Scalable and flexible inference framework for stochastic dynamic single-cell models.

Understanding the inherited nature of how biological processes dynamically change over time and exhibit intra- and inter-individual variability, due to the different responses to environmental stimuli and when interacting with other processes, has been a major focus of systems biology. The rise of single-cell fluorescent microscopy has enabled the study of those phenomena. The analysis of single-cell data with mechanistic models offers an invaluable tool to describe dynamic cellular processes and to rationalise cell-to-cell variability within the population. However, extracting mechanistic information from single-cell data has proven difficult. This requires statistical methods to infer unknown model parameters from dynamic, multi-individual data accounting for heterogeneity caused by both intrinsic (e.g. variations in chemical reactions) and extrinsic (e.g. variability in protein concentrations) noise. Although several inference methods exist, the availability of efficient, general and accessible methods that facilitate modelling of single-cell data, remains lacking. Here we present a scalable and flexible framework for Bayesian inference in state-space mixed-effects single-cell models with stochastic dynamic. Our approach infers model parameters when intrinsic noise is modelled by either exact or approximate stochastic simulators, and when extrinsic noise is modelled by either time-varying, or time-constant parameters that vary between cells. We demonstrate the relevance of our approach by studying how cell-to-cell variation in carbon source utilisation affects heterogeneity in the budding yeast Saccharomyces cerevisiae SNF1 nutrient sensing pathway. We identify hexokinase activity as a source of extrinsic noise and deduce that sugar availability dictates cell-to-cell variability.

The Effect of Lithium on the Budding Yeast Saccharomyces cerevisiae upon Stress Adaptation.

Lithium salts are used in the treatment of mood disorders, cancer, and Alzheimer's disease. It has been shown to prolong life span in several phyla; however, not yet in budding yeast. In our study, we investigate the influence of lithium on yeast cells' viability by characterizing protein aggregate formation, cell volume, and molecular crowding in the context of stress adaptation. While our data suggest a concentration-dependent growth inhibition caused by LiCl, we show an extended long-term survival rate as an effect of lithium addition upon glucose deprivation. We show that caloric restriction mitigates the negative impact of LiCl on cellular survival. Therefore, we suggest that lithium could affect glucose metabolism upon caloric restriction, which could explain the extended long-term survival observed in our study. We find furthermore that lithium chloride did not affect an immediate salt-induced Hsp104-dependent aggregate formation but cellular adaptation to H2O2 and acute glucose starvation. We presume that different salt types and concentrations interfere with effective Hsp104 recruitment or its ATP-dependent disaggregase activity as a response to salt stress. This work provides novel details of Li+ effect on live eukaryotic cells which may also be applicable in further research on the treatment of cancer, Alzheimer's, or other age-related diseases in humans.

Strong van der Waals Adhesion of a Polymer Film on Rough Substrates.

We propose that chemically inert polymeric films can enhance van der Waals (vdW) forces in the same way as nanofabrication of biomimetic adhesive materials. For the vdW adhesion of an ethylene-chlorotrifluoroethylene (ECTFE) film on rough metal and dielectric substrates, we present a model that combines microscopic quantum-chemistry simulations of the polymer response functions and the equilibrium monomer-substrate distance with a macroscopic quantum-electrodynamics calculation of the Casimir force between the polymer film and the substrate. We predict adhesive forces up to 2.22 kN/mm2, where the effect is reduced by substrate roughness and for dielectric surfaces.

Stretchable optoelectronic circuits embedded in a polymer network.

Stretchable optoelectronic circuits, incorporating chip-level LEDs and photodiodes in a silicone membrane, are demonstrated. Due to its highly miniaturized design and tissue-like mechanical properties, such an optical circuit can be conformally applied to the epidermis and be used for measurement of photoplethysmograms. This level of optical functionality in a stretchable substrate is potentially of great interest for personal health monitoring.

Optical properties of liquids for fluidic optics.

We present the dispersion characteristics of 18 liquids and one resin, which are widely used as media for liquid lenses in adaptive and tunable optics and for index matching in spectrochemical analysis. These are measured by using a refractometer operating at six different wavelengths. We provide a short description of the measurement setup and present a detailed uncertainty analysis of the measurement system to provide a measure of the reliability of the data. We conclude with a catalog of refractive indices and Sellmeier coefficients of the measured liquids and show the location of the analyzed materials in an Abbe diagram.

Array-based capture, distribution, counting and multiplexed assaying of beads on a centrifugal microfluidic platform.

We present a novel centrifugal microfluidic platform for the highly efficient manipulation and analysis of particles for applications in bead-based assays. The platform uses an array of geometrical V-cup barriers to trap particles using stopped-flow sedimentation under highly reproducible hydrodynamic conditions. The impact parameters governing the occupancy distribution and capture efficiency of the arrayed traps are investigated. The unique, nearly 100% capture efficiency paired with the capability to establish sharply peaked, single occupancy distributions enables a novel, digital readout mode for color-multiplexed, particle-based assays with low-complexity instrumentation. The presented technology marks an essential step towards a versatile platform for the integration of bead- and cell-based biological assays.

Microstructuring of polymer films for sensitive genotyping by real-time PCR on a centrifugal microfluidic platform.

We present a novel process flow enabling prototyping of microfluidic cartridges made out of polymer films. Its high performance is proven by implementation of a microfluidic genotyping assay testing 22 DNA samples including clinical isolates from patients infected by methicilin-resistant Staphylococcus aureus (MRSA). The microfluidic cartridges (disks) are fabricated by a novel process called microthermoforming by soft lithography (microTSL). Positive moulds are applied allowing for higher moulding precision and very easy demoulding when compared to conventional microthermoforming. High replication accuracies with geometric disk-to-disk variations of less than 1% are typical. We describe and characterise fabrication and application of microfluidic cartridges with wall thicknesses <188 microm thus enabling efficient thermocycling during real-time polymerase chain reaction (PCR). The microfluidic cartridges are designed for operation in a slightly modified commercial thermocycling instrument. This approach demonstrates new opportunities for both microfluidic developments and well-established laboratory instruments. The microfluidic protocol is controlled by centrifugal forces and divides the liquid sample parallely into independent aliquots of 9.8 microl (CV 3.4%, N = 32 wells). The genotyping assays are performed with pre-stored primers and probes for real-time PCR showing a limit of detection well below 10 copies of DNA per reaction well (N = 24 wells in 3 independent disks). The system was evaluated by 44 genotyping assays comprising 22 DNA samples plus duplicates in a total of 11 disks. The samples contained clinical samples of seven different genotypes of MRSA as well as positive and negative controls. The results are in excellent agreement with the reference in microtubes.