Wyss Institute for Biologically Inspired Engineering

Deeper understanding of antibiotic-induced physiological responses is critical to identifying means for enhancing our current antibiotic arsenal. Bactericidal antibiotics with diverse targets have been hypothesized to kill bacteria, in part by inducing production of damaging reactive species. This notion has been supported by many groups but has been challenged recently. Here we robustly test the hypothesis using biochemical, enzymatic, and biophysical assays along with genetic and phenotypic experiments. We first used a novel intracellular H2O2 sensor, together with a chemically diverse panel of fluorescent dyes sensitive to an array of reactive species to demonstrate that antibiotics broadly induce redox stress. Subsequent gene-expression analyses reveal that complex antibiotic-induced oxidative stress responses are distinct from canonical responses generated by supraphysiological levels of H2O2. We next developed a method to quantify cellular respiration dynamically and found that bactericidal antibiotics elevate oxygen consumption, indicating significant alterations to bacterial redox physiology. We further show that overexpression of catalase or DNA mismatch repair enzyme, MutS, and antioxidant pretreatment limit antibiotic lethality, indicating that reactive oxygen species causatively contribute to antibiotic killing. Critically, the killing efficacy of antibiotics was diminished under strict anaerobic conditions but could be enhanced by exposure to molecular oxygen or by the addition of alternative electron acceptors, indicating that environmental factors play a role in killing cells physiologically primed for death. This work provides direct evidence that, downstream of their target-specific interactions, bactericidal antibiotics induce complex redox alterations that contribute to cellular damage and death, thus supporting an evolving, expanded model of antibiotic lethality.

We describe the design, fabrication, and calibration of a highly compliant artificial skin sensor. The sensor consists of multilayered mircochannels in an elastomer matrix filled with a conductive liquid, capable of detecting multiaxis strains and contact pressure. A novel manufacturing method comprised of layered molding and casting processes is demonstrated to fabricate the multilayered soft sensor circuit. Silicone rubber layers with channel patterns, cast with 3-D printed molds, are bonded to create embedded microchannels, and a conductive liquid is injected into the microchannels. The channel dimensions are 200 μm (width) × 300 μm (height). The size of the sensor is 25 mm × 25 mm, and the thickness is approximately 3.5 mm. The prototype is tested with a materials tester and showed linearity in strain sensing and nonlinearity in pressure sensing. The sensor signal is repeatable in both cases. The characteristic modulus of the skin prototype is approximately 63 kPa. The sensor is functional up to strains of approximately 250%.

3D printing of renewable building blocks like cellulose nanocrystals offers an attractive pathway for fabricating sustainable structures. Here, viscoelastic inks composed of anisotropic cellulose nanocrystals (CNC) that enable patterning of 3D objects by direct ink writing are designed and formulated. These concentrated inks are composed of CNC particles suspended in either water or a photopolymerizable monomer solution. The shear‐induced alignment of these anisotropic building blocks during printing is quantified by atomic force microscopy, polarized light microscopy, and 2D wide‐angle X‐ray scattering measurements. Akin to the microreinforcing effect in plant cell walls, the alignment of CNC particles during direct writing yields textured composites with enhanced stiffness along the printing direction. The observations serve as an important step forward toward the development of sustainable materials for 3D printing of cellular architectures with tailored mechanical properties.

This paper presents preliminary results for the design, development and evaluation of a hand rehabilitation glove fabricated using soft robotic technology. Soft actuators comprised of elastomeric materials with integrated channels that function as pneumatic networks (PneuNets), are designed and geometrically analyzed to produce bending motions that can safely conform with the human finger motion. Bending curvature and force response of these actuators are investigated using geometrical analysis and a finite element model (FEM) prior to fabrication. The fabrication procedure of the chosen actuator is described followed by a series of experiments that mechanically characterize the actuators. The experimental data is compared to results obtained from FEM simulations showing good agreement. Finally, an open-palm glove design and the integration of the actuators to it are described, followed by a qualitative evaluation study.

The inability to predict heterologous gene expression levels precisely hinders our ability to engineer biological systems. Using well-characterized regulatory elements offers a potential solution only if such elements behave predictably when combined. We synthesized 12,563 combinations of common promoters and ribosome binding sites and simultaneously measured DNA, RNA, and protein levels from the entire library. Using a simple model, we found that RNA and protein expression were within twofold of expected levels 80% and 64% of the time, respectively. The large dataset allowed quantitation of global effects, such as translation rate on mRNA stability and mRNA secondary structure on translation rate. However, the worst 5% of constructs deviated from prediction by 13-fold on average, which could hinder large-scale genetic engineering projects. The ease and scale this of approach indicates that rather than relying on prediction or standardization, we can screen synthetic libraries for desired behavior.

Biological systems are exquisitely sensitive to the location and timing of physiologic cues and drugs. This spatiotemporal sensitivity presents opportunities for developing new therapeutic approaches. Polymer-based delivery systems are used extensively for attaining localized, sustained release of bioactive molecules. However, these devices typically are designed to achieve a constant rate of release. We hypothesized that it would be possible to create digital drug release, which could be accelerated and then switched back off, on demand, by applying ultrasound to disrupt ionically cross-linked hydrogels. We demonstrated that ultrasound does not permanently damage these materials but enables nearly digital release of small molecules, proteins, and condensed oligonucleotides. Parallel in vitro studies demonstrated that the concept of applying temporally short, high-dose "bursts" of drug exposure could be applied to enhance the toxicity of mitoxantrone toward breast cancer cells. We thus used the hydrogel system in vivo to treat xenograft tumors with mitoxantrone, and found that daily ultrasound-stimulated drug release substantially reduced tumor growth compared with sustained drug release alone. This approach of digital drug release likely will be applicable to a broad variety of polymers and bioactive molecules, and is a potentially useful tool for studying how the timing of factor delivery controls cell fate in vivo.

Exosuits show much promise as a method for augmenting the body with lightweight, portable, and compliant wearable systems. We envision that such systems can be further refined so that they can be sufficiently low profile to fit under a wearer's existing clothing. Our focus is on creating an assistive device that provides a fraction of the nominal biological torques and does not provide external load transfer. In early work, we showed that the system can substantially maintain normal biomechanics and positively affect a wearer's metabolic rate. Many basic fundamental research and development challenges remain in actuator development, textile innovation, soft sensor development, human-machine interface (control), biomechanics, and physiology, which provides fertile ground for academic research in many disciplines. While we have focused on gait assistance thus far, numerous other applications are possible, including rehabilitation, upper body support, and assistance for other motions. We look forward to a future where wearable robots provide benefits for people across many areas of our society.

In this paper we present a soft lower-extremity robotic exosuit intended to augment normal muscle function in healthy individuals. Compared to previous exoskeletons, the device is ultra-lightweight, resulting in low mechanical impedance and inertia. The exosuit has custom McKibben style pneumatic actuators that can assist the hip, knee and ankle. The actuators attach to the exosuit through a network of soft, inextensible webbing triangulated to attachment points utilizing a novel approach we call the virtual anchor technique. This approach is designed to transfer forces to locations on the body that can best accept load. Pneumatic actuation was chosen for this initial prototype because the McKibben actuators are soft and can be easily driven by an off-board compressor. The exosuit itself (human interface and actuators) had a mass of 3500 g and with peripherals (excluding air supply) is 7144 g. In order to examine the exosuit's performance, a pilot study with one subject was performed which investigated the effect of the ankle plantar-flexion timing on the wearer's hip, knee and ankle joint kinematics and metabolic power when walking. Wearing the suit in a passive unpowered mode had little effect on hip, knee and ankle joint kinematics as compared to baseline walking when not wearing the suit. Engaging the actuators at the ankles at 30% of the gait cycle for 250 ms altered joint kinematics the least and also minimized metabolic power. The subject's average metabolic power was 386.7 W, almost identical to the average power when wearing no suit (381.8 W), and substantially less than walking with the unpowered suit (430.6 W). This preliminary work demonstrates that the exosuit can comfortably transmit joint torques to the user while not restricting mobility and that with further optimization, has the potential to reduce the wearer's metabolic cost during walking.

Ice repellent coatings have been studied and keenly sought after for many years, where any advances in the durability of such coatings will result in huge energy savings across many fields. Progress in creating anti-ice and anti-frost surfaces has been particularly rapid since the discovery and development of slippery, liquid infused porous surfaces (SLIPS). Here we use SLIPS-coated differential scanning calorimeter (DSC) pans to investigate the effects of the surface modification on the nucleation of supercooled water. This investigation is inherently different from previous studies which looked at the adhesion of ice to SLIPS surfaces, or the formation of ice under high humidity conditions. Given the stochastic nature of nucleation of ice from supercooled water, multiple runs on the same sample are needed to determine if a given surface coating has a real and statistically significant effect on the nucleation temperature. We have cycled supercooling to freezing and then thawing of deionized water in hydrophilic (untreated aluminum), hydrophobic, superhydrophobic, and SLIPS-treated DSC pans multiple times to determine the effects of surface treatment on the nucleation and subsequent growth of ice. We find that SLIPS coatings lower the nucleation temperature of supercooled water in contact with statistical significance and show no deterioration or change in the coating performance even after 150 freeze-thaw cycles.

Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targeted gene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering.

The presented microrobotic platform combines together the advantages of self-folding NIR light sensitive polymer bilayers, magnetic alginate microbeads, and a 3D manipulation system, to propose a solution for targeted, on-demand drug and cell delivery. First feasibility studies are presented together with the potential of the full design. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Biofilms, surface-bound communities of microbes, are economically and medically important due to their pathogenic and obstructive properties. Among the numerous strategies to prevent bacterial adhesion and subsequent biofilm formation, surface topography was recently proposed as a highly nonspecific method that does not rely on small-molecule antibacterial compounds, which promote resistance. Here, we provide a detailed investigation of how the introduction of submicrometer crevices to a surface affects attachment of Escherichia coli. These crevices reduce substrate surface area available to the cell body but increase overall surface area. We have found that, during the first 2 h, adhesion to topographic surfaces is significantly reduced compared with flat controls, but this behavior abruptly reverses to significantly increased adhesion at longer exposures. We show that this reversal coincides with bacterially induced wetting transitions and that flagellar filaments aid in adhesion to these wetted topographic surfaces. We demonstrate that flagella are able to reach into crevices, access additional surface area, and produce a dense, fibrous network. Mutants lacking flagella show comparatively reduced adhesion. By varying substrate crevice sizes, we determine the conditions under which having flagella is most advantageous for adhesion. These findings strongly indicate that, in addition to their role in swimming motility, flagella are involved in attachment and can furthermore act as structural elements, enabling bacteria to overcome unfavorable surface topographies. This work contributes insights for the future design of antifouling surfaces and for improved understanding of bacterial behavior in native, structured environments.

Self-folding is an approach used frequently in nature for the efficient fabrication of structures, but is seldom used in engineered systems. Here, self-folding origami are presented, which consist of shape memory composites that are activated with uniform heating in an oven. These composites are rapidly fabricated using inexpensive materials and tools. The folding mechanism based on the in-plane contraction of a sheet of shape memory polymer is modeled, and parameters for the design of composites that self-fold into target shapes are characterized. Four self-folding shapes are demonstrated: a cube, an icosahedron, a flower, and a Miura pattern; each of which is activated in an oven in less than 4 min. Self-sealing is also investigated using hot melt adhesive, and the resulting structures are found to bear up to twice the load of unsealed structures.

Engineering biosynthetic pathways for chemical production requires extensive optimization of the host cellular metabolic machinery. Because it is challenging to specify a priori an optimal design, metabolic engineers often need to construct and evaluate a large number of variants of the pathway. We report a general strategy that combines targeted genome-wide mutagenesis to generate pathway variants with evolution to enrich for rare high producers. We convert the intracellular presence of the target chemical into a fitness advantage for the cell by using a sensor domain responsive to the chemical to control a reporter gene necessary for survival under selective conditions. Because artificial selection tends to amplify unproductive cheaters, we devised a negative selection scheme to eliminate cheaters while preserving library diversity. This scheme allows us to perform multiple rounds of evolution (addressing ∼10(9) cells per round) with minimal carryover of cheaters after each round. Based on candidate genes identified by flux balance analysis, we used targeted genome-wide mutagenesis to vary the expression of pathway genes involved in the production of naringenin and glucaric acid. Through up to four rounds of evolution, we increased production of naringenin and glucaric acid by 36- and 22-fold, respectively. Naringenin production (61 mg/L) from glucose was more than double the previous highest titer reported. Whole-genome sequencing of evolved strains revealed additional untargeted mutations that likely benefit production, suggesting new routes for optimization.

This paper describes an inexpensive, handheld device that couples the most common forms of electrochemical analysis directly to "the cloud" using any mobile phone, for use in resource-limited settings. The device is designed to operate with a wide range of electrode formats, performs on-board mixing of samples by vibration, and transmits data over voice using audio--an approach that guarantees broad compatibility with any available mobile phone (from low-end phones to smartphones) or cellular network (second, third, and fourth generation). The electrochemical methods that we demonstrate enable quantitative, broadly applicable, and inexpensive sensing with flexibility based on a wide variety of important electroanalytical techniques (chronoamperometry, cyclic voltammetry, differential pulse voltammetry, square wave voltammetry, and potentiometry), each with different uses. Four applications demonstrate the analytical performance of the device: these involve the detection of (i) glucose in the blood for personal health, (ii) trace heavy metals (lead, cadmium, and zinc) in water for in-field environmental monitoring, (iii) sodium in urine for clinical analysis, and (iv) a malarial antigen (Plasmodium falciparum histidine-rich protein 2) for clinical research. The combination of these electrochemical capabilities in an affordable, handheld format that is compatible with any mobile phone or network worldwide guarantees that sophisticated diagnostic testing can be performed by users with a broad spectrum of needs, resources, and levels of technical expertise.

This paper presents advancements in the design of a portable, soft robotic glove for individuals with functional grasp pathologies. The robotic glove leverages soft material actuator technology to safely distribute forces along the length of the finger and provide active flexion and passive extension. These actuators consist of molded elastomeric bladders with anisotropic fiber reinforcements that produce specific bending, twisting, and extending trajectories upon fluid pressurization. In particular, we present a method for customizing a soft actuator to a wearer's biomechanics and demonstrate in a motion capture system that the ranges of motion (ROM) of the two are nearly equivalent. The active ROM of the glove is further evaluated using the Kapandji test. Lastly, in a case study, we present preliminary results of a patient with very weak hand strength performing a timed Box-and-Block test with and without the soft robotic glove.

Sepsis is a lethal disease caused by a systemic microbial infection that spreads via the bloodstream to overwhelm the body's defenses. Current therapeutic approaches are often suboptimal, in part, because they do not fully eliminate the pathogen, and hence the source of deadly toxins. Here we describe an extracorporeal blood cleansing device to selectively remove pathogens from contaminated blood and thereby enhance the patient's response to antibiotic therapy. Immunomagnetic microbeads were modified to create magnetic opsonins that were used to cleanse flowing human whole blood of Candida albicans fungi, a leading cause of sepsis-related deaths. The micromagnetic-microfluidic blood cleansing device generates magnetic field gradients across vertically stacked channels to enable continuous and high throughput separation of fungi from flowing whole blood. A multiplexed version of the device containing four parallel channels achieved over 80% clearance of fungi from contaminated blood at a flow rate of 20 mL/h in a single pass, a rate 1000 times faster than a previously described prototype micromagnetic-microfluidic cell separation system. These results provide the first proof-of-principle that a multiplexed micromagnetic-microfluidic separation system can be used to cleanse pathogens from flowing human blood at a rate and separation efficiency that is relevant for clinical applications.

Over the past decade a massive amount of research has been dedicated to generating omics data to gain insight into a variety of biological phenomena, including cancer, obesity, biofuel production, and infection. Although most of these omics data are available publicly, there is a growing concern that much of these data sit in databases without being used or fully analyzed. Statistical inference methods have been widely applied to gain insight into which genes may influence the activities of others in a given omics data set, however, they do not provide information on the underlying mechanisms or whether the interactions are direct or distal. Biochemically, genetically, and genomically consistent knowledge bases are increasingly being used to extract deeper biological knowledge and understanding from these data sets than possible by inferential methods. This improvement is largely due to knowledge bases providing a validated biological context for interpreting the data.

A soft machine composed of a composite of elastomer and fibers resists puncture from sharp objects, and continues to operate even if punctured.

This paper describes the fabrication of pressure-driven, open-channel microfluidic systems with lateral dimensions of 45-300 microns carved in omniphobic paper using a craft-cutting tool. Vapor phase silanization with a fluorinated alkyltrichlorosilane renders paper omniphobic, but preserves its high gas permeability and mechanical properties. When sealed with tape, the carved channels form conduits capable of guiding liquid transport in the low-Reynolds number regime (i.e. laminar flow). These devices are compatible with complex fluids such as droplets of water in oil. The combination of omniphobic paper and a craft cutter enables the development of new types of valves and switches, such as "fold valves" and "porous switches," which provide new methods to control fluid flow.