Roberto Rusconi | Humanitas University ; Humanitas Clinical and Research Center (original) (raw)

Papers by Roberto Rusconi

Scientific Reports, 2017

The development of strategies to reduce the load of unwanted bacteria is a fundamental challenge ... more The development of strategies to reduce the load of unwanted bacteria is a fundamental challenge in industrial processing, environmental sciences and medical applications. Here, we report a new method to sequester motile bacteria from a liquid, based on passive, deployable micro-traps that confine bacteria using micro-funnels that open into trapping chambers. Even in low concentrations, micro-traps afford a 70% reduction in the amount of bacteria in a liquid sample, with a potential to reach >90% as shown by modelling improved geometries. This work introduces a new approach to contain the growth of bacteria without chemical means, an advantage of particular importance given the alarming growth of pan-drug-resistant bacteria.

Quorum sensing (QS) is a population-density dependent chemical process that enables bacteria to c... more Quorum sensing (QS) is a population-density dependent chemical process that enables bacteria to communicate based on the production, secretion and sensing of small inducer molecules. While recombinant constructs have been widely used to decipher the molecular details of QS, how those findings translate to natural QS systems has remained an open question. Here, we compare the activation of natural and synthetic Pseudomonas aeruginosa LasI/R QS systems in bacteria exposed to quiescent conditions and controlled flows. Quantification of QS-dependent GFP expression in suspended cultures and in surface-attached microcolonies revealed that QS onset in both systems was similar under quiescent conditions but markedly differed under flow. Moderate flow (Pe > 25) was sufficient to suppress LasI/R QS recombinantly expressed in Escherichia coli, whereas only high flow (Pe > 102) suppressed QS in wild-type P. aeruginosa. We suggest that this difference stems from the differential production of extracellular matrix and that the matrix confers resilience against moderate flow to QS in wild-type organisms. These results suggest that the expression of a biofilm matrix extends the environmental conditions under which QS-based cell-cell communication is effective and that findings from synthetic QS circuits cannot be directly translated to natural systems.

We show that thermophoresis, i.e., mass flow driven by thermal gradients, can be used to drive pa... more We show that thermophoresis, i.e., mass flow driven by thermal gradients, can be used to drive particle motion in microfluidic devices exploiting suitable temperature control strategies. Due to its high sensitivity to particle/solvent interfacial properties, this method presents several advantages in terms of selectivity compared to standard particle manipulation techniques. Moreover, we show that selective driving of particles to the cold or to the hot side can be achieved by adding specific electrolytes and exploiting the additional thermoelectric effect stemming from their differential thermal responsiveness.

Aerotaxis, the directed migration along oxygen gradients, allows many microorganisms to locate fa... more Aerotaxis, the directed migration along oxygen gradients, allows many microorganisms to locate favorable oxygen concentrations. Despite oxygen's fundamental role for life, even key aspects of aerotaxis remain poorly understood. In Bacillus subtilis, for example, there is conflicting evidence of whether migration occurs to the maximal oxygen concentration available or to an optimal intermediate one, and how aerotaxis can be maintained over a broad range of conditions. Using precisely controlled oxygen gradients in a microfluidic device, spanning the full spectrum of conditions from quasi-anoxic to oxic (60 n mol/l-1 m mol/l), we resolved B. subtilis' 'oxygen preference conundrum' by demonstrating consistent migration towards maximum oxygen concentrations ('monotonic aerotaxis'). Surprisingly, the strength of aerotaxis was largely unchanged over three decades in oxygen concentration (131 n mol/l-196 μ mol/l). We discovered that in this range B. subtilis responds to the logarithm of the oxygen concentration gradient, a rescaling strategy called 'log-sensing' that affords organisms high sensitivity over a wide range of conditions. In these experiments, high-throughput single-cell imaging yielded the best signal-to-noise ratio of any microbial taxis study to date, enabling the robust identification of the first mathematical model for aerotaxis among a broad class of alternative models. The model passed the stringent test of predicting the transient aerotactic response despite being developed on steadystate data, and quantitatively captures both monotonic aerotaxis and log-sensing. Taken together, these results shed new light on the oxygen-seeking capabilities of B. subtilis and provide a blueprint for the quantitative investigation of the many other forms of microbial taxis.

We exploit the recent developments of microfluidic technologies to investigate the collective she... more We exploit the recent developments of microfluidic technologies to investigate the collective shearinduced diffusion in suspensions of micron-sized particles. Whereas spherical particles do not diffuse on the time scale of our experiments, the results with platelike clay particles show a strong cross-stream shear-induced diffusivity at low volume fraction ( 0 0:01). Moreover, we find a linear dependence of the collective diffusion coefficient with the average shear rate (in the range 10 2 -10 4 s À1 ) and the particle concentration. These data are in good agreement with previous experimental and theoretical results for spheres when rescaled with the particle number density.

Transient hot-wire data on thermal conductivity of suspensions of silica and perfluorinated parti... more Transient hot-wire data on thermal conductivity of suspensions of silica and perfluorinated particles show agreement with the mean-field theory of Maxwell but not with the recently postulated microconvection mechanism. The influence of interfacial thermal resistance, convective effects at microscales, and the possibility of thermal conductivity enhancements beyond the Maxwell limit are discussed.

A large variety of engaging phenomena, ranging from crystallization in protein solutions to the f... more A large variety of engaging phenomena, ranging from crystallization in protein solutions to the formation of colloidal gels and glasses via depletion forces, stems from the occurrence of very shortranged attractive forces. From depolarized light scattering measurements of equilibrium sedimentation profiles, we obtain an accurate description of the equation of state and of the phase diagram of colloids where depletion forces are tuned by the addition of a surfactant. For weak depletion, a colloidal fluid fully described by Baxter's ''sticky'' hard sphere model coexists with ultradense colloidal crystals. For stronger attractive interactions, kinetically arrested looser gels form, showing an elastic modulus that scales as a power law of the local particle concentration.

Bacteria within biofilms secrete and surround themselves with an extracellular matrix, which serv... more Bacteria within biofilms secrete and surround themselves with an extracellular matrix, which serves as a first line of defense against antibiotic attack. Polysaccharides constitute major elements of the biofilm matrix and are implied in surface adhesion and biofilm organization, but their contributions to the resistance properties of biofilms remain largely elusive. Using a combination of static and continuous-flow biofilm experiments we show that Psl, one major polysaccharide in the Pseudomonas aeruginosa biofilm matrix, provides a generic first line of defense toward antibiotics with diverse biochemical properties during the initial stages of biofilm development. Furthermore, we show with mixed-strain experiments that antibiotic-sensitive ''non-producing'' cells lacking Psl can gain tolerance by integrating into Psl-containing biofilms. However, non-producers dilute the protective capacity of the matrix and hence, excessive incorporation can result in the collapse of resistance of the entire community. Our data also reveal that Psl mediated protection is extendible to E. coli and S. aureus in co-culture biofilms. Together, our study shows that Psl represents a critical first bottleneck to the antibiotic attack of a biofilm community early in biofilm development.

The deformation of a flexible filament held fixed at one end in a nonuniform viscous flow with cu... more The deformation of a flexible filament held fixed at one end in a nonuniform viscous flow with curved streamlines is considered, with a focus on the filament dynamics and steady-state shape. Our motivation arises from recent microfluidic experiments on biofilm formation in a channel with bends, where thread-like structures, or streamers, were observed, attached to the side walls downstream of each corner and connecting consecutive corners while floating in the middle plane of the channel [Rusconi et al., J. R. Soc. Interface 7, 1293 (2010)]. We discuss the time evolution and final shape of the filament in different corner geometries as a function of a non-dimensional elasticity parameter that compares viscous and elastic effects. Since the filament develops tension, when the flow has curved streamlines the filament does not align with the flow, as occurs in a rectilinear flow, but rather it crosses the streamlines.

Bacteria are the smallest and most abundant form of life. They have traditionally been considered... more Bacteria are the smallest and most abundant form of life. They have traditionally been considered as primarily planktonic organisms, swimming or floating in a liquid medium, and this view has shaped many of the approaches to microbial processes, including for example the design of most antibiotics. However, over the last few decades it has become clear that many bacteria often adopt a sessile, surface-associated lifestyle, forming complex multicellular communities called biofilms. Bacterial biofilms are found in a vast range of environments and have major consequences on human health and industrial processes, from biofouling of surfaces to the spread of diseases. Although the study of biofilms has been biologists' territory for a long time, a multitude of phenomena in the formation and development of biofilms hinges on physical processes. We are pleased to present a collection of research papers that discuss some of the latest developments in many of the areas to which physicists can contribute a deeper understanding of biofilms, both experimentally and theoretically. The topics covered range from the influence of physical environmental parameters on cell attachment and subsequent biofilm growth, to the use of local probes and imaging techniques to investigate biofilm structure, to the development of biofilms in complex environments and the modeling of colony morphogenesis. The results presented contribute to addressing some of the major challenges in microbiology today, including the prevention of surface contamination, the optimization of biofilm disruption methods and the effectiveness of antibiotic treatments.

Bacteria often live in dynamic fluid environments 1-3 and flow can a ect fundamental microbial pr... more Bacteria often live in dynamic fluid environments 1-3 and flow can a ect fundamental microbial processes such as nutrient uptake 1,4 and infection 5 . However, little is known about the consequences of the forces and torques associated with fluid flow on bacteria. Through microfluidic experiments, we show that fluid shear produces strong spatial heterogeneity in suspensions of motile bacteria, characterized by up to 70% cell depletion from low-shear regions due to 'trapping' in high-shear regions. Two mathematical models and a scaling analysis accurately capture these observations, including the maximal depletion at mean shear rates of 2.5-10 s −1 , and reveal that trapping by shear originates from the competition between the cell alignment with the flow and the stochasticity in the swimming orientation. We show that this shear-induced trapping directly impacts widespread bacterial behaviours, by hampering chemotaxis and promoting surface attachment. These results suggest that the hydrodynamic environment may directly a ect bacterial fitness and should be carefully considered in the study of microbial processes.

For many physical, chemical and biological measurements, temperature is a crucial parameter to co... more For many physical, chemical and biological measurements, temperature is a crucial parameter to control. In particular, the recent development of microreactors and chip-based technologies requires integrated thermostatic systems. However, the requirements of disposability and visual inspection of a device under a microscope cannot accommodate equipment such as external heaters. By exploiting a silver-filled epoxy that can be injected and solidified in a microfluidic chip, we demonstrate a simple and inexpensive design of a conductive path, which allows heating by the Joule effect of both sides of a microchannel. In addition to permitting the maintenance of a constant temperature along the channel walls, our method can control the temperature gradient across the channel, thus enabling nonequilibrium studies in a microfluidic geometry.

Dense suspensions of motile bacteria, possibly including the human gut microbiome, exhibit collec... more Dense suspensions of motile bacteria, possibly including the human gut microbiome, exhibit collective dynamics akin to those observed in classic, high Reynolds number turbulence with important implications for chemical and biological transport, yet this analogy has remained primarily qualitative. Here, we present experiments in which a dense suspension of Bacillus subtilis bacteria was flowed through microchannels and the velocity statistics of the flowing suspension were quantified using a recently developed velocimetry technique coupled with vortex identification methods. Observations revealed a robust intermittency phenomenon, whereby the average velocity profile of the suspension fluctuated between a plug-like flow and a parabolic flow profile. This intermittency is a hallmark of the onset of classic turbulence and Lagrangian tracking revealed that it here originates from the presence of transient vortices in the active, collective motion of the bacteria locally reinforcing the externally imposed flow. These results link together two entirely different manifestations of turbulence and show the potential of the microfluidic approach to mimic the environment characteristic of certain niches of the human microbiome.

Fluid flow, ubiquitous in natural and man-made environments, has the potential to profoundly impa... more Fluid flow, ubiquitous in natural and man-made environments, has the potential to profoundly impact the transport of microorganisms, including phytoplankton in aquatic habitats and bioreactors. Yet, the effect of ambient flow on the swimming behaviour of phytoplankton has remained poorly understood, largely owing to the difficulty of observing cell-flow interactions at the microscale. Here, we present microfluidic experiments where we tracked individual cells for four species of motile phytoplankton exposed to a spatially non-uniform fluid shear rate, characteristic of many flows in natural and artificial environments. We observed that medium-to-high mean shear rates (1-25 s 21 ) produce heterogeneous cell concentrations in the form of regions of accumulation and regions of depletion. The location of these regions relative to the flow depends on the cells' propulsion mechanism, body shape and flagellar arrangement, as captured by an effective aspect ratio. Species having a large effective aspect ratio accumulated in the high-shear regions, owing to shear-induced alignment of the swimming orientation with the fluid streamlines. Species having an effective aspect ratio close to unity exhibited little preferential accumulation at low-to-moderate flow rates, but strongly accumulated in the low-shear regions under high flow conditions, potentially owing to an active, behavioural response of cells to shear. These observations demonstrate that ambient fluid flow can strongly affect the motility and spatial distribution of phytoplankton and highlight the rich dynamics emerging from the interaction between motility, morphology and flow.

Bacterial biofilms have an enormous impact on medicine, industry and ecology. These microbial com... more Bacterial biofilms have an enormous impact on medicine, industry and ecology. These microbial communities are generally considered to adhere to surfaces or interfaces. Nevertheless, suspended filamentous biofilms, or streamers, are frequently observed in natural ecosystems where they play crucial roles by enhancing transport of nutrients and retention of suspended particles. Recent studies in streamside flumes and laboratory flow cells have hypothesized a link with a turbulent flow environment. However, the coupling between the hydrodynamics and complex biofilm structures remains poorly understood. Here, we report the formation of biofilm streamers suspended in the middle plane of curved microchannels under conditions of laminar flow. Experiments with different mutant strains allow us to identify a link between the accumulation of extracellular matrix and the development of these structures. Numerical simulations of the flow in curved channels highlight the presence of a secondary vortical motion in the proximity of the corners, which suggests an underlying hydrodynamic mechanism responsible for the formation of the streamers. Our findings should be relevant to the design of all liquid-carrying systems where biofilms are potentially present and provide new insights on the origins of microbial streamers in natural and industrial environments.

Measuring the concentration profiles induced by gravity settling is known to be an efficient rout... more Measuring the concentration profiles induced by gravity settling is known to be an efficient route to obtain the equation of state of a colloidal suspension, to inspect the fine details of the phase diagram and to provide clues on the nature of metastable phases. Here we show that a careful analysis of the transient settling profiles may add valuable information for what concerns colloidal hydrodynamics. In particular, we show that a numerical inversion of a kinetic profile yields the full hydrodynamic factor K ( ) up to the concentration of the original unsettled suspension, and that the dilute part of the profile yields a 'dynamic' gravitation length also related to K ( ). These predictions are tested on a suspension of monodisperse hard and sticky spheres. Finally we describe and test a novel optical method, allowing us to measure sedimentation profiles on a wide class of colloidal systems, even in the presence of a noticeable turbidity.

We show that thermophoresis (particle drift driven by thermal gradients) in aqueous solutions can... more We show that thermophoresis (particle drift driven by thermal gradients) in aqueous solutions can be measured by using an all-optical thermal-lensing setup, where a temperature gradient is set by a near-infrared laser beam with no need of light-absorbing dyes. After discussing the principles of the method, we study by numerical simulation the nature and extent of parasitic thermal-convection effects, and we describe an optical setup designed to limit them. We finally present preliminary results on thermophoresis in micellar solutions and colloidal dispersions.

We show that a large set of nanofluid thermal conductivity data falls within the upper and lower ... more We show that a large set of nanofluid thermal conductivity data falls within the upper and lower Maxwell bounds for homogeneous systems. This indicates that the thermal conductivity of nanofluids is largely dependent on whether the nanoparticles stay dispersed in the base fluid, form large aggregates, or assume a percolating fractal configuration. The experimental data, which are strikingly analogous to those in most solid composites and liquid mixtures, provide strong evidence for the classical nature of thermal conduction in nanofluids.

In recent microfluidic experiments with solutions of bacteria we observed the formation of biofil... more In recent microfluidic experiments with solutions of bacteria we observed the formation of biofilms in the form of thread-like structures, called 'streamers', which float in the middle plane of the channel and are connected to the side walls at the inner corners. Motivated by this observation, we discuss here the pressure-driven low-Reynolds-number flow around a corner bounded by the walls of a channel with rectangular cross-section. We numerically solve the flow field in a channel of constant cross-section, which exhibits 90 • sharp corners, or turns with constant curvature, or portions with slowly changing curvature along the flow direction, for finite, but small, values of the Reynolds numbers and including the limit of vanishingly small Reynolds numbers. In addition, we develop a matched asymptotic expansion solution for the flow around two boundaries intersecting at an angle α and spanning the small gap h between two horizontal plates. We illustrate the basic features of the flow in these channel geometries by describing the three-dimensional velocity field and the distribution of streamwise vorticity and helicity, and comparing the numerical solutions with predictions based on the asymptotic approach. We demonstrate that near a corner or a change in the curvature of the side wall the flow is three-dimensional and pairs of counter-rotating vortical structures are present, as identified by Balsa (J. Fluid Mech., vol. 372, 1998, p. 25). Finally, we discuss how this secondary flow depends on the significant geometric parameters, the aspect ratio of the channel cross-section, the radius of curvature of the turn and, more generally, the variation of the curvature of the channel side boundary. We believe that these three-dimensional secondary flow structures are relevant to transport problems where accumulation of material at the boundary is possible.

The advent of microscale technologies, such as microfluidics, has revolutionized many areas of bi... more The advent of microscale technologies, such as microfluidics, has revolutionized many areas of biology yet has only recently begun to impact the field of bacterial biofilms. By enabling accurate control and manipulation of physical and chemical conditions, these new microscale approaches afford the ability to combine important features of natural and artificial microbial habitats, such as fluid flow and ephemeral nutrient sources, with an unprecedented level of flexibility and quantification. Here, we review selected case studies to exemplify this potential, discuss limitations, and suggest that this approach opens new vistas into biofilm research over traditional setups, allowing us to expand our understanding of the formation and consequences of biofilms in a broad range of environments and applications.

Scientific Reports, 2017