Co-ordinated detection of microparticles using tunable resistive pulse sensing and fluorescence spectroscopy

Tunable resistive pulse sensing (TRPS) has emerged as a useful tool for particle-by-particle detection and analysis of microparticles and nanoparticles as they pass through a pore in a thin stretchable membrane. We have adapted a TRPS device in order to conduct simultaneous optical measurements of particles passing through the pore. High-resolution fluorescence emission spectra have been recorded for individual 1.9 μm diameter particles at a sampling period of 4.3 ms. These spectra are time-correlated with RPS pulses in a current trace sampled every 20 μs. The flow rate through the pore, controlled by altering the hydrostatic pressure, determines the rate of particle detection. At pressures below 1 kPa, more than 90% of fluorescence and RPS events were matching. At higher pressures, some peaks were missed by the fluorescence technique due to the difference in sampling rates. This technique enhances the particle-by-particle specificity of conventional RPS measurements and could be useful for a range of particle characterization and bioanalysis applications.     

光纤生物传感器的传感机制

本文综述了光学生物传感器的传感机制,按照其光学现象来进行传感可分为反应池光吸收型、敏感膜光反射与散射型、荧光型与磷光型传感,分别综述了它们的传感原理、特点及实际应用。     

On-chip microfluidic systems for determination of L-glutamate based on enzymatic recycling of substrate

Two microfluidic systems have been developed for specific analysis of L-glutamate in food based on substrate recycling fluorescence detection. L-glutamate dehydrogenase and a novel enzyme, D-phenylglycine aminotransferase, were covalently immobilized on (i) the surface of silicon microchips containing 32 porous flow channels of 235 μm depth and 25 μm width and (ii) polystyrene Poros™ beads with a particle size of 20 μm. The immobilized enzymes recycle L-glutamate by oxidation to 2-oxoglutarate followed by the transfer of an amino group from D-4-hydroxyphenylglycine to 2-oxoglutarate. The reaction was accompanied by reduction of nicotinamide adenine dinucleotide (NAD⁺) to NADH, which was monitored by fluorescence detection (ε_ex=340 nm, ε_em=460 nm). First, the microchip-based system, L-glutamate was detected within a range of 3.1–50.0 mM. Second, to be automatically determined, sequential injection analysis (SIA) with the bead-based system was investigated. The bead-based system was evaluated by both flow injection analysis and SIA modes, where good reproducibility for L-glutamate calibrations was obtained (relative standard deviation of 3.3% and 6.6%, respectively). In the case of SIA, the beads were introduced and removed from the microchip automatically. The immobilized beads could be stored in a 20% glycerol and 0.5 mM ethylenediaminetetraacetic acid solution maintained at a pH of 7.0 using a phosphate buffer for at least 15 days with 72% of the activity remaining. The bead-based system demonstrated high selectivity, where L-glutamate recoveries were between 91% and 108% in the presence of six other L-amino acids tested.     

Single molecule analysis of bacterial polymerase chain reaction products in submicrometer fluidic channels

Laser induced fluorescence in submicrometer fluidic channels was used to characterize the synthesis of polymerase chain reaction (PCR) products from a model bacterial system in order to explore the advantages and limitations of on chip real time single molecule PCR analysis. Single oligonucleotide universal bacterial primers and PCR amplicons from the 16S rDNA of Thermobifida fusca (325 bp) were directly detected at all phases of the reaction with low sample consumption and without post-amplification purification or size screening. Primers were fluorescently labeled with single Alexa Fluor 488 or Alexa Fluor 594 fluorophores, resulting in double labeled, two color amplicons. PCR products were driven electrokinetically through a fused silica channel with a 250 nm by 500 nm rectangular cross section. Lasers with 488 nm and 568 nm wavelengths were focused and overlapped on the channel for fluorescence excitation. All molecules entering the channel were rapidly and uniformly analyzed. Photon burst analysis was used to detect and identify individual primers and amplicons, and fluorescence correlation and cross-correlation spectroscopy were used to account for analyte flow speed. Conventional gel and capillary electrophoresis were also used to characterize the PCR amplification, and the results of differences in detection sensitivity and analyte discrimination were examined. Limits were imposed by the purity and labeling efficiency of the PCR reagents, which must be improved in parallel with increases in detection sensitivity.     

A droplet-based novel approach for viable and low volume consumption surface plasmon resonance bio-sensing inside a polydimethylsiloxane microchip

Over the course of last two decades, surface plasmon resonance (SPR) has emerged as a viable candidate for label-free detection and characterization for a large pool of biological interactions, ranging from hybridization of oligonucleotides to high throughput drug-screening. Conventional SPR bio-sensing involves a step-response method where the SPR sensorgram in response to a switched sequential flow of analyte and buffer is plotted in real-time and fitted to an exponential curve to extract the associative and dissociative reaction rates. Such measurement schemes involve continuous flow conditions where a substantial reagent volume is consumed and is subject to dispersive mixing at flow switching zones. In this paper, we demonstrate a new plug-train SPR technique in a microfluidic chip that separates and singulates solvent plugs in analyte and buffer by an immiscible air phase. Bio-samples are first discretized within plug droplets with volumes in order of few hundred nanoliters or less followed by pressure-driven transport onto SPR sensing sites of this hydrophobically modified SPR microdevise. The kinetic constants k_a and k_d for a model protein-small molecule interaction pair are extracted from a plug-train signal and are shown to be in reasonable agreement with our previous reports.     

Microfluidic study of the chemotactic response of Escherichia coli to amino acids,signaling molecules and secondary metabolites

Quorum sensing and chemotaxis both affect bacterial behavior on the population level. Chemotaxis shapes the spatial distribution of cells, while quorum sensing realizes a cell-density dependent gene regulation. An interesting question is if these mechanisms interact on some level: Does quorum sensing, a density dependent process, affect cell density itself via chemotaxis? Since quorum sensing often spans across species, such a feedback mechanism may also exist between multiple species. We constructed a microfluidic platform to study these questions. A flow-free, stable linear chemical gradient is formed in our device within a few minutes that makes it suitable for sensitive testing of chemoeffectors: we showed that the amino acid lysine is a weak chemoattractant for Escherichia coli, while arginine is neutral. We studied the effect of quorum sensing signal molecules of Pseudomonas aeruginosa on E. coli chemotaxis. Our results show that N-(3-oxododecanoyl)-homoserine lactone (oxo-C12-HSL) and N-(butryl)-homoserine lactone (C4-HSL) are attractants. Furthermore, we tested the chemoeffector potential of pyocyanin and pyoverdine, secondary metabolites under a quorum sensing control. Pyocyanin is proved to be a weak attractant while pyoverdine are repellent. We demonstrated the usability of the device in co-culturing experiments, where we showed that various factors released by P. aeruginosa affect the dynamic spatial rearrangement of a neighboring E. coli population, while surface adhesion of the cells is also modulated.     

Numerical modeling of DNA-chip hybridization with chaotic advection

We present numerical simulations of DNA-chip hybridization, both in the “static” and “dynamical” cases. In the static case, transport of free targets is limited by molecular diffusion; in the dynamical case, an efficient mixing is achieved by chaotic advection, with a periodic protocol using pumps in a rectangular chamber. This protocol has been shown to achieve rapid and homogeneous mixing. We suppose in our model that all free targets are identical; the chip has different spots on which the probes are fixed, also all identical, and complementary to the targets. The reaction model is an infinite sink potential of width d_h, i.e., a target is captured as soon as it comes close enough to a probe, at a distance lower than d_h. Our results prove that mixing with chaotic advection enables much more rapid hybridization than the static case. We show and explain why the potential width d_h does not play an important role in the final results, and we discuss the role of molecular diffusion. We also recover realistic reaction rates in the static case.     

Graphdiyne-based metal atomic catalysts for synthesizing ammonia

Development of novel catalysts for nitrogen reduction at ambient pressures and temperatures with ultrahigh ammonia (NH₃) yield and selectivity is challenging. In this work, an atomic catalyst with separated Pd atoms on graphdiyne (Pd-GDY) was synthesized, which shows fascinating electrocatalytic properties for nitrogen reduction. The catalyst has the highest average NH₃ yield of 4.45 ± 0.30 mg_NH3 mg_Pd⁻¹ h⁻¹, almost tens of orders larger than for previously reported catalysts, and 100% reaction selectivity in neutral media. Pd-GDY exhibits almost no decreases in NH₃ yield and Faradaic efficiency. Density functional theory calculations show that the reaction pathway prefers to perform at the (Pd, C1, C2) active area because of the strongly coupled (Pd, C1, C2), which elevates the selectivity via enhanced electron transfer. By adjusting the p–d coupling accurately, reduction of self-activated nitrogen is promoted by anchoring atom selection, and side effects are minimized.     

Spatial concentration distribution analysis of cells in electrode-multilayered microchannel by dielectric property measurement

The spatial concentration distribution of cells in a microchannel is measured by combining the dielectric properties of cells with the specific structure of the electrode-multilayered microchannel. The dielectric properties of cells obtained with the impedance spectroscopy method includes the cell permittivity and dielectric relaxation, which corresponds to the cell concentration and structure. The electrode-multilayered microchannel is constructed by 5 cross-sections, and each cross-section contains 5 electrode-layers embedded with 16 micro electrodes. In the experiment, the dielectric properties of cell suspensions with different volume concentrations are measured with different electrode-combinations corresponding to different electric field distributions. The dielectric relaxations of different cell concentrations are compared and discussed with the Maxwell-Wagner dispersion theory, and the relaxation frequencies are analysed by a cell polarization model established based on the Hanai cell model. Moreover, a significant linear relationship with AC frequency dependency between relative permittivity and cell concentration was found, which provides a promising way to on-line estimate cell concentration in microchannel. Finally, cell distribution in 1 cross-section of the microchannel (X and Y directions) was measured with different electrode-combinations using the dielectric properties of cell suspensions, and cell concentration distribution along the microchannel (Z direction) was visualized at flowing state. The present cell spatial sensing study provides a new approach for 3 dimensional non-invasive online cell sensing for biological industry.     

Optofluidic membrane interferometer: An imaging method for measuring microfluidic pressure and flow rate simultaneously on a chip

We present a novel image-based method to measure the on-chip microfluidic pressure and flow rate simultaneously by using the integrated optofluidic membrane interferometers (OMIs). The device was constructed with two layers of structured polydimethylsiloxane (PDMS) on a glass substrate by multilayer soft lithography. The OMI consists of a flexible air-gap optical cavity which upon illumination by monochromatic light generates interference patterns that depends on the pressure. These interference patterns were captured with a microscope and analyzed by computer based on a pattern recognition algorithm. Compared with the previous techniques for pressure sensing, this method offers several advantages including low cost, simple fabrication, large dynamic range, and high sensitivity. For pressure sensing, we demonstrate a dynamic range of 0-10 psi with an accuracy of ±2% of full scale. Since multiple OMIs can be integrated into a single chip for detecting pressures at multiple locations simultaneously, we also demonstrated a microfluidic flow sensing by measuring the differential pressure along a channel. Thanks to the simple fabrication that is compatible with normal microfluidics, such OMIs can be easily integrated into other microfluidic systems for in situ fluid monitoring.     

Characterization of microfluidic mixing and reaction in microchannels via analysis of cross-sectional patterns

For the diagnosis of biochemical reactions, the investigation of microflow behavior, and the confirmation of simulation results in microfluidics, experimentally quantitative measurements are indispensable. To characterize the mixing and reaction of fluids in microchannel devices, we propose a mixing quality index (M_qi) to quantify the cross-sectional patterns (also called mixing patterns) of fluids, captured with a confocal-fluorescence microscope (CFM). The operating parameters of the CFM for quantification were carefully tested. We analyzed mixing patterns, flow advection, and mass exchange of fluids in the devices with overlapping channels of two kinds. The mixing length of the two devices derived from the analysis of M_qi is demonstrated to be more precise than that estimated with a commonly applied method of blending dye liquors. By means of fluorescence resonance-energy transfer (FRET), we monitored the hybridization of two complementary oligonucleotides (a FRET pair) in the devices. The captured patterns reveal that hybridization is a progressive process along the downstream channel. The FRET reaction and the hybridization period were characterized through quantification of the reaction patterns. This analytical approach is a promising diagnostic tool that is applicable to the real-time analysis of biochemical and chemical reactions such as polymerase chain reaction (PCR), catalytic, or synthetic processes in microfluidic devices.     

Microfluidic platform integrated with worm-counting setup for assessing manganese toxicity

We reported a new microfluidic system integrated with worm responders for evaluating the environmental manganese toxicity. The micro device consists of worm loading units, worm observing chambers, and a radial concentration gradient generator (CGG). Eight T-shape worm loading units of the micro device were used to load the exact number of worms into the corresponding eight chambers with the assistance of worm responders and doorsills. The worm responder, as a key component, was employed for performing automated worm-counting assay through electric impedance sensing. This label-free and non-invasive worm-counting technique was applied to the microsystem for the first time. In addition, the disk-shaped CGG can generate a range of stepwise concentrations of the appointed chemical automatically and simultaneously. Due to the scalable architecture of radial CGG, it has the potential to increase the throughput of the assay. Dopaminergic (DAergic) neurotoxicity of manganese on C. elegans was quantitatively assessed via the observation of green fluorescence protein-tagged DAergic neurons of the strain BZ555 on-chip. In addition, oxidative stress triggered by manganese was evaluated by the quantitative fluorescence intensity of the strain CL2166. By scoring the survival ratio and stroke frequency of worms, we characterized the dose- and time-dependent mobility defects of the manganese-exposed worms. Furthermore, we applied the microsystem to investigate the effect of natural antioxidants to protect manganese-induced toxicity.     

Plasmonic hotspots of dynamically assembled nanoparticles in nanocapillaries: Towards a micro ribonucleic acid profiling platform

Plasmonic hot spots, generated by controlled 20-nm Au nanoparticle (NP) assembly, are shown to suppress fluorescent quenching effects of metal NPs, such that hair-pin FRET (Fluorescence resonance energy transfer) probes can achieve label-free ultra-sensitive quantification. The micron-sized assembly is a result of intense induced NP dipoles by focused electric fields through conic nanocapillaries. The efficient NP aggregate antenna and the voltage-tunable NP spacing for optimizing hot spot intensity endow ultra-sensitivity and large dynamic range (fM to pM). The large shear forces during assembly allow high selectivity (2-mismatch discrimination) and rapid detection (15 min) for a DNA mimic of microRNA.Irregular expressions of a panel of microRNAs (miRNA) in blood and other physiological fluids may allow early diagnosis of many diseases, including cancer and cardiovascular diseases.¹ However, quantifying all relevant miRNAs (out of 1000), with similar sequences over 22 bases² and large variations in expression level (as much as 100 fold) at small copy numbers, requires a new molecular diagnostic platform with high-sensitivity, high-selectivity, and large dynamic range. Current techniques for miRNA profiling, such as Northern blotting,³ microarray-based hybridization,⁴ and real-time quantitative polymerase chain reaction⁵ are expensive and complex. A simple and rapid miRNA array would allow broad distribution of molecular diagnostic devices for cancer and chronic diseases, eventually into homes for frequent prescreening of many diseases.At their low concentrations in untreated samples, optical sensing of miRNA is most promising. Plasmonically excited Raman scattering (SERS) and fluorescence sensors from metallic nanoparticles (NPs) or surfaces have enhanced the sensitivity of optical molecular sensors by orders of magnitude.^{6, 7, 8, 9} However, probe-less SERS sensing or fluorescent sensing of unlabeled targets are insufficiently specific for miRNA targets in heterogeneous samples. Plasmonic detection is also very compatible with FRET probes whose donor dye offers small light sources to excite fluorescently labelled targets upon hybridization.^{7, 10}A particular family of FRET reporters does offer label-free sensing: hairpin oligo probes whose end-tagged fluorophores are quenched by the Au NP to which they are functionalized.¹¹ The fluorescent signal is only detected when the hairpin is broken by the hybridizing target nucleic acid or protein (for an aptamer probe), and the more rigid paired segment separates the end fluorophore from the quenching surface to produce a fluorescent signal. It is often hoped that plasmonics on the metal surface will enhance the intensity to overcome the quenching effect, if the linearized hairpin is within the NP plasmonic penetration length. However, since fluorescent quenching decays slowly (linearly) with fluorophore-metal spacing¹⁰ whereas the plasmonic intensity decays exponentially from a flat surface, careful experimentation shows that quenching dominates and the hairpin probe actually produces a larger intensity on non-metallic surfaces,¹⁰ on which it can not function as a label-free probe. Hence, only μM limit-of-detection (LOD) has been achieved with this technique on single NPs or on flat metal surfaces,¹² with expensive laser excitation and confocal detection.Plamonic hot spots formed between metal nanostructures and sharp nanocones can further amplify the plasmonic field.^{13, 14} The hot spot intensity decays algebraically with respect to the separation or cone tip distance and hence should dominate the linear decay of the metal quenching effect at some optimum separation.¹⁵ It is hence possible that plasmonic hot spots may allow much lower LOD with inexpensive optical instruments—ideally light-emitting diode light source and miniature camera. However, the dimension of the gaps, cones, and wedges needs to be at nanoscale, and the cost is now transferred to fabrication of such hot-spot substrates like bow-ties, double crescents, bull-eyes, etc.¹⁶ Low-cost wet-etching techniques for addressable nanocones that sustain converging plasmonic hot spots¹⁷ have been reported but the fabricated nanocones are often too non-uniform to allow precise quantification. NP monolayers have been shown to exhibit plasmonic hot spots and fluorescence enhancement.^{18, 19} However, the enhancement only occurs within a range of spacing between aggregated NPs, which is difficult to control and the location or even the existence of the hotspots are not known a priori.Higher sensitivity is expected if a minimum number of NPs are used in an assembly at a known location and if the NP assembly can produce crystal-like aggregates with controllable NP spacing. Induced DC and AC NP dipoles (related to dielectrophoresis) have been used to assemble NP crystals by embedded micro-electrodes to provide the requisite high field.^{20, 21} The resulting NP crystals are ideal for plasmonic hot spots, since the spacing of the regimented NP crystal can be controlled by the applied voltage. Conic nanocapillaries^{22, 23} will be used here for such field-induced NP assembly because the submicron-tip can focus the electric field into sufficient high intensity for NP assembly without embedded-electrodes. Because the field is highest at the tip due to field focusing, the micron-sized crystal would be confined to a small volume, which will be shown to be less than typical confocal volumes, at a known location. So long as the hotspots are regimented, the quantification of target molecules is determined by the total fluorescent intensity and is hence insensitive to the exact geometry of the nanocapillary.Fluorescent microscope equipped with tungsten lamp light source and normal CCD camera from Q Imaging were used for simultaneous optical and ion current measurements, as shown in Fig. ​Fig.1a.1a. The nanocapillaries were pulled from commercial glass capillaries using laser-assisted capillary puller. SEM image of a typical pulled glass nanocapillary in Fig. ​Fig.1b1b shows an inner diameter of 111 nm and cone angle of 7.3°. The capillary was inserted into a Polydimethylsiloxane chip with two reservoirs. The 20 nm Au NPs, functionalized with fluorescently labelled dsDNA, were injected into the base reservoir. With SEM imaging (Fig. S3 in the supplementary material²⁴), the functionalized DNA is found to prevent NP aggregation even in high ionic-strength Phosphate buffered saline buffer. The NP solution is then driven into the capillary through the tip by applying a positive voltage. Fig. ​Fig.1c1c shows the ion current evolution over 2 h at +1 V packing voltage. The ion current increases rapidly in the first 10 min, then at a much slower rate. The rise of current indicates assembly of conductive Au NP assembly at the tip. This was confirmed by the strong fluorescence signal at the tip region during the packing process (inset of Fig. ​Fig.1c).1c). The one-micron region (corresponding to roughly an aggregate volume of one attoliter) near the capillary tip shows a fluorescence signal after 1 min and also appeared as a dark spot in the transmission image (supplementary material, Fig. S1²⁴). This spot darkens with longer packing time but does not grow in size, consistent with the monotonically increasing ion current with increased packing density of the NP assembly. As contrast, a strong fluorescence appeared after only 1 min of packing, but the signal became weaker after 15 min (supplementary material, Fig. S1²⁴). This reduction in fluorescence is not due to bleaching of fluorophores because we took 2 images in 15 min at 5 s exposure each and control experiments show significant bleaching only beyond an exposure time of 100 s (see supplementary material).²⁴ Instead, the non-monotonic dependence of the fluorescence intensity with respect to time is because of the optimal hotspot spacing for highest plasmonic intensity at about 5–20 nm,^{25, 26, 27} which is reached at about 10 min.Open in a separate windowFigure 1Plasmonic hotspots generated at the tip of a nano-capillary. (a) Schematic of the experimental set up. (b) SEM image of glass nanocapillary shows opening at the tip with a diameter of 111 nm. (c) Current evolution during packing of fluorescently labeled gold particles at +1 V. Inset shows strong fluorescence only after 1 min of packing.The FRET probe is designed to exploit the plasmonic hotspot.²⁴ We first electrophoretically drove the target molecules in the tip side reservoir into the nano-capillary by applying a negative voltage of −1 V. During this process, the targets are trapped within the capillary and hybridize with the hairpin probes on the Au NP in the nanocapillary. Fluorescence of the unquenched hybridized probes is too weak to be detected by our detector as shown in Fig. ​Fig.2b.2b. A reverse positive voltage of +1 V was then applied to the capillary to pack the Au NPs to the tip. Due to plasmonic hot spots of aggregated gold nanoparticles, the fluorescence signal is significantly enhanced at the tip and can be detected by our CCD camera, as shown in Fig. ​Fig.2c2c.Open in a separate windowFigure 2(a) Schematics of designed hairpin probe on gold particle. (b) Before packing gold particles, probe fluorescence signal was too weak to be detect. (c) After packing for 3 minutes, a strong fluorescence signal appears at the NP aggregate. (d) Normalized intensity (average of all pixels above a threshold (15 au) normalized with respect to the average over all pixels (with 0-250 au)) as a function of packing voltage for different samples. Black, 1 nM target ; blue, 10 pM target; purple, 10 nM 2-mismatch non-target. (e) Intensity dependence on target concentration. Measured normalized intensity before packing (black) and after packing (red), for three independent experiments with different nano-capillaries at each concentration. NT stands for non-target at 10 nM as a reference.For the same packing time, the fluorescence intensity increases initially but saturates after 10 min time of trapping (supplementary material, Fig. S2(a)²⁴). Over 10 min of trapping with a negative voltage, we found the fluorescence intensity exhibits a maximum at a packing time of 3 min (supplementary material, Fig. S2(b)²⁴). In later experiments, we used 10 min trapping time and 3 min packing time as standards.Fig. ​Fig.2d2d shows the fluorescence intensity is sensitive to the positive packing voltage at different concentration of target and non-target molecules. For target samples (1 nM and 10pM), the optimal voltage is about 1 V. We suspect that with larger voltage, the NPs are packed too tightly such that the NP spacing is smaller than the optimal distance for plasmonic hotspots. The fluorescence intensity for a nontarget with two mismatches is 7 times lower than the target even with a 10 times higher concentration (10 nM). Moreover, the optimal voltage for the non-target miRNA is reduced to 0.5 V instead 1 V for the target miRNA. Strong shear during electrophoretic packing has probably endowed this high selectivity.²⁰Using the protocol above, the LOD and dynamic range of the target was determined (Fig. ​(Fig.2e).2e). The intensity at each concentration is measured with three independent experiments with different nanocapillaries to verify insensitivity with respect to the nanocapillary. The intensity increases monotonically with respect to the concentration from 1fM to 1pM. Beyond 1pM, the fluorescence signal saturates, presumably because all hairpin probes at the tip have been hybridized. At 1 fM, the fluorescent intensity is still well above the background measured from the non-target sample. Note both auto-fluorescence of gold nanoparticles and free diffusing non-target DNA molecules contribute to the background. Given the volume of tip side reservoir (∼50 μl), there are about 30 000 target molecules in the reservoir at 1 fM. However, with a short 10 min trapping time, we estimate only a small fraction of these molecules, less than 100, have been transferred from the tip reservoir into the nanocapillary.     

Studying enzymatic bioreactions in a millisecond microfluidic flow mixer

In this study, the pre-steady state development of enzymatic bioreactions using a microfluidic mixer is presented. To follow such reactions fast mixing of reagents (enzyme and substrate) is crucial. By using a highly efficient passive micromixer based on multilaminar flow, mixing times in the low millisecond range are reached. Four lamination layers in a shallow channel reduce the diffusion lengths to a few micrometers only, enabling very fast mixing. This was proven by confocal fluorescence measurements in the channel’s cross sectional area. Adjusting the overall flow rate in the 200 μm wide and 900 μm long mixing and observation channel makes it possible to investigate enzyme reactions over several seconds. Further, the device enables changing the enzyme/substrate ratio from 1:1 up to 3:1, while still providing high mixing efficiency, as shown for the enzymatic hydrolysis using β-galactosidase. This way, the early kinetics of the enzyme reaction at multiple enzyme/substrate concentrations can be collected in a very short time (minutes). The fast and easy handling of the mixing device makes it a very powerful and convenient instrument for millisecond temporal analysis of bioreactions.     

Enhancing conjugation rate of antibodies to carboxylates: Numerical modeling of conjugation kinetics in microfluidic channels and characterization of chemical over-exposure in conventional protocols by quartz crystal microbalance

This research reports an improved conjugation process for immobilization of antibodies on carboxyl ended self-assembled monolayers (SAMs). The kinetics of antibody/SAM binding in microfluidic heterogeneous immunoassays has been studied through numerical simulation and experiments. Through numerical simulations, the mass transport of reacting species, namely, antibodies and crosslinking reagent, is related to the available surface concentration of carboxyl ended SAMs in a microchannel. In the bulk flow, the mass transport equation (diffusion and convection) is coupled to the surface reaction between the antibodies and SAM. The model developed is employed to study the effect of the flow rate, conjugating reagents concentration, and height of the microchannel. Dimensionless groups, such as the Damköhler number, are used to compare the reaction and fluidic phenomena present and justify the kinetic trends observed. Based on the model predictions, the conventional conjugation protocol is modified to increase the yield of conjugation reaction. A quartz crystal microbalance device is implemented to examine the resulting surface density of antibodies. As a result, an increase in surface density from 321 ng/cm², in the conventional protocol, to 617 ng/cm² in the modified protocol is observed, which is quite promising for (bio-) sensing applications.Microfluidics have been implemented in various bio-medical diagnostic applications, such as immunosensors and molecular diagnostic devices.¹ In the last decade, a vast number of biochemical species has been detected by microfluidic-based immunosensors. Immunosensors are sensitive transducers which translate the antibody-antigen reaction to physical signals. The detection in an immunosensor is performed through immobilization of an antibody that is specific to the analyte of interest.² The antibody is often bound to the transducing surface of the sensor covered by self-assembled monolayers (SAMs). SAMs are organic materials that form a thin, packed and robust interface on the surface of noble metals like that of gold, suitable for biosensing applications.³ Thiolic SAMs have a “head” group that shows a high affinity to being chemisorbed onto a substrate, typically gold. The SAMs'' carboxylic functional group of the “tail” end can be linked to an amine terminal of an antibody to form a SAM/antibody conjugation.^3,4 The conjugation process is usually accomplished in the presence of carbodiimides, such as 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC). A yield increasing additive, N-Hydroxysuccinimide (NHS), is often used to enhance the surface loading density of the antibody.^4,5A typical reaction for coupling the carboxylic acid groups of SAMs with the amine residue of antibodies in the presence of EDC/NHS is depicted in Figure ​Figure11.⁴ NHS promotes the generation of an active NHS ester (k₂ reaction path). The NHS ester is capable of efficient acylation of amines, including antibodies (k₃ reaction path). As a result, the amide bond formation reaction, which typically does not progress efficiently, can be enhanced using NHS as a catalyst.⁴Open in a separate windowFIG. 1.NHS catalyzed conjugation of antibodies to carboxylic-acid ended SAMs through EDC mediation (Adapted from G. T. Hermanson, Bioconjugate Techniques, 2nd. Edition. Copyright 2008 by Elsevier⁴). EDC reacts with the carboxylic acid and forms o-acylisourea, a highly reactive chemical that reacts with NHS and forms an NHS ester, which quickly reacts with an amine (i.e., antibody) to form an amide.A number of groups have studied EDC/NHS mediated conjugation reactions such as the ones depicted in Figure ​Figure1.1. The general stoichiometry of the reaction involves a carboxylic acid (SAM), an amine (antibody), and EDC to produce the final amide (antibody conjugated SAM) and urea. However, the recommended concentration ratio of the crosslinking reagents inside the buffer, i.e., the ratio of EDC and NHS with respect to adsorbates and each other, varies from one study to another.⁶ The kinetics of the reactions outlined in Figure ​Figure11 have also been investigated,^4,6–8 but only in the absence of NHS for EDC or carboxylic acids in aqueous solutions.⁸ A relatively recent experimental study verified the catalytic role of the yield-increasing reagent N-hydroxybenzotriazole (HOBt), which acts similarly to NHS.⁷ In this study, the amide formation rate (k₃ reaction path, Figure ​Figure1)1) was found to be dependent on the concentration of the carboxylic acid and EDC in the buffer solution, and independent of the amine and catalyst reagent concentration. The same group also showed that the amide bond formation kinetics is controlled by the reaction between the carboxylic acid and the EDC to give the O-acylisourea, which they marked as the rate-determining step (k₁ reaction path, Figure ​Figure11).The k₁ reaction path, or the conjugation reaction, is usually a lengthy process and takes between 1 and 3 h.^4,9 Compared to k₁, the k₂ and ?k₃ reactions are considerably faster. Microfluidics has the potential to enhance the kinetics of these reactions using the flow-through mode.^10,11 This improvement occurs because while conventional methods rely only on diffusion as the primary reagent transport mode, microfluidics adds convection to better replenish the reagents to the reaction surfaces. However, there are many fundamental fluidic and geometrical parameters that might affect the process time and reagents consumption in a microfluidics environment, such as concentration of antibodies and reagents, flow rate, channel height, and final surface density of antibodies. A model that studies the kinetics of conjugation reaction against all these parameters would therefore be helpful for the optimization of this enhanced kinetics.There are a number of reports on numerical examination of the kinetics of binding reactions in microfluidic immunoassays.^12–15 All these models developed so far couple the transport of reagents, by diffusion and convection, to the binding on the reaction surface. Myszka''s model assumes a spatially homogeneous constant concentration of reagents throughout the reaction chamber, thus fails to describe highly transport-limited conditions due to the presence of spatial heterogeneity and depletion of the bulk fluid from reagents.^16,17 In transport-limited conditions, the strength of reaction is superior to the rate of transport of reagents to the reaction surface.^18,19 More recently, the convection effects were included in a number of studies, describing the whole kinetic spectrum from reaction-limited conditions to transport-limited reactions.^20–22 Immunoreaction kinetics has also been examined with a variety of fluid driving forces, from capillary-driven flows,²⁰ to electrokinetic flows in micro-reaction patches,²¹ pressure-driven flows in a variety of geometric designs.²² Despite these comprehensive numerical investigations, the fundamental interrelations between the constitutive kinetic parameters, such as concentration, flow velocity, microchannel height, and antibody loading density, have not been studied in detail. In addition, the conjugation kinetics has not yet been exclusively examined.In this paper, a previous model for immunoreaction is modified to study the antibody/SAM conjugation reaction in a microfluidic system. Model findings are used to examine the process times recommended in the literature and possible modification scenarios are proposed. The new model connects the convective and diffusive transport of reagents in the bulk fluid to their surface reaction. The conjugation reaction is studied against fluidic and geometrical parameters such as flow rate, concentration, microchannel height and surface density of antibodies. Damköhler number is used to compare the reaction and fluidic phenomena present and justify the kinetic trends observed. Model predictions are discussed and the main finding on possible overexposure of carboxylates to crosslinking reagents, in conventional protocols, is verified by comparing the resultant antibody loading densities obtained using a quartz crystal microbalance (QCM) set up. The results demonstrate an improved receptor (antibody) loading density which is quite promising for a number of (bio-) sensing applications.^23,24 Major application areas include antibody-based sensors for on-site, rapid, and sensitive analysis of pathogens such as Bacillus anthracis,²³ Escherichia coli, and Listeria monocytogenes, and toxins such as fungal pathogens, viruses, mycotoxins, marine toxins, and parasites.²⁴     

Quantifying the volume of single cells continuously using a microfluidic pressure-driven trap with media exchange

We demonstrate a microfluidic device capable of tracking the volume of individual cells by integrating an on-chip volume sensor with pressure-activated cell trapping capabilities. The device creates a dynamic trap by operating in feedback; a cell is periodically redirected back and forth through a microfluidic volume sensor (Coulter principle). Sieve valves are positioned on both ends of the sensing channel, creating a physical barrier which enables media to be quickly exchanged while keeping a cell firmly in place. The volume of individual Saccharomyces cerevisiae cells was tracked over entire growth cycles, and the ability to quickly exchange media was demonstrated.Measuring cell growth is of primary interest to researchers who seek to study the effects of drugs, nutrients, disease, and environmental stress. This has traditionally been accomplished by monitoring the optical transmittance of large ensembles of cells and applying the Beer-Lambert Law.^1,2 Such population-scale measurements provide important culture statistics, but averaging obscures the behaviour of individual cells. In addition, these techniques often require cell synchronicity in order to correlate growth with specific points in the cell cycle, but synchronicity typically decays rapidly in many cell lines including Saccharomyces cerevisiae (yeast) cultures.³ Researchers have thus adopted methods that study the growth of individual cells. Quantifying cellular growth is especially challenging since proliferating cells such as yeast or Escherichia coli are irregularly shaped, and will only increase in size by a factor of two.⁴ Growth will affect the mass, volume, and density of the cell; having access to each of these characteristics is important in obtaining a complete picture of this process. Time-lapse fluorescence microscopy can provide valuable information as to the cell cycle progression of individual cells,⁵ but 2D optics requires geometric assumptions, and, thus, can provide an incomplete picture of growth.^6,7Microfluidic lab-on-chip devices with integrated sensors can provide high-resolution growth tracking of individual cells, either through mass, volume, or density monitoring.^4,7,8 Recently, a microfluidic mass sensor was used to track the buoyant mass of individual cells using a suspended microchannel resonator (SMR).^4,9 Monitoring growth can also be accomplished by tracking volume using microfluidic volume sensors⁷ operating on the Coulter principle.¹⁰ Trapping can be achieved by either (1) cycling the target back and forth through the sensor (pressure-driven⁴ and electrokinetic⁷) or (2) holding a cell in place (posts,¹¹ chevron structure,¹² and E-Field¹³). The former, dynamic approach, allows a single cell to be sampled periodically by reversing flow directions after a cell is detected. Simple in its implementation, this technique also has the ability to compensate for a drifting baseline current resulting from parasitic ionic changes within the sensing channel or other sources of noise. On the other hand, static traps allow cells to be held in place while the buffer is rapidly exchanged.¹² The ability to dynamically change cellular growth conditions during an experiment can lead to significant insight into the behaviour of cells in environments of varying salinity,¹⁴ oxidative,^15,16 or osmotic conditions,¹⁷ as well as the effect of nutrients¹⁸ and drugs.¹⁹In this work, we propose a device capable of tracking growth using high-resolution volume measurements, combining the best attributes of both types of measurement systems; continuous baseline correction and the ability to rapidly exchange cell media. This is accomplished by using a pressure-driven, feedback-based dynamic trap, whereby a cell is cycled back and forth through the sensor within a microfluidic channel. On-chip sieve valves positioned at both ends of the sensing channel are able to selectively capture a cell while the solution is being replaced. As proof of principle, the volume of several individual yeast cells was monitored over the course of their respective growth cycles, and the ability to quantify growth response to media exchange was demonstrated.Devices were fabricated using multilayered soft lithography with polydimethylsiloxane (PDMS) molding.²⁰ The completed device is pictured in Figure 1(a); full fabrication protocols are presented as supplementary material.²¹ To maximize measurement sensitivity, it is optimal to choose a channel width and height slightly larger than the dimensions of the target cell.²² However, yeast cells are asymmetrically shaped and tend to tumble as they traverse the sensor. Preliminary testing suggested this effect could be mitigated by having cells flow along trajectories far from the electrodes (through buoyancy), where electric field is more uniform. Thus, a channel height of 20 μm was chosen as a compromise. Channel height increases to 28 μm in the wider part of the central and bypass channels, a result of using a mold made out of reflowed photoresist.²³ Channel width was set at 25 μm through the sensor, and widens to 80 μm at the sieve valves to facilitate valve actuation, which requires a high width to height ratio.²⁰ The fluidic layer is integrated in a 35 μm thick PDMS spin-coated layer, above which sits a 50 μm tall valve channel in a 4 mm PDMS layer. Tubing connects I1 and I2 to a common inlet vial, V1 and V2 to vials filled with deionised water and O1 and O2 connect to empty vials (not pictured). Inlet pressures I1 and I2, and valve pressures V1 and V2 are controlled with manual regulators (SMC IR2000-N02-R and SMC IR2010-N02-R); outlet pressures are computer-controlled (SMC ITV-1011). This pressure scheme is detailed elsewhere.²⁴ Current pulses caused by transiting particles/cells (Figure 1(d)) were acquired by applying a 50 kHz, 220 mV AC voltage between a pair of electrodes and measuring the drawn current. This frequency is sufficiently elevated to avoid the electrical double layer capacitance at the electrode-electrolyte interface,²⁵ but low enough to avoid sensitivity to cell impedance or substrate.²⁶ The electrical setup used for these experiments has been described previously.^24,27 A temperature controller maintains the device at 30 °C.Open in a separate windowFIG. 1.(a) Micrograph of the microfluidic device. Two parallel bypass channels are connected by a sensing channel with sensing electrodes. Pressure is applied at inlets (I1, I2) and outlets (O1, O2) to control flow conditions. Valves (V1, V2) are positioned over each end of the sensing channel. Food coloring is used to highlight the valve (red) and fluidic layers (blue). (b) Flow mode: valves are unpressurized, and cells flow freely through the device. (c) Trapping mode: valves are pressurized to capture a cell within the central channel. Pressure-driven flow cycles the cell back and forth across the sensor. (d)Typical current pulses measured for a yeast cell.The cell capture, media exchange, and detection process occurs as follows. A cell suspension is loaded into the bypass channel and made to flow through the central sensing channel by imposing a pressure gradient (Figure 1(b)). Cells flowing through the sensor are observed optically; once a cell of interest is observed (a cell without a bud), valves are sealed (V1 = V2 = 35 psi). This stops all flow through the sensor, and enables bypass channels to be flushed and replaced with fresh media. After 2 min, valve channels are pressurized to 24 psi where they compress the channel to a sufficient height to physically restrict the passage of yeast cells, while allowing the media to flow through the central channel (Figure 1(c)). The pressure gradient between bypasses causes the media in the central channel to be flushed out, while the target cell is physically trapped. Replacing the media in the central channel takes 2 min. At this stage, a pressure-driven feedback-based dynamic trap can be initiated. In this dynamic trap mode, the pressure settings at O1 and O2 are adjusted to redirect the cell back and forth through the sensor, based on current pulses measured from cells transiting through the sensor. Through custom LabView® software, these outlet pressure settings are feedback-adjusted to maintain a speed of 250 μm/s in both directions at a detection frequency of 30 cells/min (Figure 1(d)). To minimize the effects of channel stretching/shrinking, the sum of pressures at O1 and O2 is held constant. This precaution was taken since the sensing channel structured within the flexible PDMS polymer will alter its geometry based on internal pressure.²⁸ The short central channel ensures steady nutrient replenishment from the bypasses. For example, a glucose molecule takes ∼4 min to diffuse from the bypass to the electrodes. In practice, Taylor-Aris dispersion will reduce this replenishment time considerably. Based on video analysis, 25% of the central channel''s media is replenished every pressure reversal (video presented as supplementary material²¹). Polystyrene microspheres of 3.9 ± 0.3 μm, 5.6 ± 0.2 μm, and 8.3 ± 0.7 μm (NIST size standards) were used to calibrate the sensor, and obtain the current pulse-to-volume calibration for every solution (supplementary material²¹). The validity of this calibration method is discussed elsewhere.²⁹ Care was taken to limit trajectory-based variations in signal: the device is positioned with electrodes at the top of the sensing channel, and with the negatively buoyant cells/particles flowing along the bottom. Based on previous experimental and theory work, we found that signal amplitude can vary as much as 3.5 fold for different heights.²⁷ The effect of trajectory on current pulse amplitude has also been reported elsewhere.^30,31 In this work, buoyancy is used to ensure that the cell flows along a trajectory at the same distance from the electrodes for every measurement.Saccharomyces cerevisiae (BY4743 Mat a/alpha, genotype: his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met15Δ0/MET15 ura3Δ0/ura3Δ0 ade2::LEU2/ade2::URA3) was cultured to exponential phase at 30 °C in an incubator/shaker in yeast bacto-peptone (YPD) with 2% w/v glucose, supplemented with 0.2 M NaCl, 0.05% bovine serum albumin (BSA) and 42 mg/l adenine. Sodium chloride was added to enable the current pulse measurement, at a concentration where cells are viable;³² BSA was used to prevent cell agglomeration; adenine was supplemented since this particular yeast mutant does not produce its own supply. A cell suspension was introduced into the device, from which a cell at the early stages of its cell cycle was captured, and dynamically trapped for 100 min. Three typical cell growth results are shown in Figure 2(a). Since the culture was not synchronized, this leads to variability between “initial” cell volumes: there is a 27% difference in initial volume between the cells identified by red squares and green triangles. This is caused by (1) optical limits, whereby cells chosen for study are not all at the exact same cell cycle stage and (2) differences in the age of the mother cell: the more buds a mother cell has produced, the larger it becomes.³³ On average, captured yeast cell demonstrated a doubling time consistent with growth rates under ideal incubator/shaker conditions; nutrient depletion, electric field, and shear stresses are not affecting growth. Optical inspection of budding cells confirms that most growth is occurring at the daughter cell, as expected.³³ An elevated signal-to-noise ratio allows for high resolution volumetric measurements (4 μm³); cell asymmetry⁷ and trajectory variability^27,30,31 lead to a relative standard deviation of 6% for cells and 4% for microspheres of similar size. While mass or protein synthesis methods have indicated linear³⁴ or exponential^4,6,35,36 growth curves, volume-based methods have suggested sigmoidal patterns.^7,37 Prior to daughter cell emergence, and later in the cycle as the daughter cell emerges, volumetric growth rate declines.³⁸ In this work, it is difficult to ascertain with mathematical rigor the shape of the growth profile; however, for each cell, volume increases steadily throughout the growth cycle before declining near the end of the cycle.Open in a separate windowFIG. 2.(a) Growth curves for 3 cells trapped in succession. Simultaneous optical and electrical measurements allow cell cycle stage to be correlated with volume. Pictures of cell corresponding to the red squares are presented in 15 min increments. A cell is cycled through the sensor every 2 s. For clarity, each data point for yeast volume represents the average of data points over a period of 5 min, with standard deviation. (b) Demonstration of an interrupted growth cycle, where YPD + 0.2 M NaCl was replaced with 0.2 M NaCl at 40 min, and then again returned to YPD + 0.2 M NaCl at 80 min. The media exchange process takes 4 min.To demonstrate our ability to easily exchange media while maintaining a trap, the solution was exchanged 40 min into a yeast growth cycle; culture media was replaced with a pure saline solution 0.2 M NaCl + 0.05% BSA, and then replaced again with culture media at 80 min (Figure 2(b)). Cell growth is halted temporarily while in saline solution, before resuming normal growth thereafter. The cell cycle time is extended by this period. The cell volume drifts downward after the initial solution change at 40 min. Though this drift lies within our uncertainty bounds, cellular responses to osmotic shock on similar timescales have been documented elsewhere.³⁹ This result demonstrates an ability to quickly exchange cell media, and observe cellular response.In conclusion, we have demonstrated a microfluidic device capable of maintaining a dynamic, pressure-driven cell trap, which can monitor cellular volume over the cell cycle. Concurrent optical microscopy allows for real-time visual inspection of the cells. In addition, sieve valve integration provides for the exchange of media or the addition of drugs. Such a platform could also be key in cancer cell cytotoxicity assays,⁴⁰ where growth response to anticancer drugs could be monitored.     

Microfluidic devices fitted with “flowver” paper pumps generate steady,tunable gradients for extended observation of chemotactic cell migration

Microfluidics approaches have gained popularity in the field of directed cell migration, enabling control of the extracellular environment and integration with live-cell microscopy; however, technical hurdles remain. Among the challenges are the stability and predictability of the environment, which are especially critical for the observation of fibroblasts and other slow-moving cells. Such experiments require several hours and are typically plagued by the introduction of bubbles and other disturbances that naturally arise in standard microfluidics protocols. Here, we report on the development of a passive pumping strategy, driven by the high capillary pressure and evaporative capacity of paper, and its application to study fibroblast chemotaxis. The paper pumps—flowvers (flow + clover)—are inexpensive, compact, and scalable, and they allow nearly bubble-free operation, with a predictable volumetric flow rate on the order of μl/min, for several hours. To demonstrate the utility of this approach, we combined the flowver pumping strategy with a Y-junction microfluidic device to generate a chemoattractant gradient landscape that is both stable (6+ h) and predictable (by finite-element modeling calculations). Integrated with fluorescence microscopy, we were able to recapitulate previous, live-cell imaging studies of fibroblast chemotaxis to platelet derived growth factor (PDGF), with an order-of-magnitude gain in throughput. The increased throughput of single-cell analysis allowed us to more precisely define PDGF gradient conditions conducive for chemotaxis; we were also able to interpret how the orientation of signaling through the phosphoinositide 3-kinase pathway affects the cells’ sensing of and response to conducive gradients.     

Micromixing visualization and quantification in a microscale multi-inlet vortex nanoprecipitation reactor using confocal-based reactive micro laser-induced fluorescence

A technique for visualizing and quantifying reactive mixing for laminar and turbulent flow in a microscale chemical reactor using confocal-based microscopic laser induced fluorescence (confocal μ-LIF) was demonstrated in a microscale multi-inlet vortex nanoprecipitation reactor. Unlike passive scalar μ-LIF, the reactive μ-LIF technique is able to visualize and quantify micromixing effects. The confocal imaging results indicated that the flow in the reactor was laminar and steady for inlet Reynolds numbers of 10, 53, and 93. Mixing and reaction were incomplete at each of these Reynolds numbers. The results also suggested that although mixing by diffusion was enhanced near the midplane of the reactor at Re_j = 53 and 93 due to very thin bands of acidic and basic fluid forming as the fluid spiraled towards the center of the reactor, near the top, and bottom walls of the reactor, the lower velocities due to fluid friction with the walls hindered the formation of these thin bands, and, thus, resulted in large regions of unmixed and unreacted fluid. At Re_j = 240, the flow was turbulent and unsteady. The mixing and reaction processes were still found to be incomplete even at this highest Reynolds number. At the reactor midplane, the flow images at Re_j = 240 showed unmixed base fluid near the center of the reactor, suggesting that just as in the Re_j = 53 and 93 cases, lower velocities near the top and bottom walls of the reactor hinder the mixing and rection of the acidic and basic streams. Ensemble averages of line-scan profiles for the Re_j = 240 were then calculated to provide statistical quantification of the microscale mixing in the reactor. These results further demonstrate that even at this highest Reynolds number investigated, mixing and reaction are incomplete. Visualization and quantification of micromixing using this reactive μ-LIF technique can prove useful in the validation of computational fluid dynamics models of micromixing within microscale chemical reactors.     

Bacteria under the physical constraints of periodic micro-nanofluidic junctions reveal morphological plasticity and dynamic shifting of Min patterns

Morphological plasticity is an important survival strategy for bacteria adapting to stressful environments in response to new physical constraints. Here, we demonstrate Escherichia coli morphological plasticity can be induced by switching stress levels through the physical constraints of periodic micro-nanofluidic junctions. Moreover, the generation of diverse morphological aberrancies requires the intact functions of the divisome- and elongasome-directed pathways. It is also intriguing that the altered morphologies are developed in bacteria undergoing morphological reversion as stresses are removed. Cell filamentation underlies the most dominant morphological phenotypes, in which transitions between the novel pattern formations by the spatial regulators of the divisome, i.e., the Min system, are observed, suggesting their potential linkage during morphological reversion.Most bacteria have evolved sophisticated systems to manage their characteristic morphology by orchestrating the spatiotemporal synthesis of the murein sacculus (peptidoglycan exoskeleton), which is known to be the stress-bearing component of cell wall and presides over de novo generation of cell shape.¹ Morphological plasticity is attributed to a bacterial survival strategy as responding to stressful environments such as innate immune effectors, antimicrobial therapy, quorum sensing, and protistan predation.² It comes of no surprise that stress-induced diversified morphology and mechanisms, ascribed to shape control and determination, have drawn great attention in both fundamental and clinical studies.^3–6 The molecular mechanism to form filamentous bacteria has been revealed that both β-lactam antibiotics³ and oxidative radicals produced by phagocytic cells⁵ trigger the SOS response, promoting cell elongation by inactivating cell division via the blockade of tubulin-like FtsZ, known as the divisome initiator. While apart from the scenario of length control by the divisome-directed filamentation, the elongasome assembled by proteins associated with actin-like MreB complex^1,7,8 helps the insertion of peptidoglycans into lateral cell wall, suggesting the role in the determination of cell diameter during cell elongation.Recently, additional mechanisms other than the divisome/elongasome-directed pathways of shape maintenance are discovered to regenerate normal morphology de novo from wall-less lysozyme-induced (LI) spheroplasts of E. coli via a plethora types of aberrant division intermediates.⁹ Similar morphological reversion from different aberrant bacterial shapes has been observed as squashed wild-type bacteria generated through sub-micron constrictions are released into connected microchambers.¹⁰ Previous work using the microfluidic approach focuses on the septation accuracy and robustness of constricted bacteria,¹¹ but the reversion process of stress-released bacteria is not well studied and analyzed. In particular, the aberrant bacterial shape is mainly branched-type with bent and curved variants in the reverting bacteria, analogous to the aberrant intermediate found in the morphological reversion of LI spheroplasts with PBP5-defective mutant.⁹ Since bacteria suffering from starvation¹² or confronting mechanical stresses exerted by phagocytosis and protistan grazing⁶ can induce morphological alterations, one could manipulate the stress levels of physical constraints by adopting repeated structures of sub-micron constricted channels (nanoslits) and microchambers,^10,11 to select and enrich bacteria converting to specified aberrant intermediates. The stress incurred by the nanoslit on bacteria is about the mechanical intervention over de novo synthesis of the cell wall, which is the major factor causing morphological aberrancy, while the second environmental stress comes from bacterial growth in the restricted space of microchamber as bacteria proliferate to full confluency, resulting in growth pressure of high population density, nutrient deficiency, and the size reduction of bacteria.Here, we report the selection of distinctive bacterial morphologies by size shrinkage in the outlet cross-section (W × H = 1.5 × 1.5 μm) of the terminal microchamber in the periodic structures of nanoslit-microchamber (Figs. 1(a) and 1(b)). The fluidic structures were micropatterned on fused silica wafers by photolithography, fabricated through reactive ion etching (RIE) and inductively coupled plasma (ICP) etching, and encapsulated by cover glasses coated with polydimethylsiloxane (PDMS) or polysilsesquioxane (PSQ) layer as described earlier.^13,14 Two days after the outgrowth of Escherichia coli (imp4213 [MC4100 ΔlamB106 imp4213]) loaded to the microfluidic device at 25 °C, bacteria started to penetrate into the nanoslit as they proliferated to full confluency in the first microchamber (Fig. 1(c)). It takes about 10 days for bacteria traversing 500 μm long (5 repeated nanoslit-microchamber units) via proliferations and being released from the outlet of the terminal microchamber. The narrowed outlet allows only bacteria with smaller diameters to be squeezed into the spacious and nutrient-rich region, thus it acts as a spatial filter to avoid the passage of branching bacteria with cross-sectional size larger than that of the outlet. The rationale of this design is to select aberrant bacteria prone to promote de novo shape regeneration other than the branched-type, which is the dominant morphology of reverting bacteria in the prior microfluidic constriction study.¹⁰ As anticipated, the stress-released bacteria through the narrowed outlet are therefore mostly filamentous (see statistical analysis for cell morphology in the supplementary material).¹⁵ However, it is noted that the aberrant morphology of lemon-like shape with tubular poles (Figs. 1(d-1), 1(d-3), and 1(d-11)) is developed about 3 h after the stress-released bacteria escaped through the outlet. Though the generation of the lemon-like aberrancy in bacteria has been reported in PBP5/7-defective E. coli mutant subjected to a high-level inhibition of both MreB and FtsZ, while the same mutant treated with low-level MreB inhibitor, together with antagonized-FtsZ, displays filamentous shape with varying diameters,¹⁶ these morphological aberrances can be observed in our system (Figs. 1(d-2) and 1(d-12)). Besides, a high-level inhibition of MreB in E. coli with an intact divisome function is known to cause round bacteria, resembling to the cell morphology of the bacteria shown in Fig. 1(d-4). Interestingly, parallel experiments using bacteria mutants carrying impaired regulatory functions in either the divisome (Min⁻) or the elongasome (MreB⁻) do not develop morphological plasticity (supplementary Fig. S1).¹⁵ Taken together, the filamentous and lemon-like variants selected from our microfluidic platform, while elaborating the morphological plasticity and reverting progression, require both the functional divisome/elongasome. Alternatively, the selection by the spatial filter does not fully exclude cells with aberrant shapes such as the branched-type with initial budding (Fig. 1(d-7)), cells with asymmetric cross-section perpendicular to the longitudinal axis (Figs. 1(d-2), 1(d-8), 1(d-9), 1(d-9′), and 1(d-10)), and those resembling to the morphological phenotypes of the division intermediates reported in the LI-spheroplasts carrying genetic defects on some non-cytoskeletal proteins (Figs. 1(d-5) and 1(d-6)). In particular, intracellular vesicles and cell autolysis are observed in some reverting bacteria (Figs. 1(d-5) and 1(d-6)), which are reminiscent to the phenomena reported in the division intermediates of the LI-spheroplasts lacking stress response system (Rcs) or some accessory proteins (PBP1B and LpoB). Unlike the bacteria grow with odd shapes under the stress of nanofluidic confinement only¹⁰ (Fig. 1(c)), all the morphological aberrancy reported here are developed in the reverting bacteria, which grow in the spacious and nutrition-rich environment and are free from physical constraints. Further investigations over the expression levels of the divisome/elongasome networks and the stress-response system in bacterial cells subjected to micro-nanofluidic junctions could be insightful in understanding their role in bacterial shape control.⁹Open in a separate windowFIG. 1.(a) Schematics of the microfluidic device used in this study with an H-shaped geometry (left upper panel), where repeated nanoslit (L×W×H = 50×10×0.4 μm)−microchamber (L×W×H = 50×50×1.5 μm) structures are bridged between two arms of the H-shaped microchannels (left lower panel and enlarged view in right panel). (b) Top-view layout of an individual channel in (a) with close view of the outlet in the terminal microchamber (orange: nanoslits; blue: microchambers). (c) Fluorescence micrograph of E. coli imp4213 penetrating a nanoslit (scale bar: 5 μm). (d) Bright-field micrographs for various cell morphology of the selected imp4213 released from the outlet (magenta arrows: cells with vesicles; scale bar: 5 μm). (e) Sequential bright-field micrographs of morphological reversion. T1–T3 indicate the time after bacteria escaping from the outlet. T1: 3 h; T2: 6 h; T3: 24 h. Scale bar: 10 μm.During the morphological reversion, the stress-released bacteria rapidly increase their size in the first 3 h after escaping from the terminal microchamber (T1 in Fig. 1(e)). Some filamentous bacteria even grow over 50 μm long, though such a morphological phenotype implicates the cessation of functional divisome. With active growth and proliferation, the progeny of stress-released bacteria increase their population but gradually reduce their size about 6 h after being released from the constriction stress (T2 in Fig. 1(e)). Fig. ​Fig.22 displays the marginal histograms for different shape factors, where Fig. 2(a) is the plot of the minimal Feret diameter (cell diameter) versus Feret diameter (cell length), i.e., the shortest versus the longest distance between any two points with parallel tangents along the cell peripheral, respectively, indicating that cell diameters are larger for reverting bacteria at T1 (mean ± S.E.M. = 1.89 ± 0.08 μm) with respect to T2 (1.51 ± 0.06 μm). Moreover, the histogram of Feret diameter depicts two major populations of the cell length for reverting bacteria at T1, which mostly resume to typical cell length at T2 (the median of Feret diameter = 3.33 μm; see statistical analysis for Fig. ​Fig.22 in the supplementary material).¹⁵ The shape factors of circularity (4π × [area]/[perimeter]²) and aspect ratio ([major axis]/[minor axis] for the cell geometry fitted to an ellipse) confirm the existence of dual populations for bacteria at T1 as well (Fig. 2(b)). About 24 h after escaping (T3 in Fig. 1(e)), almost all the progeny of stress-released bacteria regained the rod shape.Open in a separate windowFIG. 2.Marginal histograms for shape factors measured from the reverting imp4213 at T1 and T2. (a) Minimal Feret diameter (cell diameter) versus Feret diameter (cell length). (b) Circularity versus aspect ratio. N = 366 for T1 and N = 494 for T2.The bacterial size reduction of filamentous and lemon-like shape variants, though involving negative control of the divisome positioning by the spatial regulators of MinCDE system,¹⁷ is not completely understood as to how they coordinate in aberrant geometries. Besides, the filamentation of stress-released bacteria during the period of T1 to T2 implicates the inhibition of functional divisome. With minimal perturbation of the divisome by leaky expression of GFP-MinD and MinE (imp4213/P_lac-gfpmut2::minD minE), the patterning dynamics of GFP-MinD in different bacterial morphology were time-lapse imaged during morphological reversion. Intriguingly, more than the standing-wave-like pattern of MinD denoted in filamentous E. coli,¹⁸ we discovered bidirectional drifting of two standing-wave-like patterns of MinD occur in most reverting bacteria filaments (supplementary Figs. S2(a) and S2(b)).¹⁵ The bidirectional drifting in the longitudinal direction of the cells may be emanating from the cell poles (the blue upper panel of Fig. 3(a) and supplementary Fig. S2(c)¹⁵) and the cylinder region (the blue lower panel of Fig. 3(a) and supplementary Fig. S2(d)¹⁵). Furthermore, the MinD pattern transitions from the standing to traveling waves are occasionally observed (the lower panel of Figs. 3(a) and supplementary Fig. S2(e)¹⁵). Notably, the standing-wave-like MinD patterns exhibit bidirectional drifting along the cell longitudinal direction and intermittently change directions, implying the competition between coexisting MinD patterns can be supported under filamentous geometry. Despite there have been observations of multiple wave-packet of traveling waves in filamentous cells,¹⁹ the mixture of distinct wave-like MinD patterns have never been experimentally reported. While most intriguingly, multiple drifting movements of wave-like MinD patterns potentiate the mitigation of periodic minima in time-averaged Min gradient in the reverting filamentous bacteria, suggesting the disability of proper divisome positioning for recovering the typical rod shape. Apart from the wave-like movements, amoeba-like motion of Min proteins has been shown in vitro upon synthetic minimal system, but never been verified in vivo.²⁰ Strikingly, here amoeba-like motion of MinD is the dominant mode in lemon-like bacteria and the transitions between wave-like patterns and amoeba-like motion are supported even under filamentous geometry (Figs. 3(b) and 3(c), Multimedia view).Open in a separate windowFIG. 3.Kymographs for GFP-MinD dynamics in selected imp4213 cells during morphological reversion: (a) Mixture modes of standing wave packets and traveling wave. The left panel is the stacked fluorescence micrograph displaying cell shape (scale bar = 5 μm). The kymograph is derived from the filamentous cell indicated by the green arrow (scale bar: 120 s horizontal; 5 μm vertical), where the lower panel follows the upper panel in time. The yellow windows indicate bidirectional-drifting standing wave packets, while the green indicates traveling waves (see also supplementary Fig. S2).¹⁵ (b) Sequential fluorescence micrographs of GFP-MinD in lemon-shape imp4213 show amoeba-like motion, with the first left a bright-field image (scale bar: 10 μm). (c) Mixed modes of amoeba-like motion and waves in selected filamentous imp4213 cell indicated by the green arrow in the left panel (scale bar = 5 μm). The filamentous cells depicted in (a) and (c) locate at the top region while the lemon-shape cell in (b) at the central region of the movie (time stamp in min:s). (Multimedia view) [URL: http://dx.doi.org/10.1063/1.4892860.1]In summary, we have demonstrated that the development of bacterial morphological plasticity can be stress-induced by periodic physical constraints with intact functions of the divisome and elongasome-directed pathways. Through size exclusion, the constricted outlet structure designed in our microfluidic device is useful in selecting bacteria with plethora morphological aberrancies other than the branched type. Interestingly, disparate morphological changes, rather than those being directly induced under a stressful environment, can be generated in the stress-released bacteria experiencing morphological reversion. Further, the discovery of novel transitions between the Min patterns in most reverting bacteria implicates its regulatory effect of cell filamentation. However, by exploiting the micro-nanofluidic approach, further investigations of the mechanism underlying the development of morphological plasticity in bacteria adapting to physical constraints are expected in future studies to gain more insights into the molecular basis of shape generation.     

Adaptive robust control for planar n-link underactuated manipulator based on radial basis function neural network and online iterative correction method

This paper presents an adaptive robust control strategy based on a radial basis function neural network (RBFNN) and an online iterative correction method (OICM) for a planar n-link underactuated manipulator with a passive first joint to realize its position control objective. An uncertain model of the planar n-link underactuated manipulator is built, which contains the parameter perturbation and the external disturbance. The adaptive robust controllers based on the RBFNN are designed to realize the model reduction, which makes the system reduce to a planar virtual three-link underactuated manipulator (PVTUM) and simplifies the complexity of the system control. An online differential evolution (DE) algorithm is used to calculate the target angles of the PVTUM based on the nominal model parameters. The control of the PVTUM is divided into two stages, and the adaptive robust controllers are still employed to realize the control objective of each stage. Then, the OICM is used to correct the deviations of all link angles of the PVTUM caused by the parameter perturbation, which makes the end-point of the system gradually approach to its target position. Finally, simulation results of a planar four-link underactuated manipulator demonstrate the effectiveness of the proposed adaptive robust control strategy.