Immiscible Rayleigh-Taylor turbulence: Implications for bacterial degradation in oil spills.

An unstable density stratification between two fluids mixes spontaneously under the effect of gravity, a phenomenon known as Rayleigh-Taylor (RT) turbulence. If the two fluids are immiscible, for example, oil and water, surface tension prevents intermixing at the molecular level. However, turbulence fragments one fluid into the other, generating an emulsion in which the typical droplet size decreases over time as a result of the competition between the rising kinetic energy and the surface energy density. Even though the first phenomenological theory describing this emulsification process was derived many years ago, it has remained elusive to experimental verification, hampering our ability to predict the fate of oil in applications such as deep-water spills. Here, we provide the first experimental and numerical verification of the immiscible RT turbulence theory, unveiling a unique turbulent state that originates at the oil-water interface due to the interaction of multiple capillary waves. We show that a single, non-dimensional, and time-independent parameter controls the range of validity of the theory. Our findings have wide-ranging implications for the understanding of the mixing of immiscible fluids. This includes in particular oil spills, where our work enables the prediction of the oil-water interface dynamics that ultimately determine the rate of oil biodegradation by marine bacteria.

TMED2 binding restricts SMO to the ER and Golgi compartments.

Hedgehog (HH) signaling is important for embryonic pattering and stem cell differentiation. The G protein-coupled receptor (GPCR) Smoothened (SMO) is the key HH signal transducer modulating both transcription-dependent and transcription-independent responses. We show that SMO protects naive mouse embryonic stem cells (ESCs) from dissociation-induced cell death. We exploited this SMO dependency to perform a genetic screen in haploid ESCs where we identify the Golgi proteins TMED2 and TMED10 as factors for SMO regulation. Super-resolution microscopy shows that SMO is normally retained in the endoplasmic reticulum (ER) and Golgi compartments, and we demonstrate that TMED2 binds to SMO, preventing localization to the plasma membrane. Mutation of TMED2 allows SMO accumulation at the plasma membrane, recapitulating early events after HH stimulation. We demonstrate the physiologic relevance of this interaction in neural differentiation, where TMED2 functions to repress HH signal strength. Identification of TMED2 as a binder and upstream regulator of SMO opens the way for unraveling the events in the ER-Golgi leading to HH signaling activation.

Internal Biofilm Heterogeneities Enhance Solute Mixing and Chemical Reactions in Porous Media.

Bacterial biofilms can form in porous media that are of interest in industrial applications ranging from medical implants to biofilters as well as in environmental applications such as in situ groundwater remediation, where they can be critical locations for biogeochemical reactions. The presence of biofilms modifies porous media topology and hydrodynamics by clogging pores and consequently solutes transport and reactions kinetics. The interplay between highly heterogeneous flow fields found in porous media and microbial behavior, including biofilm growth, results in a spatially heterogeneous biofilm distribution in the porous media as well as internal heterogeneity across the thickness of the biofilm. Our study leverages highly resolved three-dimensional X-ray computed microtomography images of bacterial biofilms in a tubular reactor to numerically compute pore-scale fluid flow and solute transport by considering multiple equivalent stochastically generated internal permeability fields for the biofilm. We show that the internal heterogeneous permeability mainly impacts intermediate velocities when compared with homogeneous biofilm permeability. While the equivalent internal permeability fields of the biofilm do not impact fluid-fluid mixing, they significantly control a fast reaction. For biologically driven reactions such as nutrient or contaminant uptake by the biofilm, its internal permeability field controls the efficiency of the process. This study highlights the importance of considering the internal heterogeneity of biofilms to better predict reactivity in industrial and environmental bioclogged porous systems.

SOX17 in cellular reprogramming and cancer.

SOX17 is a transcription factor directing the specification and development of the primitive endoderm, primitive germ cells, definitive endoderm and, subsequently, is involved in the cardiovascular system and several endoderm-derived organs. The analysis of cancer genome sequencing data classified SOX17 as mutated cancer driver gene in endometrial cancer. These studies identified hotspot missense mutations within its DNA binding and transactivation domains. In somatic cell reprogramming, structure-based protein re-engineering showed a single missense mutation in SOX17 can change the DNA dependent heterodimer formation with OCT4 and enables the replacement of SOX2 with SOX17 mutants to induce pluripotency. This reveals the profound impact of specific missense mutations on gene function and regulatory activity. Here, we review the roles of SOX17 in cancer and discuss its cross-talk with the WNT/ß-catenin pathway, potentially reconciling its activity as re-engineered reprogramming factor and mutated cancer driver gene.

Toward an accurate estimation of wall shear stress from 4D flow magnetic resonance downstream of a severe stenosis.

PURPOSE: First, to investigate the agreement between velocity, velocity gradient, and Reynolds stress obtained from four-dimensional flow magnetic resonance (4D flow MRI) measurements and direct numerical simulation (DNS). Second, to propose and optimize based on DNS, 2 alternative methods for the accurate estimation of wall shear stress (WSS) when the resolution of the flow measurements is limited. Thirdly, to validate the 2 methods based on 4D flow MRI data. METHODS: In vitro 4D MRI has been conducted in a realistic rigid stenosed aorta model under a constant flow rate of 12 L/min. A DNS of transitional stenotic flow has been performed using the same geometry and boundary conditions. RESULTS: Time-averaged velocity and Reynolds stresses are in good agreement between in vitro 4D MRI data and DNS (errors between 2% and 8% of the reference downsampled data). WSS estimation based on the 2 proposed methods applied to MRI data provide good agreement with DNS for slice-averaged values (maximum error is less than 15% of the mean reference WSS for the first method and 25% for the second method). The performance of both models is not strongly sensitive to spatial resolution up to 1.5 mm voxel size. While the performance of model 1 deteriorates appreciably at low signal-to-noise ratios, model 2 remains robust. CONCLUSIONS: The 2 methods for WSS magnitude give an overall better agreement than the standard approach used in the literature based on direct calculation of the velocity gradient close to the wall (relative error of 84%).

Zooplankton can actively adjust their motility to turbulent flow.

Calanoid copepods are among the most abundant metazoans in the ocean and constitute a vital trophic link within marine food webs. They possess relatively narrow swimming capabilities, yet are capable of significant self-locomotion under strong hydrodynamic conditions. Here we provide evidence for an active adaptation that allows these small organisms to adjust their motility in response to background flow. We track simultaneously and in three dimensions the motion of flow tracers and planktonic copepods swimming freely at several intensities of quasi-homogeneous, isotropic turbulence. We show that copepods synchronize the frequency of their relocation jumps with the frequency of small-scale turbulence by performing frequent relocation jumps of low amplitude that seem unrelated to localized hydrodynamic signals. We develop a model of plankton motion in turbulence that shows excellent quantitative agreement with our measurements when turbulence is significant. We find that, compared with passive tracers, active motion enhances the diffusion of organisms at low turbulence intensity whereas it dampens diffusion at higher turbulence levels. The existence of frequent jumps in a motion that is otherwise dominated by turbulent transport allows for the possibility of active locomotion and hence to transition from being passively advected to being capable of controlling diffusion. This behavioral response provides zooplankton with the capability to retain the benefits of self-locomotion despite turbulence advection and may help these organisms to actively control their distribution in dynamic environments. Our study reveals an active adaptation that carries strong fitness advantages and provides a realistic model of plankton motion in turbulence.

Performance analysis of the transcatheter aortic valve implantation on blood flow hemodynamics: An optical imaging-based in vitro study.

Cardiac implants may have a strong influence on the hemodynamics of the circulatory system. In this study, we aimed at investigating the impact of transcatheter aortic valve implantation (TAVI) devices on blood flow patterns that develop in the ascending aorta under physiological flow conditions in vitro. For this purpose, a noninvasive optical measurement tool, three-dimensional particle tracking velocimetry (3D-PTV), was used in a realistic compliant silicone aortic model. The performance and the influence of two TAVIs and one surgical valve on the aortic flow were investigated. Our results showed that valve design and materials may have a distinct influence on relevant hemodynamic properties, namely kinetic energy, production of turbulence, and shear stresses in the ascending aorta. All properties varied considerably between the different valve models. We found that the total aortic regurgitation composed of the closing volume, transvalvular and paravalvular leakages varied for the three valves investigated. Furthermore, peak mean kinetic energy (MKE) ranged from 61 to 116 J/m3 , whereas peak turbulent kinetic energy (TKE) ranged from 23 to 36 J/m3 . The analysis of shear showed that all the three studied devices had minimal overall risk for thrombus formation. We conclude that the characteristics and material designs of TAVI devices have strong influences on the hemodynamics in the ascending aorta.

A Novel Approach for 3D-Structural Identification through Video Recording: Magnified Tracking.

Advancements in optical imaging devices and computer vision algorithms allow the exploration of novel diagnostic techniques for use within engineering systems. A recent field of application lies in the adoption of such devices for non-contact vibrational response recordings of structures, allowing high spatial density measurements without the burden of heavy cabling associated with conventional technologies. This, however, is not a straightforward task due to the typically low-amplitude displacement response of structures under ambient operational conditions. A novel framework, namely Magnified Tracking (MT), is proposed herein to overcome this limitation through the synergistic use of two computer vision techniques. The recently proposed phase-based motion magnification (PBMM) framework, for amplifying motion in a video within a defined frequency band, is coupled with motion tracking by means of particle tracking velocimetry (PTV). An experimental campaign was conducted to validate a proof-of-concept, where the dynamic response of a shear frame was measured both by conventional sensors as well as a video camera setup, and cross-compared to prove the feasibility of the proposed non-contact approach. The methodology was explored both in 2D and 3D configurations, with PTV revealing a powerful tool for the measurement of perceptible motion. When MT is utilized for tracking "imperceptible" structural responses (i.e., below PTV sensitivity), via the use of PBMM around the resonant frequencies of the structure, the amplified motion reveals the operational deflection shapes, which are otherwise intractable. The modal results extracted from the magnified videos, using PTV, demonstrate MT to be a viable non-contact alternative for 3D modal identification with the benefit of a spatially dense measurement grid.

On the accuracy of viscous and turbulent loss quantification in stenotic aortic flow using phase-contrast MRI.

PURPOSE: To investigate the limits of phase contrast MRI (PC-MRI)-based measurements of viscous losses and turbulent kinetic energy (TKE) pertaining to spatial resolution, signal-to-noise ratio (SNR), and non-Gaussian intravoxel velocity distributions. THEORY AND METHODS: High-resolution particle tracking velocimetry data obtained in a realistic aortic phantom with stenotic flow were used to simulate PC-MRI measurements at different resolutions and noise levels. Laminar viscous losses were computed using the spatial gradients of the mean velocity vector field, and TKE levels were derived based on the intravoxel phase dispersion of flow-sensitized PC-MRI measurements. RESULTS: Increasing the voxel size from 0.625 to 2.5 mm resulted in an underestimation of viscous losses of up to 83%, whereas total TKE values showed errors of <15% and reduced sensitivity to voxel size. Relative errors in viscous loss quantification were found to be less dependent on noise levels when compared with TKE values. In general, a SNR of 20-30 is required for both methods. CONCLUSION: At spatial resolutions feasible in clinical three-dimensional PC-MRI measurements, viscous losses of stenotic flows are significantly underestimated, whereas TKE shows smaller errors and reduced sensitivity to spatial resolution. Magn Reson Med 76:191-196, 2016. © 2015 Wiley Periodicals, Inc.

Breakup of Finite-Size Colloidal Aggregates in Turbulent Flow Investigated by Three-Dimensional (3D) Particle Tracking Velocimetry.

Aggregates grown in mild shear flow are released, one at a time, into homogeneous isotropic turbulence, where their motion and intermittent breakup is recorded by three-dimensional particle tracking velocimetry (3D-PTV). The aggregates have an open structure with a fractal dimension of ∼2.2, and their size is 1.4 ± 0.4 mm, which is large, compared to the Kolmogorov length scale (η = 0.15 mm). 3D-PTV of flow tracers allows for the simultaneous measurement of aggregate trajectories and the full velocity gradient tensor along their pathlines, which enables us to access the Lagrangian stress history of individual breakup events. From this data, we found no consistent pattern that relates breakup to the local flow properties at the point of breakup. Also, the correlation between the aggregate size and both shear stress and normal stress at the location of breakage is found to be weaker, when compared with the correlation between size and drag stress. The analysis suggests that the aggregates are mostly broken due to the accumulation of the drag stress over a time lag on the order of the Kolmogorov time scale. This finding is explained by the fact that the aggregates are large, which gives their motion inertia and increases the time for stress propagation inside the aggregate. Furthermore, it is found that the scaling of the largest fragment and the accumulated stress at breakup follows an earlier established power law, i.e., dfrag ∼ σ(-0.6) obtained from laminar nozzle experiments. This indicates that, despite the large size and the different type of hydrodynamic stress, the microscopic mechanism causing breakup is consistent over a wide range of aggregate size and stress magnitude.

Elasto-inertial turbulence.

Turbulence is ubiquitous in nature, yet even for the case of ordinary Newtonian fluids like water, our understanding of this phenomenon is limited. Many liquids of practical importance are more complicated (e.g., blood, polymer melts, paints), however; they exhibit elastic as well as viscous characteristics, and the relation between stress and strain is nonlinear. We demonstrate here for a model system of such complex fluids that at high shear rates, turbulence is not simply modified as previously believed but is suppressed and replaced by a different type of disordered motion, elasto-inertial turbulence. Elasto-inertial turbulence is found to occur at much lower Reynolds numbers than Newtonian turbulence, and the dynamical properties differ significantly. The friction scaling observed coincides with the so-called "maximum drag reduction" asymptote, which is exhibited by a wide range of viscoelastic fluids.

Characterization of intermittency in zooplankton behaviour in turbulence.

We consider Lagrangian velocity differences of zooplankters swimming in still water and in turbulence. Using cumulants, we quantify the intermittency properties of their motion recorded using three-dimensional particle tracking velocimetry. Copepods swimming in still water display an intermittent behaviour characterized by a high probability of small velocity increments, and by stretched exponential tails. Low values arise from their steady cruising behaviour while heavy tails result from frequent relocation jumps. In turbulence, we show that at short time scales, the intermittency signature of active copepods clearly differs from that of the underlying flow, and reflects the frequent relocation jumps displayed by these small animals. Despite these differences, we show that copepods swimming in still and turbulent flow belong to the same intermittency class that can be modelled by a log-stable model with non-analytical cumulant generating function. Intermittency in swimming behaviour and relocation jumps may enable copepods to display oriented, collective motion under strong hydrodynamic conditions and thus, may contribute to the formation of zooplankton patches in energetic environments.

Mapping mean and fluctuating velocities by Bayesian multipoint MR velocity encoding-validation against 3D particle tracking velocimetry.

PURPOSE: To validate Bayesian multipoint MR velocity encoding against particle tracking velocimetry for measuring velocity vector fields and fluctuating velocities in a realistic aortic model. METHODS: An elastic cast of a human aortic arch equipped with an 80 or 64% stenotic section was driven by a pulsatile pump. Peak velocities and peak turbulent kinetic energies of more than 3 m/s and 1000 J/m(3) could be generated. Velocity vector fields and fluctuating velocities were assessed using Bayesian multipoint MR velocity encoding with varying numbers of velocity encoding points and particle tracking velocimetry in the ascending aorta. RESULTS: Velocities and turbulent kinetic energies measured with 5-fold k-t undersampled 10-point MR velocity encoding and particle tracking velocimetry were found to reveal good correlation with mean differences of -4.8 ± 13.3 cm/s and r(2) = 0.98 for velocities and -21.8 ± 53.9 J/m(3) and r(2) = 0.98 for turbulent kinetic energies, respectively. Three-dimensional velocity patterns of fast flow downstream of the stenoses and regions of elevated velocity fluctuations were found to agree well. CONCLUSION: Accelerated Bayesian multipoint MR velocity encoding has been demonstrated to be accurate for assessing mean and fluctuating velocities against the reference standard particle tracking velocimetry. The MR method holds considerable potential to map velocity vector fields and turbulent kinetic energies in clinically feasible exam times of <15 min.

Experimental characterization of breakage rate of colloidal aggregates in axisymmetric extensional flow.

Aggregates prepared under fully destabilized conditions by the action of Brownian motion were exposed to an extensional flow generated at the entrance of a sudden contraction. Two noninvasive techniques were used to monitor their breakup process [i.e. light scattering and three-dimensional (3D) particle tracking velocimetry (3D-PTV)]. While the first one can be used to measure the size and the morphology of formed fragments after the breakage event, the latter is capable of resolving trajectories of individual aggregates up to the breakage point as well as the trajectories of formed fragments. Furthermore, measured velocity gradients were used to determine the local hydrodynamic conditions at the breakage point. All this information was combined to experimentally determine for the first time the breakage rate of individual aggregates, given in the form of a size reduction rate K(R), as a function of the applied strain rate, as well as the properties of the formed fragments (i.e., the number of formed fragments and the size ratio between the largest fragment and the original aggregate). It was found that K(R) scales with the applied strain rate according to a power law with the slope being dependent on the initial fractal dimension only, while the obtained data indicates a linear dependency of K(R) with the initial aggregate size. Furthermore, the probability distribution function (PDF) of the number of formed fragments and the PDF of the size ratio between the largest fragment and the original aggregate indicate that breakage will result with high probability (75%) in the formation of two to three fragments with a rather asymmetric ratio of sizes of about 0.8. The obtained results are well in agreement with the results from the numerical simulations published in the literature.

Applying Spinal Cord Organoids as a quantitative approach to study the mammalian Hedgehog pathway.

The Hedgehog (HH) pathway is crucial for embryonic development, and adult homeostasis. Its dysregulation is implicated in multiple diseases. Existing cellular models used to study HH signal regulation in mammals do not fully recapitulate the complexity of the pathway. Here we show that Spinal Cord Organoids (SCOs) can be applied to quantitively study the activity of the HH pathway. During SCO formation, the specification of different categories of neural progenitors (NPC) depends on the intensity of the HH signal, mirroring the process that occurs during neural tube development. By assessing the number of NPCs within these distinct subgroups, we are able to categorize and quantify the activation level of the HH pathway. We validate this system by measuring the effects of mutating the HH receptor PTCH1 and the impact of HH agonists and antagonists on NPC specification. SCOs represent an accessible and reliable in-vitro tool to quantify HH signaling and investigate the contribution of genetic and chemical cues in the HH pathway regulation.

Impact of heteroaggregation between microplastics and algae on particle vertical transport.

Understanding the impacts of microplastics (MPs) on aqueous environments requires understanding their transport dynamics and how their presence affects other natural processes and cycles. In this context, one aspect to consider is how MPs interact with freshwater snow (FWS), a mixture of algae and natural particles. FWS is one of the primary drivers of the flux of organic matter from the water surface to the bottom sediment, where zooplankton, diurnal migration, fish faecal pellets settling and turbulent mixing can also play prominent roles. Understanding how MPs and FWS heteroaggregation affects their respective settling velocities is important to assess not only MPs fate and transport but also their ecological impacts by altering FWS deposition and thereby nutrient cycling. In this present study, we obtained a mechanistic understanding of the processes controlling MPs settling dynamics and heteroaggregation with FWS and the subsequent impacts on the settling rates of both MPs and ballasted FWS. Here we used a plexiglass column equipped with a stereoscopic camera system to track the settling velocities of (1) MPs of various compositions, densities and morphologies, (2) FWS flocs and (3) MP-FWS agglomerates. For each experimental set, thousands of particles were tracked over a series of image sequences. We found that agglomerates with high-density MPs settled at least twofold faster than FWS alone, implying a much smaller residence time in the water column, except for cases with MP fibres or low-density plastics. These findings will help to refine MP fate models and, while contingent on MPs number, may impact biogeochemical cycles by changing the flux of nutrients contained in FWS to the sediment.

In vitro investigation of the blood flow downstream of a 3D-printed aortic valve.

The hemodynamics in the aorta as well as the durability of aortic valve prostheses vary greatly between different types of devices. Although placement and sizing of surgical aortic valve prostheses are excellent, the valve geometry of common devices cannot be customized to fit the patient's anatomy perfectly. Similarly, transcatheter aortic valve implantation (TAVI) devices are not customizable and may be orientated unfavorably during implantation. Imperfect fit of an aortic valve prosthesis may result in suboptimal performance and in some cases the need for additional surgery. Leveraging the advent of precision, multi-material 3D-printing, a bioinspired silicone aortic valve was developed. The manufacturing technique makes it fully customizable and significantly cheaper to develop and produce than common prostheses. In this study, we assess the hemodynamic performance of such a 3D-printed aortic valve and compare it to two TAVI devices as well as to a severely stenosed valve. We investigate the blood flow distal to the valve in an anatomically accurate, compliant aorta model via three-dimensional particle tracking velocimetry measurements. Our results demonstrate that the 3D-printed aortic valve induces flow patterns and topology compatible with the TAVI valves and showing similarity to healthy aortic blood flow. Compared to the stenosis, the 3D-printed aortic valve reduces turbulent kinetic energy levels and irreversible energy losses by over 75%, reaching values compatible with healthy subjects and conventional TAVIs. Our study substantiates that the 3D-printed heart valve displays a hemodynamic performance similar to established devices and underscores its potential for driving innovation towards patient specific valve prostheses.

Universal alignment in turbulent pair dispersion.

Countless processes in nature and industry, from rain droplet nucleation to plankton interaction in the ocean, are intimately related to turbulent fluctuations of local concentrations of advected matter. These fluctuations can be described by considering the change of the separation between particle pairs, known as pair dispersion, which is believed to obey a cubic in time growth according to Richardson's theory. Our work reveals a universal, scale-invariant alignment between the relative velocity and position vectors of dispersing particles at a mean angle that we show to be a universal constant of turbulence. We connect the value of this mean angle to Richardson's traditional theory and find agreement with data from a numerical simulation and a laboratory experiment. While the Richardson's cubic regime has been observed for small initial particle separations only, the constancy of the mean angle manifests throughout the entire inertial range of turbulence. Thus, our work reveals the universal nature of turbulent pair dispersion through a geometrical paradigm whose validity goes beyond the classical theory, and provides a framework for understanding and modeling transport and mixing processes.

Global warming accelerates soil heterotrophic respiration.

Carbon efflux from soils is the largest terrestrial carbon source to the atmosphere, yet it is still one of the most uncertain fluxes in the Earth's carbon budget. A dominant component of this flux is heterotrophic respiration, influenced by several environmental factors, most notably soil temperature and moisture. Here, we develop a mechanistic model from micro to global scale to explore how changes in soil water content and temperature affect soil heterotrophic respiration. Simulations, laboratory measurements, and field observations validate the new approach. Estimates from the model show that heterotrophic respiration has been increasing since the 1980s at a rate of about 2% per decade globally. Using future projections of surface temperature and soil moisture, the model predicts a global increase of about 40% in heterotrophic respiration by the end of the century under the worst-case emission scenario, where the Arctic region is expected to experience a more than two-fold increase, driven primarily by declining soil moisture rather than temperature increase.

An engineered Sox17 induces somatic to neural stem cell fate transitions independently from pluripotency reprogramming.

Advanced strategies to interconvert cell types provide promising avenues to model cellular pathologies and to develop therapies for neurological disorders. Yet, methods to directly transdifferentiate somatic cells into multipotent induced neural stem cells (iNSCs) are slow and inefficient, and it is unclear whether cells pass through a pluripotent state with full epigenetic reset. We report iNSC reprogramming from embryonic and aged mouse fibroblasts as well as from human blood using an engineered Sox17 (eSox17FNV). eSox17FNV efficiently drives iNSC reprogramming while Sox2 or Sox17 fail. eSox17FNV acquires the capacity to bind different protein partners on regulatory DNA to scan the genome more efficiently and has a more potent transactivation domain than Sox2. Lineage tracing and time-resolved transcriptomics show that emerging iNSCs do not transit through a pluripotent state. Our work distinguishes lineage from pluripotency reprogramming with the potential to generate more authentic cell models for aging-associated neurodegenerative diseases.