput assay to identify substances that reduce the frequency of conjugation in Gram-negative bacteria. Bacterial conjugation is largely responsible for the spread of multiple antibiotic resistances in human pathogens. Conjugation inhibitors may provide a means to control the spread of antibiotic resistance. An automated conjugation assay was developed that used plasmid R388 and a laboratory strain of Escherichia coli as a model system, and bioluminescence as a reporter for conjugation activity. Frequencies of conjugation could be measured continuously in real time by the amount of light produced, and thus the effects of inhibitory compounds could be determined quantitatively. A control assay, run in parallel, allowed elimination of compounds affecting cell growth, plasmid stability or gene expression. The automated conjugation assay was used to screen a database of more than 12 000 microbial extracts known to contain a wide variety of bioactive compounds (the NatChem library). The initial hit rate was 1·4 %. From these, 48 extracts containing active compounds and representing a variety of organisms and extraction conditions were subjected to fractionation (24 fractions per extract). The 52 most active fractions were subjected to a secondary analysis to determine the range of plasmid inhibition. Plasmids R388, R1 and RP4 were used as representatives of a variety of plasmid transfer systems. Only one fraction (of complex composition) affected transfer of all three plasmids, while four other fractions were active against two of them. Two separate compounds were identified from these fractions: linoleic acid and dehydrocrepenynic acid. Downstream analysis showed that the chemical class of unsaturated fatty acids act as true inhibitors of conjugation

LETTER Communicated by Benjamin Schrauwen Regularized Variational Bayesian Learning of Echo State Networks with Delay&Sum Readout

In this work, a variational Bayesian framework for efficient training of echo state networks (ESNs) with automatic regularization and delay&sum (D&S) readout adaptation is proposed. The algorithm uses a classical batch learning of ESNs. By treating the network echo states as fixed basis functions parameterized with delay parameters, we propose a variational Bayesian ESN training scheme. The variational approach allows for a seamless combination of sparse Bayesian learning ideas and a variational Bayesian space-alternating generalized expectationmaximization (VB-SAGE) algorithm for estimating parameters of superimposed signals. While the former method realizes automatic regularization of ESNs, which also determines which echo states and input signals are relevant for "explaining" the desired signal, the latter method provides a basis for joint estimation of D&S readout parameters. The proposed training algorithm can naturally be extended to ESNs with fixed filter neurons. It also generalizes the recently proposed expectationmaximization-based D&S readout adaptation method. The proposed algorithm was tested on synthetic data prediction tasks as well as on dynamic handwritten character recognition. Neural Computation 24, 967-995 (2012

Evaluation of the thermal stability of TiW/Cu heterojunctions using a combined SXPS and HAXPES approach

Power semiconductor device architectures require the inclusion of a diffusion barrier to suppress or at best prevent the interdiffusion between the copper metallization interconnects and the surrounding silicon substructure. The binary pseudo-alloy of titanium–tungsten (TiW), with >70 at. % W, is a well-established copper diffusion barrier but is prone to degradation via the out-diffusion of titanium when exposed to high temperatures ([Formula: see text]400 [Formula: see text]C). Here, the thermal stability of physical vapor deposited TiW/Cu bilayer thin films in Si/SiO[Formula: see text](50 nm)/TiW(300 nm)/Cu(25 nm) stacks were characterized in response to annealing at 400 [Formula: see text]C for 0.5 h and 5 h, using a combination of soft and hard x-ray photoelectron spectroscopy and transmission electron microscopy. Results show that annealing promoted the segregation of titanium out of the TiW and interdiffusion into the copper metallization. Titanium was shown to be driven toward the free copper surface, accumulating there and forming a titanium oxide overlayer upon exposure to air. Annealing for longer timescales promoted a greater out-diffusion of titanium and a thicker oxide layer to grow on the copper surface. However, interface measurements suggest that the diffusion is not significant enough to compromise the barrier integrity, and the TiW/Cu interface remains stable even after 5 h of annealing

An activation domain of plasmid R1 TraI protein delineates stages of gene transfer initiation

Bacterial conjugation is a form of type IV secretion that transports protein and DNA to recipient cells. Specific bacteriophage exploit the conjugative pili and cell envelope spanning protein machinery of these systems to invade bacterial cells. Infection by phage R17 requires F-like pili and coupling protein TraD, which gates the cytoplasmic entrance of the secretion channel. Here we investigate the role of TraD in R17 nucleoprotein uptake and find parallels to secretion mechanisms. The relaxosome of IncFII plasmid R1 is required. A ternary complex of plasmid oriT, TraD and a novel activation domain within the N-terminal 992 residues of TraI contributes a key mechanism involving relaxase-associated properties of TraI, protein interaction and the TraD ATPase. Helicase-associated activities of TraI are dispensable. These findings distinguish for the first time specific protein domains and complexes that process extracellular signals into distinct activation stages in the type IV initiation pathway. The study also provided insights into the evolutionary interplay of phage and the plasmids they exploit. Related plasmid F adapted to R17 independently of TraI. It follows that selection for phage resistance drives not only variation in TraA pilins but diversifies TraD and its binding partners in a plasmid-specific manner

Transgenic Mice Expressing Lipoprotein Lipase in Adipose Tissue: ABSENCE OF THE PROXIMAL 3′-UNTRANSLATED REGION CAUSES TRANSLATIONAL UPREGULATION

Lipoprotein lipase (LPL) is a key enzyme in lipoprotein and adipocyte metabolism. Defects in LPL can lead to hypertriglyceridemia and the subsequent development of atherosclerosis. The mechanisms of regulation of this enzyme are complex and may occur at multiple levels of gene expression. Because the 3′-untranslated region (UTR) is involved in LPL translational regulation, transgenic mice were generated with adipose tissue expression of an LPL construct either with or without the proximal 3′-UTR and driven by the aP2 promoter. Both transgenic mouse colonies were viable and expressed the transgene, resulting in a 2-fold increase in LPL activity in white adipose tissue. Neither mouse colony exhibited any obvious phenotype in terms of body weight, plasma lipids, glucose, and non-esterified fatty acid levels. In the mice expressing hLPL with an intact 3′-UTR, hLPL mRNA expression approximately paralleled hLPL activity. However in the mice without the proximal 3′-UTR, hLPL mRNA was low in the setting of large amounts of hLPL protein and LPL activity. In previous studies, the 3′-UTR of LPL was critical for the inhibitory effects of constitutively expressed hormones, such as thyroid hormone and catecholamines. Therefore, these data suggest that the absence of the 3′-UTR results in a translationally unrepressed LPL, resulting in a moderate overexpression of adipose LPL activity