Spatial determinants of quorum signaling in a Pseudomonas aeruginosa infection model.

Quorum sensing (QS) is a bacterial communication system that involves production and sensing of extracellular signals. In laboratory models, QS allows bacteria to monitor and respond to their own cell density and is critical for fitness. However, how QS proceeds in natural, spatially structured bacterial communities is not well understood, which significantly hampers our understanding of the emergent properties of natural communities. To address this gap, we assessed QS signaling in the opportunistic pathogen Pseudomonas aeruginosa in a cystic fibrosis (CF) lung infection model that recapitulates the biogeographical aspects of the natural human infection. In this model, P. aeruginosa grows as spatially organized, highly dense aggregates similar to those observed in the human CF lung. By combining this natural aggregate system with a micro-3D-printing platform that allows for confinement and precise spatial positioning of P. aeruginosa aggregates, we assessed the impact of aggregate size and spatial positioning on both intra- and interaggregate signaling. We discovered that aggregates containing ∼2,000 signal-producing P. aeruginosa were unable to signal neighboring aggregates, while those containing ≥5,000 cells signaled aggregates as far away as 176 µm. Not all aggregates within this "calling distance" responded, indicating that aggregates have differential sensitivities to signal. Overexpression of the signal receptor increased aggregate sensitivity to signal, suggesting that the ability of aggregates to respond is defined in part by receptor levels. These studies provide quantitative benchmark data for the impact of spatial arrangement and phenotypic heterogeneity on P. aeruginosa signaling in vivo.

In Situ Imprinting of Topographic Landscapes at the Cell-Substrate Interface.

In their native environments, adherent cells encounter dynamic topographical cues involved in promoting differentiation, orientation, and migration. Ideally, such processes would be amenable to study in cell culture using tools capable of imposing dynamic, arbitrary, and reversible topographic features without perturbing environmental conditions or causing chemical and/or structural disruptions to the substrate surface. To address this need, we report here development of an in vitro strategy for challenging cells with dynamic topographical experiences in which protein-based hydrogel substrate surfaces are modified in real time by positioning a pulsed, near-infrared laser focus within the hydrogel, promoting chemical cross-linking which results in local contraction of the protein matrix. Scanning the laser focus through arbitrary patterns directed by a dynamic reflective mask creates an internal contraction pattern that is projected onto the hydrogel surface as features such as rings, pegs, and grooves. By subjecting substrates to a sequence of scan patterns, we show that topographic features can be created, then eliminated or even reversed. Because laser-induced shrinkage can be confined to 3D voxels isolated from the cell-substrate interface, hydrogel modifications are made without damaging cells or disrupting the chemical or structural integrity of the surface.

Towards mapping electrostatic interactions between Kdo2-lipid A and cationic antimicrobial peptides via ultraviolet photodissociation mass spectrometry.

Cationic antimicrobial peptides (CAMPs) have been known to act as multi-modal weapons against Gram-negative bacteria. As a new approach to investigate the nature of the interactions between CAMPs and the surfaces of bacteria, native mass spectrometry and two MS/MS strategies (ultraviolet photodissociation (UVPD) and higher energy collisional activation (HCD)) are used to examine formation and disassembly of saccharolipid·peptide complexes. Kdo2-lipid A (KLA) is used as a model saccharolipid to evaluate complexation with a series of cationic peptides (melittin and three analogs). Collisional activation of the KLA·peptide complexes results in the disruption of electrostatic interactions, resulting in apo-sequence ions with shifts in the distribution of ions compared to the fragmentation patterns of the apo-peptides. UVPD of the KLA·peptide complexes results in both apo- and holo-sequence ions of the peptides, the latter in which the KLA remains bound to the truncated peptide fragment despite cleavage of a covalent bond of the peptide backbone. Mapping both the N- and C-terminal holo-product ions gives insight into the peptide motifs (specifically an electropositive KRKR segment and a proline residue) that are responsible for mediating the electrostatic interactions between the cationic peptides and saccharolipid.

Transparent Carbon Ultramicroelectrode Arrays for the Electrochemical Detection of a Bacterial Warfare Toxin, Pyocyanin.

Pyocyanin is a virulence factor produced as a secondary metabolite by the opportunistic human pathogen, Pseudomonas aeruginosa. Fast and direct detection of pyocyanin is of importance as it could provide important insights regarding P. aeruginosa's virulence mechanisms. Here, we present an electrochemical sensing platform of redox-active pyocyanin using transparent carbon ultramicroelectrode arrays (T-CUAs), which were made using a previously reported simple fabrication process ( Duay et al. Anal. Chem. 2015 , 87 , 10109 ). Square-wave voltammetry was used to quantify pyocyanin concentrations on T-CUAs with and without chitosan gold nanoparticles (CS/GNP) and planar transparent macroelectrodes (T-Macro). The response time (RT), limit of detection (LOD), and linear dynamic range (LDR) differ for each electrode type due to subtle influences in how the detectable signal varies in relation to the charging time and resistive and capacitive noise. In general lower LODs can be achieved at the consequence of smaller LDRs. The LOD for T-Macro was 0.75 ± 0.09 µM with a LDR of 0.75-25 µM, and the LOD for the CS/GNP 1.54 T-CUA was determined to be 1.6 ± 0.2 µM with a LDR of 1-100 µM, respectively. The LOD for the 1.54T-CUA with a larger LDR of 1-250 µM was 1.0 ± 0.3 µM. These LODs and LDRs fall within the range of PYO concentrations for a variety of in vitro and in vivo cellular environments and offer promise of the application of T-CUAs for the quantitative study of biotoxins, quorum sensing, and pathogenesis. Finally, we demonstrate the successful use of T-CUAs for the electrochemical detection of pyocyanin secreted from P. aeruginosa strains while optically imaging the cells. The secreted pyocyanin levels from two bacterial strains, PA11 and PA14, were measured to have concentrations of 45 ± 5 and 3 ± 2 µM, respectively.

Gold Nanoparticle Modified Transparent Carbon Ultramicroelectrode Arrays for the Selective and Sensitive Electroanalytical Detection of Nitric Oxide.

Transparent carbon ultramicroelectrode arrays (T-CUAs) were made using a previously reported facile fabrication method (Duay et al. Anal. Chem. 2015, 87, 10109). Two modifications introduced to the T-CUAs were examined for their analytical response to nitric oxide (NO•). The first modification was the application of a cellulose acetate (CA) gas permeable membrane. Its selectivity to NO• was extensively characterized via chronoamperometry, electrochemical impedance spectroscopy (EIS), and atomic force microscopy (AFM). The thickness of the CA membrane was determined to be 100 nm and 88 ± 15 nm using AFM and EIS, respectively. Furthermore, the partition and diffusion coefficients of NO• within the CA membrane were determined to be 0.0500 and 2.44 × 10-13 m2/s using EIS measurements. The second modification to the 1.54T-CUA was the introduction of chitosan and gold nanoparticles (CS/GNPs) to enhance its catalytic activity, sensitivity, and limit of detection (LOD) to NO•. Square wave voltammetry was used to quantify the NO• concentration at the CA membrane covered 1.54T-CUA with and without CS/GNPs; the LODs were determined to be 0.2 ± 0.1 and 0.44 ± 0.02 µM (S/N = 3), with sensitivities of 9 ± 9 and 1.2 ± 0.4 nA/µM, respectively. Our results indicate that this modification to the arrays results in a significant catalytic enhancement to the electrochemical oxidation of NO•. Hence, these electrodes allow for the in situ mechanistic and kinetic characterization of electrochemical reactions with high electroanalytical sensitivity.

Real-time monitoring of quorum sensing in 3D-printed bacterial aggregates using scanning electrochemical microscopy.

Microbes frequently live in nature as small, densely packed aggregates containing ∼10(1)-10(5) cells. These aggregates not only display distinct phenotypes, including resistance to antibiotics, but also, serve as building blocks for larger biofilm communities. Aggregates within these larger communities display nonrandom spatial organization, and recent evidence indicates that this spatial organization is critical for fitness. Studying single aggregates as well as spatially organized aggregates remains challenging because of the technical difficulties associated with manipulating small populations. Micro-3D printing is a lithographic technique capable of creating aggregates in situ by printing protein-based walls around individual cells or small populations. This 3D-printing strategy can organize bacteria in complex arrangements to investigate how spatial and environmental parameters influence social behaviors. Here, we combined micro-3D printing and scanning electrochemical microscopy (SECM) to probe quorum sensing (QS)-mediated communication in the bacterium Pseudomonas aeruginosa. Our results reveal that QS-dependent behaviors are observed within aggregates as small as 500 cells; however, aggregates larger than 2,000 bacteria are required to stimulate QS in neighboring aggregates positioned 8 µm away. These studies provide a powerful system to analyze the impact of spatial organization and aggregate size on microbial behaviors.

Three-Dimensional Printing of Photoresponsive Biomaterials for Control of Bacterial Microenvironments.

Advances in microscopic three-dimensional (µ3D) printing provide a means to microfabricate an almost limitless range of arbitrary geometries, offering new opportunities to rapidly prototype complex architectures for microfluidic and cellular applications. Such 3D lithographic capabilities present a tantalizing prospect for engineering micromechanical components, for example, pumps and valves, for cellular environments composed of smart materials whose size, shape, permeability, stiffness, and other attributes might be modified in real time to precisely manipulate ultralow-volume samples. Unfortunately, most materials produced using µ3D printing are synthetic polymers that are inert to biologically tolerated chemical and light-based triggers and provide low compatibility as materials for cell culture and encapsulation applications. We previously demonstrated feasibility for µ3D printing environmentally sensitive, microstructured protein hydrogels that undergo volume changes in response to pH, ionic strength, and thermal triggers, cues that may be incompatible with sensitive chemical and biological systems. Here, we report the systematic investigation of photoillumination as a minimally invasive and remotely applied means to trigger morphological change in protein-based µ3D-printed smart materials. Detailed knowledge of material responsiveness is exploited to develop individually addressable "smart" valves that can be used to capture, "farm", and then dilute motile bacteria at specified times in multichamber picoliter edifices, capabilities that offer new opportunities for studying cell-cell interactions in ultralow-volume environments.

3D printing of microscopic bacterial communities.

Bacteria communicate via short-range physical and chemical signals, interactions known to mediate quorum sensing, sporulation, and other adaptive phenotypes. Although most in vitro studies examine bacterial properties averaged over large populations, the levels of key molecular determinants of bacterial fitness and pathogenicity (e.g., oxygen, quorum-sensing signals) may vary over micrometer scales within small, dense cellular aggregates believed to play key roles in disease transmission. A detailed understanding of how cell-cell interactions contribute to pathogenicity in natural, complex environments will require a new level of control in constructing more relevant cellular models for assessing bacterial phenotypes. Here, we describe a microscopic three-dimensional (3D) printing strategy that enables multiple populations of bacteria to be organized within essentially any 3D geometry, including adjacent, nested, and free-floating colonies. In this laser-based lithographic technique, microscopic containers are formed around selected bacteria suspended in gelatin via focal cross-linking of polypeptide molecules. After excess reagent is removed, trapped bacteria are localized within sealed cavities formed by the cross-linked gelatin, a highly porous material that supports rapid growth of fully enclosed cellular populations and readily transmits numerous biologically active species, including polypeptides, antibiotics, and quorum-sensing signals. Using this approach, we show that a picoliter-volume aggregate of Staphylococcus aureus can display substantial resistance to ß-lactam antibiotics by enclosure within a shell composed of Pseudomonas aeruginosa.

Transparent carbon ultramicroelectrode arrays: figures of merit for quantitative spectroelectrochemistry for biogenic analysis of reactive oxygen species.

Opaque and transparent carbon ultramicro- to nanoelectrode arrays were made using a previously reported facile versatile fabrication method (Duay et al. Anal. Chem. 2014, 86, 11528). First, opaque carbon ultramicroelectrode arrays (CUAs) were characterized for their analytical response to hydrogen peroxide (H2O2) oxidation using cyclic voltammetry. The alumina blocking layer was found to contribute to the noise and thus had undesirable effects on the array's limit of detection (LOD) for H2O2 at fast scan rates. Nonetheless, at slower scan rates (ν ≤ 250 mV s(-1)), the LODs for H2O2 for both opaque (O-CUAs) and transparent arrays (T-CUAs) were found to be lower than previously reported levels for array-based UMEs. LODs as low as 35 nM H2O2 are obtained for T-CUA at a 2.5 mV s(-1) scan rate. Furthermore, the transparent arrays were analyzed for their spectroelectrochemical response during the oxidation/reduction of ferrocenemethanol. Results showed very good correlation between the optical and electrochemical response for ferrocenemethanol at a UV wavelength of 254 nm. Thus, these electrodes allow for the in situ mechanistic and kinetic characterization of heterogeneous electrochemical and intermediate homogeneous chemical reactions with high electroanalytical sensitivity, low detection limits, and wide dynamic range.

3D-printed microfluidic microdissector for high-throughput studies of cellular aging.

Due to their short lifespan, rapid division, and ease of genetic manipulation, yeasts are popular model organisms for studying aging in actively dividing cells. To study replicative aging over many cell divisions, individual cells must be continuously separated from their progeny via a laborious manual microdissection procedure. Microfluidics-based soft-lithography devices have recently been used to automate microdissection of the budding yeast Saccharomyces cerevisiae. However, little is known about replicative aging in Schizosaccharomyces pombe, a rod-shaped yeast that divides by binary fission and shares many conserved biological functions with higher eukaryotes. In this report, we develop a versatile multiphoton lithography method that enables rapid fabrication of three-dimensional master structures for polydimethylsiloxane (PDMS)-based microfluidics. We exploit the rapid prototyping capabilities of multiphoton lithography to create and characterize a cell-capture device that is capable of high-resolution microscopic observation of hundreds of individual S. pombe cells. By continuously removing the progeny cells, we demonstrate that cell growth and protein aggregation can be tracked in individual cells for over ~100 h. Thus, the fission yeast lifespan microdissector (FYLM) provides a powerful on-chip microdissection platform that will enable high-throughput studies of aging in rod-shaped cells.

Generating arbitrary chemical patterns for multipoint dosing of single cells.

Living cells reside within anisotropic microenvironments that orchestrate a broad range of polarized responses through physical and chemical cues. To unravel how localized chemical signals influence complex behaviors, tools must be developed for establishing patterns of chemical gradients that vary over subcellular dimensions. Here, we present a strategy for addressing this critical need in which an arbitrary number of chemically distinct, subcellular dosing streams are created in real time within a microfluidic environment. In this approach, cells are cultured on a thin polymer membrane that serves as a barrier between the cell-culture environment and a reagent chamber containing multiple reagent species flowing in parallel under low Reynolds number conditions. Focal ablation of the membrane creates pores that allow solution to flow from desired regions within this reagent pattern into the cell-culture chamber, resulting in narrow, chemically distinct dosing streams. Unlike previous dosing strategies, this system provides the capacity to tailor arbitrary patterns of reagents on the fly to suit the geometry and orientation of specific cells.

Laser-imprinting of micro-3D printed protein hydrogels enables real-time independent modification of substrate topography and elastic modulus.

Independent control over the Young's modulus and topography of a hydrogel cell culture substrate is necessary to characterize how attributes of its adherent surface affect cellular responses. Arbitrary, real-time manipulation of these parameters at the micron scale would further provide cellular biologists and bioengineers with the tools to study and control numerous highly dynamic behaviors including cellular adhesion, motility, metastasis, and differentiation. Although physical, chemical, thermal, and light-based strategies have been developed to influence Young's modulus and topography of hydrogel substrates, independent control of these physical attributes has remained elusive, spatial resolution is often limited, and features commonly must be pre-patterned. We recently reported a strategy in which biomaterials having specified three-dimensional (3D) morphologies are micro-3D printed in a two-step process: laser-scanning bioprinting of a protein-based hydrogel, followed by biocompatible hydrogel re-scanning to create microscale imprinted features at user-defined times. In this approach, a pulsed near-infrared laser beam is focused within the printed hydrogel to promote matrix contraction through multiphoton crosslinking, where scanning the laser focus projects a user-defined topographical pattern on the surface without subjecting the hydrogel-solution interface to damaging light intensities. Here, we extend this strategy, demonstrating the ability to decouple dynamic topographical changes from changes in hydrogel Young's modulus at the substrate surface by increasing the isolation distance between the surface and re-scanning planes. Using atomic force microscopy, we show that robust topographic changes can be imposed without altering the Young's modulus measured at the substrate surface by scanning at a depth of greater than ~6 µm. Transmission electron microscopy of hydrogel thin sections reveals changes to hydrogel porosity and density distribution within scanned regions, and that such changes to the hydrogel matrix are highly localized to regions of laser exposure. These results represent valuable new capabilities for deconvolving the effects of substrate dynamic physical attributes on the behavior of adherent cells.

Multiphoton fabrication of chemically responsive protein hydrogels for microactuation.

We report a method for creating stimuli-responsive biomaterials in which scanning nonlinear excitation is used to photocrosslink proteins at submicrometer 3D coordinates. Proteins with differing hydration properties can be combined to achieve tunable volume changes that are rapid and reversible in response to changes in chemical environment. Protein matrices having arbitrary 3D topographies and definable density gradients over micrometer dimensions provide the ability to effect rapid (<1 sec) and precise mechanical manipulations by means of changes in hydrogel size and shape, and applicability of these materials to cell biology is shown through the fabrication of responsive bacterial cages.

Dynamic remodeling of subcellular chemical gradients using a multi-directional flow device.

Elucidation of the mechanisms by which external chemical cues regulate polarized cellular behaviors requires tools that can rapidly recast chemical landscapes with subcellular resolution. Here, we describe an approach for creating steep microscopic gradients of cellular effectors at any desired position in culture that can be reoriented rapidly to evaluate dynamic responses. In this approach, micrometre pores are ablated in a membrane that supports cell adherence, allowing dosing reagent from an underlying reservoir to enter the cell-culture flow chamber as sharp streams that are directed at subcellular targets by using a system of paired sources and drains to specify flow direction. This tool substantially extends capabilities for chemical interaction with cultured cells, enabling investigations of chemotaxis via precise placement and reorientation of peptide gradients formed at the boundaries of dosing streams. These studies demonstrate that neutrophil precursor cells can repolarize and redirect their migration paths using morphological responses that depend on the subcellular localization of chemoattractant gradients.

A highly selective low-background fluorescent imaging agent for nitric oxide.

We introduce a novel sensing mechanism for nitric oxide (NO) detection with a particular easily synthesized embodiment (NO(550)), which displays a rapid and linear response to NO with a red-shifted 1500-fold turn-on signal from a dark background. Excellent selectivity was observed against other reactive oxygen/nitrogen species, pH, and various substances that interfere with existing probes. NO(550) crosses cell membranes but not nuclear membranes and is suitable for both intra- and extracellular NO quantifications. Good cytocompatibility was found during in vitro studies with two different cell lines. The high specificity, dark background, facile synthesis, and low pH dependence make NO(550) a superior probe for NO detection when used as an imaging agent.

Multiphoton lithography using a high-repetition rate microchip laser.

Multiphoton lithography (MPL) provides a means to create prototype, three-dimensional (3D) materials for numerous applications in analysis and cell biology. A major impediment to the broad adoption of MPL in research laboratories is its reliance on high peak-power light sources, a requirement that typically has been met using expensive femtosecond titanium:sapphire lasers. Development of affordable microchip laser sources has the potential to substantially extend the reach of MPL, but previous lasers have provided relatively low pulse repetition rates (low kilohertz range), thereby limiting the rate at which microforms could be produced using this direct-write approach. In this report, we examine the MPL capabilities of a new, high-repetition-rate (36.6 kHz) microchip Nd:YAG laser. We show that this laser enables an approximate 4-fold decrease in fabrication times for protein-based microforms relative to the existing state-of-the-art microchip source and demonstrate its utility for creating complex 3D microarchitectures.

2-Amino-3'-dialkylaminobiphenyl-based fluorescent intracellular probes for nitric oxide surrogate N2O3.

Fluorescent probes for nitric oxide (NO), or more frequently for its oxidized surrogate dinitrogen trioxide (N2O3), have enabled scientists to study the contributions of this signaling molecule to many physiological processes. Seeking to improve upon limitations of other probes, we have developed a family of fluorescent probes based on a 2-amino-3'-dialkylaminobiphenyl core. This core condenses with N2O3 to form benzo[c]cinnoline structures, incorporating the analyte into the newly formed fluorophore, which results in product fluorescence with virtually no background contribution from the initial probe. We varied the substituents in the core in order to optimize both the reactivity of the probes with N2O3 and their cinnoline products' fluorescence wavelengths and brightness. The top candidates were then applied to cultured cells to verify that they could respond to NO within cellular milieus, and the top performer, NO530, was compared with a "gold standard" commercial probe, DAF-FM, in a macrophage-derived cell line, RAW 264.7, stimulated to produce NO. NO530 demonstrated similar or better sensitivity and higher selectivity for NO than DAF, making it an attractive potential alternative for NO tracking in various applications.

High-throughput design of microfluidics based on directed bacterial motility.

Use of motile cells as sensors and actuators in microfabricated devices requires precise design of interfaces between living and non-living components, a process that has relied on slow revision of device architectures as prototypes are sequentially evaluated and re-designed. In this report, we describe a microdesign and fabrication approach capable of iteratively refining three-dimensional bacterial interfaces in periods as short as 10 minutes, and demonstrate its use to drive fluid transport by harnessing flagellar motion. In this approach, multiphoton excitation is used to promote protein photocrosslinking in a direct-write procedure mediated by static and dynamic masking, with the resultant microstructures serving to capture motile bacteria from the surrounding fluidic environment. Reproducible steering and patterning of flagellated E. coli cells drive microfluidic currents capable of guiding micro-objects on predictable trajectories with velocities reaching 150 microm s(-1) and achieving bulk flow through microchannels. We show that bacteria can be dynamically immobilized at specified positions, an approach that frees such devices from limitations imposed by the functional lifetime of cells. These results provide a foundation for the development of sophisticated microfluidic devices powered by cells.

Microsecond analysis of transient molecules using bi-directional capillary electrophoresis.

We demonstrate the feasibility for minimizing electrophoretic analysis times of transient chemical species by inducing nascent, oppositely charged photochemical products to migrate in opposite directions from their point of creation. In this approach, separate probe sites are positioned within an electrophoretic channel both upfield and downfield from a photoreaction site formed by high-numerical-aperture optics, with positively charged (and in some cases neutral) components migrating toward one probe site and negatively charged species migrating in the opposite direction, toward the second probe site. As a proof-of-concept, fluorescent photoproducts of the hydroxyindoles, 5-hydroxytryptamine (serotonin), 5-hydroxytrptophan, and 5-hydroxyindole-2-carboxylic acid, are formed within a geometrically modified capillary and are transported electrophoretically and electroosmotically to probe sites several micrometers away. Although it is possible to detect all components in a single channel, or to use a two-channel imaging approach to independently detect positive and negative components, we have found the most rapid analysis approach involves a protocol in which laser light is alternately directed to opposing probe sites at high frequency (1 kHz), a strategy that allows positive and negative species to be detected with no cross-talk, even when components have overlapping detection times. Fluorescence-signal-averaging is performed on each temporal channel via summation of the two sequences of interdigitized electrophoretic traces. This approach allows photoproducts to be detected free from interferences from oppositely charged species, enabling positive and negative species in a mixture to be analyzed electrophoretically in ca. 6 micros, a period several-fold faster than was previously feasible using unidirectional electrophoresis.

Microreplication and design of biological architectures using dynamic-mask multiphoton lithography.

A strategy for rapidly printing three-dimensional (3D) microscopic replicas using multiphoton lithography directed by a dynamic electronic mask is reported. Morphological descriptions of 3D structures are encoded as stacks of 2D slices created from tomographic and computer-designed instruction sets. In this manner, digital images serve as input for a sequence of reflective photomasks on a digital micromirror device to direct replication of a structure. By scanning a laser focus across the face of the intrinsically aligned masks, tomographic and computed data can be translated into protein-based 3D reproductions with submicrometer feature sizes within 1 min. This straightforward and highly versatile approach may provide improved routes for the development of 3D cellular scaffolds, rapid prototyping of microanalytical devices, and production of custom tissue replacements.