Functionality integration in stereolithography 3D printed microfluidics using a "print-pause-print" strategy.

Stereolithography 3D printing, although an increasingly used fabrication method for microfluidic chips, has the main disadvantage of producing monolithic chips in a single material. We propose to incorporate during printing various objects using a "print-pause-print" strategy. Here, we demonstrate that this novel approach can be used to incorporate glass slides, hydrosoluble films, paper pads, steel balls, elastic or nanoporous membranes and silicon-based microdevices, in order to add microfluidic functionalities as diverse as valves, fluidic diodes, shallow chambers, imaging windows for bacteria tracking, storage of reagents, blue energy harvesting or filters for cell capture and culture.

Modeling oxygen transport in the brain: An efficient coarse-grid approach to capture perivascular gradients in the parenchyma.

Recent progresses in intravital imaging have enabled highly-resolved measurements of periarteriolar oxygen gradients (POGs) within the brain parenchyma. POGs are increasingly used as proxies to estimate the local baseline oxygen consumption, which is a hallmark of cell activity. However, the oxygen profile around a given arteriole arises from an interplay between oxygen consumption and delivery, not only by this arteriole but also by distant capillaries. Integrating such interactions across scales while accounting for the complex architecture of the microvascular network remains a challenge from a modelling perspective. This limits our ability to interpret the experimental oxygen maps and constitutes a key bottleneck toward the inverse determination of metabolic rates of oxygen. We revisit the problem of parenchymal oxygen transport and metabolism and introduce a simple, conservative, accurate and scalable direct numerical method going beyond canonical Krogh-type models and their associated geometrical simplifications. We focus on a two-dimensional formulation, and introduce the concepts needed to combine an operator-splitting and a Green's function approach. Oxygen concentration is decomposed into a slowly-varying contribution, discretized by Finite Volumes over a coarse cartesian grid, and a rapidly-varying contribution, approximated analytically in grid-cells surrounding each vessel. Starting with simple test cases, we thoroughly analyze the resulting errors by comparison with highly-resolved simulations of the original transport problem, showing considerable improvement of the computational-cost/accuracy balance compared to previous work. We then demonstrate the model ability to flexibly generate synthetic data reproducing the spatial dynamics of oxygen in the brain parenchyma, with sub-grid resolution. Based on these synthetic data, we show that capillaries distant from the arteriole cannot be overlooked when interpreting POGs, thus reconciling recent measurements of POGs across cortical layers with the fundamental idea that variations of vascular density within the depth of the cortex may reveal underlying differences in neuronal organization and metabolic load.

A versatile micromodel technology to explore biofilm development in porous media flows.

Bacterial biofilms that grow in porous media are critical to ecosystem processes and applications ranging from soil bioremediation to bioreactors for treating wastewater or producing value-added products. However, understanding and engineering the complex phenomena that drive the development of biofilms in such systems remains a challenge. Here we present a novel micromodel technology to explore bacterial biofilm development in porous media flows. The technology consists of a set of modules that can be combined as required for any given experiment and conveniently tuned for specific requirements. The core module is a 3D-printed micromodel where biofilm is grown into a perfusable porous substrate. High-precision additive manufacturing, in particular stereolithography, is used to fabricate porous scaffolds with precisely controlled architectures integrating flow channels with diameters down to several hundreds of micrometers. The system is instrumented with: ultraviolet-C light-emitting diodes; on-line measurements of oxygen consumption and pressure drop across the porous medium; camera and spectrophotometric cells for the detection of biofilm detachment events at the outlet. We demonstrate how this technology can be used to study the development of Pseudomonas aeruginosa biofilm for several days within a network of flow channels. We find complex dynamics whereby oxygen consumption reaches a steady-state but not the pressure drop, which instead features a permanent regime with large fluctuations. We further use X-ray computed microtomography to image the spatial distribution of biofilms and computational fluid dynamics to link biofilm development with local flow properties. By combining the advantages of additive manufacturing for the creation of reproducible 3D porous microarchitectures with the flow control and instrumentation accuracy of microfluidics, our system provides a platform to study the dynamics of biofilm development in 3D porous media and to rapidly test new concepts in process engineering.

Ultraviolet control of bacterial biofilms in microfluidic chips.

Polydimethylsiloxane (PDMS) microfluidic systems have been instrumental in better understanding couplings between physical mechanisms and bacterial biofilm processes, such as hydrodynamic effects. However, precise control of the growth conditions, for example, the initial distribution of cells on the substrate or the boundary conditions in a flow system, has remained challenging. Furthermore, undesired bacterial colonization in crucial parts of the systems, in particular, in mixing zones or tubing, is an important factor that strongly limits the duration of the experiments and, therefore, impedes our ability to study the biophysics of biofilm evolving over long periods of time, as found in the environment, in engineering, or in medicine. Here, we develop a new approach that uses ultraviolet-C (UV-C) light-emitting diodes (LEDs) to confine bacterial development to specific zones of interest in the flow channels. The LEDs are integrated into a 3D printed light guide that is positioned upon the chip and used to irradiate germicidal UV-C directly through the PDMS. We first demonstrate that this system is successful in controlling undesired growth of Pseudomonas aeruginosa biofilm in inlet and outlet mixing zones during 48 h. We further illustrate how this can be used to define the initial distribution of bacteria to perturb already formed biofilms during an experiment and to control colonization for seven days-and possibly longer periods of time-therefore opening the way toward long-term biofilm experiments in microfluidic devices. Our approach is easily generalizable to existing devices at low cost and may, thus, become a standard in biofilm experiments in PDMS microfluidics.

A few upstream bifurcations drive the spatial distribution of red blood cells in model microfluidic networks.

The physics of blood flow in small vessel networks is dominated by the interactions between Red Blood Cells (RBCs), plasma and blood vessel walls. The resulting couplings between the microvessel network architecture and the heterogeneous distribution of RBCs at network-scale are still poorly understood. The main goal of this paper is to elucidate how a local effect, such as RBC partitioning at individual bifurcations, interacts with the global structure of the flow field to induce specific preferential locations of RBCs in model microfluidic networks. First, using experimental results, we demonstrate that persistent perturbations to the established hematocrit profile after diverging bifurcations may bias RBC partitioning at the next bifurcations. By performing a sensitivity analysis based upon network models of RBC flow, we show that these perturbations may propagate from bifurcation to bifurcation, leading to an outsized impact of a few crucial upstream bifurcations on the distribution of RBCs at network-scale. Based on measured hematocrit profiles, we further construct a modified RBC partitioning model that accounts for the incomplete relaxation of RBCs at these bifurcations. This model allows us to explain how the flow field results in a single pattern of RBC preferential location in some networks, while it leads to the emergence of two different patterns of RBC preferential location in others. Our findings have important implications in understanding and modeling blood flow in physiological and pathological conditions.

The evolution of tit-for-tat in bacteria via the type VI secretion system.

Tit-for-tat is a familiar principle from animal behavior: individuals respond in kind to being helped or harmed by others. Remarkably some bacteria appear to display tit-for-tat behavior, but how this evolved is not understood. Here we combine evolutionary game theory with agent-based modelling of bacterial tit-for-tat, whereby cells stab rivals with poisoned needles (the type VI secretion system) after being stabbed themselves. Our modelling shows tit-for-tat retaliation is a surprisingly poor evolutionary strategy, because tit-for-tat cells lack the first-strike advantage of preemptive attackers. However, if cells retaliate strongly and fire back multiple times, we find that reciprocation is highly effective. We test our predictions by competing Pseudomonas aeruginosa (a tit-for-tat species) with Vibrio cholerae (random-firing), revealing that P. aeruginosa does indeed fire multiple times per incoming attack. Our work suggests bacterial competition has led to a particular form of reciprocation, where the principle is that of strong retaliation, or 'tits-for-tat'.

Brain Capillary Networks Across Species: A few Simple Organizational Requirements Are Sufficient to Reproduce Both Structure and Function.

Despite the key role of the capillaries in neurovascular function, a thorough characterization of cerebral capillary network properties is currently lacking. Here, we define a range of metrics (geometrical, topological, flow, mass transfer, and robustness) for quantification of structural differences between brain areas, organs, species, or patient populations and, in parallel, digitally generate synthetic networks that replicate the key organizational features of anatomical networks (isotropy, connectedness, space-filling nature, convexity of tissue domains, characteristic size). To reach these objectives, we first construct a database of the defined metrics for healthy capillary networks obtained from imaging of mouse and human brains. Results show that anatomical networks are topologically equivalent between the two species and that geometrical metrics only differ in scaling. Based on these results, we then devise a method which employs constrained Voronoi diagrams to generate 3D model synthetic cerebral capillary networks that are locally randomized but homogeneous at the network-scale. With appropriate choice of scaling, these networks have equivalent properties to the anatomical data, demonstrated by comparison of the defined metrics. The ability to synthetically replicate cerebral capillary networks opens a broad range of applications, ranging from systematic computational studies of structure-function relationships in healthy capillary networks to detailed analysis of pathological structural degeneration, or even to the development of templates for fabrication of 3D biomimetic vascular networks embedded in tissue-engineered constructs.

Neutrophil adhesion in brain capillaries reduces cortical blood flow and impairs memory function in Alzheimer's disease mouse models.

Cerebral blood flow (CBF) reductions in Alzheimer's disease patients and related mouse models have been recognized for decades, but the underlying mechanisms and resulting consequences for Alzheimer's disease pathogenesis remain poorly understood. In APP/PS1 and 5xFAD mice we found that an increased number of cortical capillaries had stalled blood flow as compared to in wild-type animals, largely due to neutrophils that had adhered in capillary segments and blocked blood flow. Administration of antibodies against the neutrophil marker Ly6G reduced the number of stalled capillaries, leading to both an immediate increase in CBF and rapidly improved performance in spatial and working memory tasks. This study identified a previously uncharacterized cellular mechanism that explains the majority of the CBF reduction seen in two mouse models of Alzheimer's disease and demonstrated that improving CBF rapidly enhanced short-term memory function. Restoring cerebral perfusion by preventing neutrophil adhesion may provide a strategy for improving cognition in Alzheimer's disease patients.

Cooperation, competition and antibiotic resistance in bacterial colonies.

Bacteria commonly live in dense and genetically diverse communities associated with surfaces. In these communities, competition for resources and space is intense, and yet we understand little of how this affects the spread of antibiotic-resistant strains. Here, we study interactions between antibiotic-resistant and susceptible strains using in vitro competition experiments in the opportunistic pathogen Pseudomonas aeruginosa and in silico simulations. Selection for intracellular resistance to streptomycin is very strong in colonies, such that resistance is favoured at very low antibiotic doses. In contrast, selection for extracellular resistance to carbenicillin is weak in colonies, and high doses of antibiotic are required to select for resistance. Manipulating the density and spatial structure of colonies reveals that this difference is partly explained by the fact that the local degradation of carbenicillin by ß-lactamase-secreting cells protects neighbouring sensitive cells from carbenicillin. In addition, we discover a second unexpected effect: the inducible elongation of cells in response to carbenicillin allows sensitive cells to better compete for the rapidly growing colony edge. These combined effects mean that antibiotic treatment can select against antibiotic-resistant strains, raising the possibility of treatment regimes that suppress sensitive strains while limiting the rise of antibiotic resistance. We argue that the detailed study of bacterial interactions will be fundamental to understanding and overcoming antibiotic resistance.

Multiscale modelling of blood flow in cerebral microcirculation: Details at capillary scale control accuracy at the level of the cortex.

Aging or cerebral diseases may induce architectural modifications in human brain microvascular networks, such as capillary rarefaction. Such modifications limit blood and oxygen supply to the cortex, possibly resulting in energy failure and neuronal death. Modelling is key in understanding how these architectural modifications affect blood flow and mass transfers in such complex networks. However, the huge number of vessels in the human brain-tens of billions-prevents any modelling approach with an explicit architectural representation down to the scale of the capillaries. Here, we introduce a hybrid approach to model blood flow at larger scale in the brain microcirculation, based on its multiscale architecture. The capillary bed, which is a space-filling network, is treated as a porous medium and modelled using a homogenized continuum approach. The larger arteriolar and venular trees, which cannot be homogenized because of their fractal-like nature, are treated as a network of interconnected tubes with a detailed representation of their spatial organization. The main contribution of this work is to devise a proper coupling model at the interface between these two components. This model is based on analytical approximations of the pressure field that capture the strong pressure gradients building up in the capillaries connected to arterioles or venules. We evaluate the accuracy of this model for both very simple architectures with one arteriole and/or one venule and for more complex ones, with anatomically realistic tree-like vessels displaying a large number of coupling sites. We show that the hybrid model is very accurate in describing blood flow at large scales and further yields a significant computational gain by comparison with a classical network approach. It is therefore an important step towards large scale simulations of cerebral blood flow and lays the groundwork for introducing additional levels of complexity in the future.

Cell morphology drives spatial patterning in microbial communities.

The clearest phenotypic characteristic of microbial cells is their shape, but we do not understand how cell shape affects the dense communities, known as biofilms, where many microbes live. Here, we use individual-based modeling to systematically vary cell shape and study its impact in simulated communities. We compete cells with different cell morphologies under a range of conditions and ask how shape affects the patterning and evolutionary fitness of cells within a community. Our models predict that cell shape will strongly influence the fate of a cell lineage: we describe a mechanism through which coccal (round) cells rise to the upper surface of a community, leading to a strong spatial structuring that can be critical for fitness. We test our predictions experimentally using strains of Escherichia coli that grow at a similar rate but differ in cell shape due to single amino acid changes in the actin homolog MreB. As predicted by our model, cell types strongly sort by shape, with round cells at the top of the colony and rod cells dominating the basal surface and edges. Our work suggests that cell morphology has a strong impact within microbial communities and may offer new ways to engineer the structure of synthetic communities.

Chaste: an open source C++ library for computational physiology and biology.

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to 're-invent the wheel' with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.

Comment on "Frequency-dependent dispersion in porous media".

In a recent paper, Valdès-Parada and Alvarez-Ramirez [Phys. Rev. E 84, 031201 (2011)] used the technique of volume averaging to derive a "frequency-dependent" dispersion tensor, D(γ)(*), the goal of which is to describe solute transport in porous media undergoing periodic processes. We describe two issues related to this dispersion tensor. First, we demonstrate that the definition of D(γ)(*) is erroneous and derive a corrected version, D(γ)(*c). With this modification, the approach of Valdès-Parada and Alvarez-Ramirez becomes strictly equivalent to the one devised by Moyne [Adv. Water Res. 20, 63 (1997)]. Second, we show that the term "frequency-dependent dispersion" is misleading because D(γ)(*) and D(γ)(*c) do not depend on the process operating frequency, χ. The study carried out by Valdès-Parada and Alvarez-Ramirez represents a spectral analysis of the relaxation of D(γ)(*) towards its steady-state, independent of any periodic operation or excitation.