A tractable physical model for the yeast polarity predicts epistasis and fitness.

Accurate phenotype prediction based on genetic information has numerous societal applications, such as crop design or cellular factories. Epistasis, when biological components interact, complicates modelling phenotypes from genotypes. Here we show an approach to mitigate this complication for polarity establishment in budding yeast, where mechanistic information is abundant. We coarse-grain molecular interactions into a so-called mesotype, which we combine with gene expression noise into a physical cell cycle model. First, we show with computer simulations that the mesotype allows validation of the most current biochemical polarity models by quantitatively matching doubling times. Second, the mesotype elucidates epistasis emergence as exemplified by evaluating the predicted mutational effect of key polarity protein Bem1p when combined with known interactors or under different growth conditions. This example also illustrates how unlikely evolutionary trajectories can become more accessible. The tractability of our biophysically justifiable approach inspires a road-map towards bottom-up modelling complementary to statistical inferences. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.

Deep demersal fish communities respond rapidly to warming in a frontal region between Arctic and Atlantic waters.

The assessment of climate impact on marine communities dwelling deeper than the well-studied shelf seas has been hampered by the lack of long-term data. For a long time, the prevailing expectation has been that thermal stability in deep ocean layers will delay ecosystem responses to warming. Few observational studies have challenged this view and indicated that deep organisms can respond exceptionally fast to physical change at the sea surface. To address the depth-specific impact of climate change, we investigated spatio-temporal changes in fish community structure along a bathymetry gradient of 150-1500 m between 1998 and 2016 in East Greenland. Here, the Arctic East Greenland Current and the Atlantic Irminger Current meet and mix, representing a sub-Arctic transition zone. We found the strongest signals of community reorganizations at depths between 350 and 1000 m and only weak responses in the shallowest and deepest regions. Changes were in synchrony with atmospheric warming, loss in sea ice and variability in physical sea surface conditions both within our study region and North of the Denmark Strait. These results suggest that interannual variability and long-term climate trends of the larger ecoregion can rapidly affect fish communities down to 1000-m depth through atmospheric ocean coupling and food web interactions.

The Path towards Predicting Evolution as Illustrated in Yeast Cell Polarity.

A bottom-up route towards predicting evolution relies on a deep understanding of the complex network that proteins form inside cells. In a rapidly expanding panorama of experimental possibilities, the most difficult question is how to conceptually approach the disentangling of such complex networks. These can exhibit varying degrees of hierarchy and modularity, which obfuscate certain protein functions that may prove pivotal for adaptation. Using the well-established polarity network in budding yeast as a case study, we first organize current literature to highlight protein entrenchments inside polarity. Following three examples, we see how alternating between experimental novelties and subsequent emerging design strategies can construct a layered understanding, potent enough to reveal evolutionary targets. We show that if you want to understand a cell's evolutionary capacity, such as possible future evolutionary paths, seemingly unimportant proteins need to be mapped and studied. Finally, we generalize this research structure to be applicable to other systems of interest.

PVDF Sensor Foils Employed to Measure Shear Stress and Temperature of Friction Welding.

Friction welding is a popular process for joining metal and polymer work pieces by rubbing them against each other. This way, friction heat is generated in a zone of the faying surfaces, thinner than 1 mm. After cooling down, the heated surfaces establish a tight and strong bond. To improve this joining process, a method is desirable allowing measuring generated temperature and shear stress in the zone between the joining work pieces. Unfortunately, this is a very difficult task because the welding zone cannot be accessed with a sensor without significantly altering the process and thereby the desired measurement results. This paper describes how shear stress and temperature change generated by rubbing polymer pieces in a friction welding machine have been measured between the faying surfaces by employing sensor foils from the piezoelectric and pyroelectric polymer polyvinylidene fluoride (PVDF). This way, heating and cooling rates, pressure rise of the pneumatic system, frequency rise of the starting machine, the duration of starting and stopping, the damping of the vibrations after the drive was stopped, and the stress generated by the pullback of the machine head have been measured. A careful characterization of the sensor was necessary to enable distinguishing the measured voltage due to straining, shearing and temperature change.

Rapid calcification propensity testing in blood using a temperature controlled microfluidic polymer chip.

Phosphate toxicity is a major threat to cardiovascular health in chronic kidney disease. It is associated with oxidative stress, inflammation and the accumulation of calcium phosphate commonly known as calcification in soft tissues leading to functional disorders of blood vessels. An improved calcification propensity test for the assessment of phosphate toxicity was developed, which measures the velocity of calcium phosphate mineralization from colloidal precursors in vitro. This so called T50 test measures the transformation from a primary into a secondary form of nanosized colloidal plasma protein-calcium phosphate particles known as calciprotein particles. The T50 test in its previous form required a temperature controlled nephelometer and several hours of continuous measurement, which precluded rapid bed side testing. We miniaturized the test using microfluidic polymer chips produced by ultrasonic hot embossing. A cartridge holder contained a laser diode for illumination, light dependent resistor for detection and a Peltier element for thermo control. Increasing the assay temperature from 37°C to 75°C reduced the T50 test time 36-fold from 381 ± 10 min at 37°C to 10.5 ± 0.3 min at 75°C. Incorporating sputtered micro mirrors into the chip design increased the effective light path length, and improved signal-to-noise ratio 9-fold. The speed and reproducibility of the T50 chip-based assay run at 75°C suggest that it may be suitable for rapid measurements, preferably in-line in a dialyser or in a portable microfluidic analytic device with the chip inserted as a disposable cartridge.

Five-Stage Approach for a Systematic Screening and Development of Etravirine Amorphous Solid Dispersions by Hot-Melt Extrusion.

The aim of this study was to develop a fast, effective, and material sparing screening method to design amorphous solid dispersions (ASDs) of etravirine to drive more effectively the development process, leading to improved bioavailability (BA) and stability. A systematic step-by-step approach was followed by combining theoretical calculations with high-throughput screening (HTS) and software-assisted multivariate statistical analysis. The thermodynamic miscibility and interaction of the drug in several polymers were predicted using Hansen solubility parameters (δ). The selected polymers were evaluated by HTS, using solvent evaporation. Binary compositions were evaluated by their solubilization capacity and physical stability over 2 months. JMP 14.0 was used for multivariate statistical analysis using principal components analysis. Extrusion was performed in Thermo Scientific HAAKE MiniLab II, and extrudates were characterized by assay, related substances, dissolution, and physical state (polarized light microscopy (PLM), Raman spectroscopy, and X-ray powder diffraction (XRPD)). A short stability study was performed where milled extrudates were exposed to 25 °C/60%RH and 40 °C/75%RH for 3 months. Through thermodynamic predictions, five main polymers were selected. The HTS enabled the evaluation of 42 formulations for solubilization capacity and physical stability. The three most promising compositions were selected for hot-melt extrusion (HME) tests. In general, a good correlation was found among the results of theoretical predictions, HTS, and HME. Poly(vinylpyrrolidone) (PVP)-based formulations were shown to be easily extrudable, with low degradation and complete amorphicity, whereas in Soluplus, the drug was not miscible, leading to a high crystalline content. The drug release rate was improved more than two times with PVP, and the manufactured ASD was demonstrated to be stable physically and chemically. A fast and effective screening technique to develop stable ASDs for a poorly soluble drug was successfully developed as applied to etravirine. The given method is easy to use, requires a low amount of drug, and is fairly accurate in predicting the amorphization of the drug when formulated. The success of HME formulation development of etravirine was undoubtedly enhanced with this high-throughput tool, which led to the identification of extrudates with improved biopharmaceutical properties. The structural characterization performed by PLM, XRPD, and Raman spectroscopy demonstrated that the HME prototype was essentially amorphous. The unexpected stability at 40 °C/75%RH was correlated with the presence of molecular interaction characterized by Raman spectroscopy.