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M.E. Aubin-Tam

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By leveraging the unique qualities of microorganisms, engineered living materials (ELMs) offer functional and economic advantages in everyday applications along with notable ecological benefits. This study contributes to the growing field of biodesign by examining the potential of Flavobacteria for thermochromic ELMs. Many Flavobacteria, commonly found in marine environments, produce iridescent structural colorations as their colonies expand on semi-solid surfaces through gliding motility. In this study, we analyzed the effects of temperature variations on flavobacterium Cellulophaga lytica PLY-A2, characterizing distinct changes in colony growth and iridescent colorations at a macroscopic and microscopic scale. Using scanning electron microscopy, we investigated the relationship between iridescent color and the underlying cell-based optical structures. By providing insights into the temperature-responsive behavior of Flavobacteria, our findings highlight their potential for future thermochromic ELMs—with applications ranging from sustainable food packaging to smart textiles—while encouraging further characterization studies within biodesign research. ...
Journal article (2026) - Lisa Laura Dreesens, Igor Rutka, Kyriacos Nicolaou, Marie Eve Aubin-Tam
The ability of a bacteriophage to distinguish between a suitable and a non-suitable bacterial host is critical for its survival. The series of events occurring between first contact and irreversible binding of a phage to its host is likely playing an essential role in the phage reproduction cycle. However, crucial information about the dynamic interaction between phages and bacterial cell surfaces is still lacking. Until now, most studies have focused on bulk measurements or on analyzing static interactions between phage and host using electron microscopy. These studies generally lack the ability to reveal the spatiotemporal dynamics that are key to understanding the "decision-making" process before the phage commits to infection. Here, we investigated nanoscopic on-cell dynamics using single-particle fluorescence microscopy, which allowed us to track the interaction between fluorescently labeled phage T4 and its host Escherichia coli B with high spatial and temporal resolution. We provide the first direct evidence that phage T4 exhibits long-range motion on or near the cell surface, facilitated by repeated shifts in mean positions of its tethering location. IMPORTANCE: We study the interaction of the virus bacteriophage T4 with bacteria. By tagging fluorescent dyes to bacteriophage T4, we can follow the movement of individual viruses when they approach the bacteria, which revealed that these bacteriophages perform a long-range walking motion on the surface of the bacteria. ...
This paper explores the potential of microbial biomineralisation—a biological phenomenon where microorganisms drive mineral formation, generating structures with exceptional mechanical properties—for sustainable design futures. In particular, we discuss how leveraging microbial biomineralisation in designing living artefacts can support regenerative ecologies. Although a few pioneering biodesigners have begun to explore the potentials of microbial biomineralisation for design, a vast design space remains under-explored in the realm of living artefacts. In response, we first characterise a design space by analysing 22 microbial biomineralisation cases from art, design, architecture, materials science, and engineering. We examine the specifics of the organisms and substrates used, the fabrication or growing techniques developed, and the unique design outcomes. Following this, we further analyse these cases through a five-pillar framework of living artefacts for regenerative ecologies, speculating on potential pathways where these cases can be further developed as living artefacts to achieve the specific goals related to these pillars. Our results signal a promising era for designing living artefacts that promote cleaner production practices, foster biodiversity, and cultivate care and sensibilities towards other-than-human entities in our daily lives, by integrating the unique properties of microbial biomineralisation into everyday interactions with living artefacts. ...
Engineered living materials (ELMs) integrate aspects of material science and biology into a unique platform, leading to materials and devices with features of life. Among those, ELMs containing microalgae have received increased attention due to the many benefits photosynthetic organisms provide. Due to their relatively recent occurrence, photosynthetic ELMs still face many challenges related to reliability, lifetime, scalability, and more, often based on the complicated crosstalk of cellular, material-based, and environmental variables in time. This Viewpoint aims to summarize potential avenues for improving ELMs, beginning with an emphasis on understanding the cell’s perspective and the potential stresses imposed on them due to recurring flaws in many current ELMs. Potential solutions and their ease of implementation will be discussed, ranging from choice of organism, adjustments to the ELM design, to various genetic modification tools, so as to achieve ELMs with longer lifetime and improved functionality. ...
Journal article (2025) - Fan Jiang, Kui Yu, Roland Kieffer, Djanick de Jong, Richard M. Parker, Silvia Vignolini, Marie Eve Aubin-Tam
Growing environmental concerns are driving demand for energy-saving strategies. Thermochromic smart windows offer a practical solution by passively regulating sunlight in homes and offices. Despite recent progress, current technologies still face challenges in achieving the thermal durability and mechanical robustness necessary for long-term use, combined with a rapid transition below 30 °C. Here we report a thermochromic hydrogel assembled from poly(N,N-dimethylaminoethyl methacrylate) and 2,2,2-trifluoroethyl methacrylate that produces flexible films on a large scale. This hydrogel rapidly (~ 3 s) and reversibly becomes turbid above a tunable transition temperature spanning the human comfort zone, and maintains its thermochromic property even when mechanically stretched with 500% strain. The film’s high modulation of solar transmittance (70.6%) and luminous transmittance (85.7%) enables efficient sunlight screening in hot weather and clear vision in cool weather. Such ‘smart windows’ remain stable for over 10,000 heating/cooling cycles. These combined features indicate the hydrogel suitability for applications ranging from heat-modulating smart windows (architectural, automotive, etc.) to passive temperature indicators and even wearables. ...
Photosynthetic organisms convert solar light into chemical energy through the process of photosynthesis. The employment of photosynthetic organisms in novel materials and devices provides them with a solar-powered and sustainable functionality. In general, photosynthesis utilizes light, water, and CO2 to generate various organic compounds while releasing secondary valuable products such as O2, extracellular electrons, carbohydrates, or H2. The light-dependent inputs and outputs are harnessed for environmental purification, biomedical applications, and production of biofuel, electricity, nanomaterials, or bioplastics. In this review, we summarize photosynthesis-assisted materials and engineering applications based on the products and substrates of photosynthetic processes, and we highlight key challenges that remain to be addressed. ...
The cell membrane is a crucial biological interface to consider in biomedical research, as a significant proportion of drugs interacts with this barrier. While understanding membrane–drug interactions is important, existing in vitro platforms for drug screening predominantly focus on interactions with whole cells or tissues. This preference is partly due to the instability of membrane-based systems and the technical challenges associated with buffer replacement around lipid membranes formed on microfluidic chips. Here, we introduce a novel microfluidic design capable of forming stable freestanding lipid bilayers with efficient replacement of the media in their local environment for molecular delivery to the membrane. With the use of bubble traps and resistance channels, we achieved sufficient hydrodynamic control to maintain membrane stability during the membrane formation and the molecular delivery phases. As a proof of concept, we successfully formed 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) bilayers on the chip and delivered the antibiotic azithromycin at low (5 μM) and high (250 μM) doses. Using optical tweezers, we characterized how azithromycin influenced the membrane elastic properties, including tension and bending rigidity. This microfluidic device is a versatile tool that can deliver various buffers, molecules or nano-/microparticles to freestanding membranes, and study the resulting impact on the membranes' properties. ...
Journal article (2025) - Jeong Joo Oh, Franka H. van der Linden, Koray Malcı, Ramon A. van der Valk, Tom Ellis, Marie Eve Aubin-Tam
Inspired by naturally occurring biomaterials, autonomously grown engineered living materials (ELMs) feature cell-driven growth and programmable biological functions. However, the "livingness" of cells poses a short life span and low tolerance to harsh conditions, limiting the practical use of such materials. Here, we developed materials with programmable and dormant functionalities, grown from a mixture of Komagataeibacter rhaeticus and Bacillus endospores under engineered medium conditions. K. rhaeticus produces the bacterial cellulose (BC) matrix that integrates Bacillus spores within, whereas the confined spores keep dormant and are resistant to harsh conditions in the environment. Bacillus spores can germinate and confer desired functions to the materials. Modulating the binding affinity of spores to the BC matrix with genetic engineering can improve cell loading and therefore enhance the material functionality. These materials can serve as a versatile on-demand platform for applications as biosensors, biocatalytic materials, and in situ transformation of mechanically robust cellulose-based composites. ...
Journal article (2024) - Stefan U. Egelhaaf, Xiaoming Mao, Marjolijn Dijkstra, David J Pine, Sanat K. Kumar, M.E. Aubin-Tam, G.H. Koenderink, More authors..., Jean-Louis Barrat, Emanuela Del Gado
Soft materials are usually defined as materials made of mesoscopic entities, often self-organised, sensitive to thermal fluctuations and to weak perturbations. Archetypal examples are colloids, polymers, amphiphiles, liquid crystals, foams. The importance of soft materials in everyday commodity products, as well as in technological applications, is enormous, and controlling or improving their properties is the focus of many efforts. From a fundamental perspective, the possibility of manipulating soft material properties, by tuning interactions between constituents and by applying external perturbations, gives rise to an almost unlimited variety in physical properties. Together with the relative ease to observe and characterise them, this renders soft matter systems powerful model systems to investigate statistical physics phenomena, many of themrelevant as well to hard condensed matter systems. Understanding the emerging properties from mesoscale constituents still poses enormous challenges, which have stimulated a wealth of new experimental approaches, including the synthesis of new systems with, e.g. tailored self-assembling properties, or novel experimental techniques in imaging, scattering or rheology. Theoretical and
numerical methods, and coarse-grained models, have become central to predict physical propertiesof soft materials, while computational approaches that also use machine learning tools are playing a progressively major role in many investigations. This Roadmap intends to give a broad overview of recent and possible future activities in the field of soft materials, with experts covering various developments and challenges in material synthesis and characterisation, instrumental, simulation and theoretical methods as well as general concepts. ...
Inspired by biological functions of living systems, researchers have engineered cells as independent functional materials or integrated them within a natural or synthetic matrix to create engineered living materials (ELMs). However, the ‘livingness’ of cells in such materials poses serious drawbacks, such as a short lifespan and the need for cold-chain logistics. Bacterial spores have emerged as a game changer to bypass these shortcomings as a result of their intrinsic dormancy and resistance against harsh conditions. Emerging synthetic biology tools tailored for engineering spores and better understanding of their physical properties have led to novel applications of spore-based materials. Here, we review recent advances in such materials and discuss future challenges for the development of time- and cost-efficient spore-based materials with high performance. ...
Coexistence of lipid domains in cell membranes is associated with vital biological processes. Here, we investigate two such membranes: a multi-component membrane composed of DOPC and DPPC lipids with gel and fluid separated domains, and a single component membrane composed of PMPC lipids forming ripples. We characterize their mechanical properties below their melting point, where ordered and disordered regions coexist, and above their melting point, where they are in fluid phase. To conduct these inquiries, we create lipid bilayers in a microfluidic chip interfaced with a heating system and optical tweezers. The chip features a bubble trap and enables high-throughput formation of planar bilayers. Optical tweezers experiments reveal interfacial hydrodynamics (fluid-slip) and elastic properties (membrane tension and bending rigidity) at various temperatures. For PMPC bilayers, we demonstrate a higher fluid slip at the interface in the fluid-phase compared to the ripple phase, while for the DOPC:DPPC mixture, similar fluid slip is measured below and above the transition point. Membrane tension for both compositions increases after thermal fluidization. Bending rigidity is also measured using the forces required to extend a lipid nanotube pushed out of the freestanding membranes. This novel temperature-controlled microfluidic platform opens numerous possibilities for thermomechanical studies on freestanding planar membranes. ...
Journal article (2024) - D. Wei, G. Quaranta, M.E. Aubin-Tam, D.S.W. Tam
Eukaryotes swim with coordinated flagellar (ciliary) beating and steer by fine-tuning the coordination. The model organism for studying flagellate motility, Chlamydomonas reinhardtii, employs synchronous, breaststroke-like flagellar beating to swim, and it modulates the beating amplitudes differentially to steer. This strategy hinges on both inherent flagellar asymmetries (e.g. different response to chemical messengers) and such asymmetries being effectively coordinated in the synchronous beating. In C. reinhardtii, the synchrony of beating is known to be supported by a mechanical connection between flagella; however, how flagellar asymmetries persist in the synchrony remains elusive. For example, it has been speculated for decades that one flagellum leads the beating, as its dynamic properties (i.e. frequency, waveform, etc.) appear to be copied by the other one. In this study, we combine experiments, computations, and modeling efforts to elucidate the roles played by each flagellum in synchronous beating. With a non-invasive technique to selectively load each flagellum, we show that the coordinated beating essentially only responds to load exerted on the cis flagellum; and that such asymmetry in response derives from a unilateral coupling between the two flagella. Our results highlight a distinct role for each flagellum in coordination and have implication for biflagellates’ tactic behaviors. ...
Engineered living materials (ELMs) are a novel class of functional materials that typically feature spatial confinement of living components within an inert polymer matrix to recreate biological functions. Understanding the growth and spatial configuration of cellular populations within a matrix is crucial to predicting and improving their responsive potential and functionality. Here, this work investigates the growth, spatial distribution, and photosynthetic productivity of eukaryotic microalga Chlamydomonas reinhardtii (C. reinhardtii) in three-dimensionally shaped hydrogels in dependence of geometry and size. The embedded C. reinhardtii cells photosynthesize and form confined cell clusters, which grow faster when located close to the ELM periphery due to favorable gas exchange and light conditions. Taking advantage of location-specific growth patterns, this work successfully designs and prints photosynthetic ELMs with increased CO2 capturing rate, featuring high surface to volume ratio. This strategy to control cell growth for higher productivity of ELMs resembles the already established adaptations found in multicellular plant leaves. ...
Biofilms are three-dimensional (3D) bacterial communities that exhibit a highly self-organized nature in terms of their composition and complex architecture. Bacteria in biofilms display emergent biological properties, such as resistance to antimicrobials and disinfectants that the individual planktonic cells lack. Bacterial biofilms possess specialized architectural features including unique extracellular matrix compositions and a distinct spatially patterned arrangement of cells and matrix components within the biofilm. It is unclear which of these architectural elements of bacterial biofilms lead to the development of their emergent biological properties. Here, we report a 3D printing-based technique for studying the emergent resistance behaviors of Escherichia coli biofilms as a function of their architecture. Cellulose and curli are the major extracellular-matrix components in E. coli biofilms. We show that 3D-printed biofilms expressing either curli alone or both curli and cellulose in their extracellular matrices show higher resistance to exposure against disinfectants than 3D prints expressing either cellulose alone or no biofilm-matrix components. The 3D-printed biofilms expressing cellulose and/or curli also show thicker anaerobic zones than nonbiofilm-forming E. coli 3D prints. Thus, the matrix composition plays a crucial role in the emergent spatial patterning and biological endurance of 3D-printed biofilms. In contrast, initial spatial distribution of bacterial density or curli-producing cells does not have an effect on biofilm resistance phenotypes. Further, these 3D-printed biofilms could be reversibly attached to different surfaces (bacterial cellulose, glass, and polystyrene) and display resistance to physical distortions by retaining their shape and structure. This physical robustness highlights their potential in applications including bioremediation, protective coatings against pathogens on medical devices, or wastewater treatment, among many others. This new understanding of the emergent behavior of bacterial biofilms could aid in the development of novel engineered living materials using synthetic biology and materials science approaches. ...
Journal article (2021) - Guillermo J. Amador, Dennis van Dijk, Roland Kieffer, Marie Eve Aubin-Tam, Daniel Tam
Vital biological processes, such as trafficking, sensing, and motility, are facilitated by cellular lipid membranes, which interact mechanically with surrounding fluids. Such lipid membranes are only a few nanometers thick and composed of a liquid crystalline structure known as the lipid bilayer. Here, we introduce an active, noncontact, two-point microrheology technique combining multiple optical tweezers probes with planar freestanding lipid bilayers accessible on both sides. We use the method to quantify both fluid slip close to the bilayer surface and transmission of fluid flow across the structure, and we use numerical simulations to determine the monolayer viscosity and the intermonolayer friction. We find that these physical properties are highly dependent on the molecular structure of the lipids in the bilayer. We compare ordered-phase with liquid disordered-phase lipid bilayers, and we find the ordered-phase bilayers to be 10 to 100 times more viscous but with 100 times less intermonolayer friction. When a local shear is applied by the optical tweezers, the ultralow intermonolayer friction results in full slip of the two leaflets relative to each other and as a consequence, no shear transmission across the membrane. Our study sheds light on the physical principles governing the transfer of shear forces by and through lipid membranes, which underpin cell behavior and homeostasis. ...
The swift deformations of flagella and cilia are crucial for locomotion and fluid transport on the micron scale. Most hydrodynamic models of flagellar and ciliary flows assume the zero Reynolds number limit and model the flow using Stokes equations. Recent work has demonstrated that this quasi-steady approximation breaks down at increasing distances from the cilia. Here, we use optical tweezer-based velocimetry to measure the flow velocity with high temporal accuracy, and to reconstruct the entire unsteady flow field around beating cilia. We report both the steady and the unsteady component of the ciliary flow and compare them with the solutions to both the Stokes and the Navier-Stokes equations. Our experimental measurements of the velocity and vorticity fields are in agreement with the numerical solution to the Navier-Stokes equations and show significant differences with the solution to the Stokes equations. We characterize the phase difference between the flow oscillations and the oscillations of the ciliary motion and evidence a significant anisotropic phase lag. We show that this phase lag presents the spatiotemporal characteristics of the unsteady Stokes equations and that the flow field around beating cilia is well represented by the fundamental solution to the unsteady Stokes equations: the oscillet. ...
Journal article (2021) - Srikkanth Balasubramanian, Kui Yu, Anne S. Meyer, Elvin Karana, Marie Eve Aubin-Tam
Living materials, which are fabricated by encapsulating living biological cells within a non-living matrix, have gained increasing attention in recent years. Their fabrication in spatially defined patterns that are mechanically robust is essential for their optimal functional performance but is difficult to achieve. Here, a bioprinting technique employing environmentally friendly chemistry to encapsulate microalgae within an alginate hydrogel matrix is reported. The bioprinted photosynthetic structures adopt pre-designed geometries at millimeter-scale resolution. A bacterial cellulose substrate confers exceptional advantages to this living material, including strength, toughness, flexibility, robustness, and retention of physical integrity against extreme physical distortions. The bioprinted materials possess sufficient mechanical strength to be self-standing, and can be detached and reattached onto different surfaces. Bioprinted materials can survive stably for a period of at least 3 days without nutrients, and their life can be further extended by transferring them to a fresh source of nutrients within this timeframe. These bioprints are regenerative, that is, they can be reused and expanded to print additional living materials. The fabrication of the bioprinted living materials can be readily up-scaled (up to ≥70 cm × 20 cm), highlighting their potential product applications including artificial leaves, photosynthetic bio-garments, and adhesive labels. ...
FtsH is a membrane-bound protease that plays a crucial role in proteolytic regulation of many cellular functions. It is universally conserved in bacteria and responsible for the degradation of misfolded or misassembled proteins. A recent study has determined the structure of bacterial FtsH in detergent micelles. To properly study the function of FtsH in a native-like environment, we reconstituted the FtsH complex into lipid nanodiscs. We found that FtsH in membrane scaffold protein (MSP) nanodiscs maintains its native hexameric conformation and is functionally active. We further investigated the effect of the lipid bilayer composition (acyl chain length, saturation, head group charge and size) on FtsH proteolytic activity. We found that the lipid acyl chain length influences AaFtsH activity in nanodiscs, with the greatest activity in a bilayer of di-C18:1 PC. We conclude that MSP nanodiscs are suitable model membranes for further in vitro studies of the FtsH protease complex. ...
Sustainable structural materials with excellent impact-resistance properties are urgently needed but challenging to produce, especially in a scalable fashion and with control over 3D shape. Here, we show that bacterial cellulose (BC) and bacterially precipitated calcium carbonate self-assemble into a layered structure reminiscent of tough biomineralized materials in nature (nacre, bone, dentin). The fabrication method consists of biomineralizing BC to form an organic/inorganic mixed slurry, in which calcium carbonate crystal size is controlled with bacterial poly(γ-glutamic acid) and magnesium ions. This slurry self-assembles into a layered material that combines high toughness and high impact and fire resistance. The rapid fabrication is readily scalable, without involving toxic chemicals. Notably, the biomineralized BC can be repeatedly recycled and molded into any desired 3D shape and size using a simple kitchen blender and sieve. This fully biodegradable composite is well suited for use as a component in daily life, including furniture, helmets, and protective garments. ...
Journal article (2020) - Kuang Liang, Ewa M. Spiesz, Dominik T. Schmieden, An Wu Xu, Anne S. Meyer, Marie Eve Aubin-Tam
Graphene oxide (GO) has recently been highlighted as a promising multipurpose two-dimensional material. However, free-standing graphene oxide films suffer from poor strength and flexibility, which limits scaling-up of production and lifetime structural robustness in applications. Inspired by the relationship between the organic and inorganic components of the hierarchical structure of nacre found in mollusk shells, we have fabricated self-assembled, layered graphene-based composite films. The organic phase of our composite is produced via environmentally friendly and economical methods based on bacterial production of γ-poly(glutamic acid) (PGA). Composite films made of GO, PGA, and divalent cations (Ca2+) were prepared through a slow solvent evaporation method at ambient temperature, resulting in a nacre-like layered structure. These biobased nanocomposite films showed impressive mechanical properties, which resulted from a synergistic combination of hydrogen bonding with the bacterially produced PGA and ionic bonding with calcium ions (Ca2+). The GO/PGA/Ca2+ composite films possessed a high strength of 150 ± 51.9 MPa and a high Young's modulus of 21.4 ± 8.7 GPa, which represents an increase of 120% and over 70% with respect to pure GO films. We provide rational design strategies for the production of graphene-based films with improved mechanical performance, which can be applied in filtration purification of wastewater in the paper, food, beverage, pigment, and pharmaceuticals industries, as well as for manufacturing of functional membranes and surface coatings. ...