Quantifying spatio-temporal dynamics of biomarker pre-concentration and depletion in microfluidic systems by intensity threshold analysis

A novel ultralow conductivity electromanipulation buffer improves cell viability and enhances dielectrophoretic consistency

Cell separation has become a critical diagnostic, research, and treatment tool for personalized medicine. Despite significant advances in cell separation, most widely used applications require the use of multiple, expensive antibodies to known markers in order to identify subpopulations of cells for separation. Dielectrophoresis (DEP) provides a biophysical separation technique that can target cell subpopulations based on phenotype without labels and return native cells for downstream analysis. One challenge in employing any DEP device is the sample being separated must be transferred into an ultralow conductivity medium, which can be detrimental in retaining cells' native phenotypes for separation. Here, we measured properties of traditional DEP reagents and determined that after just 1-2 h of exposure and subsequent culture, cells' viability was significantly reduced below 50%. We developed and tested a novel buffer (Cyto Buffer) that achieved 6 weeks of stable shelf-life and demonstrated significantly improved viability and physiological properties. We then determined the impact of Cyto Buffer on cells' dielectric properties and morphology and found that cells retained properties more similar to that of their native media. Finally, we vetted Cyto Buffer's usability on a cell separation platform (Cyto R1) to determine combined efficacy for cell separations. Here, more than 80% of cells from different cell lines were recovered and were determined to be >70% viable following exposure to Cyto Buffer, flow stimulation, electromanipulation, and downstream collection and growth. The developed buffer demonstrated improved opportunities for electrical cell manipulation, enrichment, and recovery for next generation cell separations.

Mito Hacker: a set of tools to enable high-throughput analysis of mitochondrial network morphology

Mitochondria are highly dynamic organelles that can exhibit a wide range of morphologies. Mitochondrial morphology can differ significantly across cell types, reflecting different physiological needs, but can also change rapidly in response to stress or the activation of signaling pathways. Understanding both the cause and consequences of these morphological changes is critical to fully understanding how mitochondrial function contributes to both normal and pathological physiology. However, while robust and quantitative analysis of mitochondrial morphology has become increasingly accessible, there is a need for new tools to generate and analyze large data sets of mitochondrial images in high throughput. The generation of such datasets is critical to fully benefit from rapidly evolving methods in data science, such as neural networks, that have shown tremendous value in extracting novel biological insights and generating new hypotheses. Here we describe a set of three computational tools, Cell Catcher, Mito Catcher and MiA, that we have developed to extract extensive mitochondrial network data on a single-cell level from multi-cell fluorescence images. Cell Catcher automatically separates and isolates individual cells from multi-cell images; Mito Catcher uses the statistical distribution of pixel intensities across the mitochondrial network to detect and remove background noise from the cell and segment the mitochondrial network; MiA uses the binarized mitochondrial network to perform more than 100 mitochondria-level and cell-level morphometric measurements. To validate the utility of this set of tools, we generated a database of morphological features for 630 individual cells that encode 0, 1 or 2 alleles of the mitochondrial fission GTPase Drp1 and demonstrate that these mitochondrial data could be used to predict Drp1 genotype with 87% accuracy. Together, this suite of tools enables the high-throughput and automated collection of detailed and quantitative mitochondrial structural information at a single-cell level. Furthermore, the data generated with these tools, when combined with advanced data science approaches, can be used to generate novel biological insights.

Quantifying bacterial spore germination by single-cell impedance cytometry for assessment of host microbiota susceptibility to Clostridioides difficile infection

The germination of ingested spores is often a necessary first step required for enabling bacterial outgrowth and host colonization, as in the case of Clostridioides difficile (C. difficile) infection. Spore germination rate in the colon depends on microbiota composition and its level of disruption by antibiotic treatment since secretions by commensal bacteria modulate primary to secondary bile salt levels to control germination. Assessment of C. difficile spore germination typically requires measurement of colony-forming units, which is labor intensive and takes at least 24 h to perform but is regularly required due to the high recurrence rates of nosocomial antibiotic-associated diarrhea. We present a rapid method to assess spore germination by using high throughput single-cell impedance cytometry (>300 events/s) to quantify live bacterial cells, by gating for their characteristic electrophysiology versus spores, so that germination can be assessed after just 4 h of culture at a detection limit of ~100 live cells per 50 μL sample. To detect the phenotype of germinated C. difficile bacteria, we utilize its characteristically higher net conductivity versus that of spore aggregates and non-viable C. difficile forms, which causes a distinctive high-frequency (10 MHz) impedance phase dispersion within moderately conductive media (0.8 S/m). In this manner, we can detect significant differences in spore germination rates within just 4 h, with increasing primary bile salt levels in vitro and using ex vivo microbiota samples from an antibiotic-treated mouse model to assess susceptibility to C. difficile infection. We envision a rapid diagnostic tool for assessing host microbiota susceptibility to bacterial colonization after key antibiotic treatments.

Rapid in Vitro Assessment of Clostridioides difficile Inhibition by Probiotics Using Dielectrophoresis to Quantify Cell Structure Alterations

Clostridioides difficile (C. difficile) infection (CDI) is the primary cause of nosocomial antibiotic-associated diarrhea, with high recurrence rates following initial antibiotic treatment regimens. Restoration of the host gut microbiome through probiotic therapy is under investigation to reduce recurrence. Current in vitro methods to assess C. difficile deactivation by probiotic microorganisms are based on C. difficile growth inhibition, but the cumbersome and time-consuming nature of the assay limits the number of assessed permutations. Phenotypic alterations to the C. difficile cellular structure upon interaction with probiotics can potentially enable rapid assessment of the inhibition without the need for extended culture. Because supernatants from cultures of commensal microbiota reflect the complex metabolite milieu that deactivates C. difficile, we explore coculture of C. difficile with an optimal dose of supernatants from probiotic culture to speed growth inhibition assays and enable correlation with alterations to its prolate ellipsoidal structure. Based on sensitivity of electrical polarizability to C. difficile cell shape and subcellular structure, we show that the inhibitory effect of Lactobacillus spp. supernatants on C. difficile can be determined based on the positive dielectrophoresis level within just 1 h of culture using a highly toxigenic strain and a clinical isolate, whereas optical and growth inhibition measurements require far greater culture time. We envision application of this in vitro coculture model, in conjunction with dielectrophoresis, to rapidly screen for potential probiotic combinations for the treatment of recurrent CDI.

Conductance-Based Biophysical Distinction and Microfluidic Enrichment of Nanovesicles Derived from Pancreatic Tumor Cells of Varying Invasiveness

Diagnostics based on exosomes and other extracellular vesicles (EVs) are emerging as strategies for informing cancer progression and therapies, since the lipid content and macromolecular cargo of EVs can provide key phenotypic and genotypic information on the parent tumor cell and its microenvironment. We show that EVs derived from more invasive pancreatic tumor cells that express high levels of tumor-specific surface proteins and are composed of highly unsaturated lipids that increase membrane fluidity, exhibit significantly higher conductance versus those derived from less invasive tumor cells, based on dielectrophoresis measurements. Furthermore, through specific binding of the EVs to gold nanoparticle-conjugated antibodies, we show that these conductance differences can be modulated in proportion to the type as well as level of expressed tumor-specific antigens, thereby presenting methods for selective microfluidic enrichment and cytometry-based quantification of EVs based on invasiveness of their parent cell.

Isolation and identification of Listeria monocytogenes utilizing DC insulator-based dielectrophoresis

Foodborne pathogens pose one of the greatest challenges facing public health in the modern day. One important pathogen, Listeria monocytogenes, is known to be challenging to detect and identify. Three serovars cause most of the Listeria related food-borne illnesses, which the Centers for Disease Control currently utilizes a combination of pulsed-field gel electrophoresis and whole genome sequencing for identification and the determination of clusters and outbreaks. There is a potential method for rapid collection of epidemiological information by exploiting the electrokinetic and dielectrophoretic properties of the L. monocytogenes serovars. Using dielectrophoresis, the three most commonly identified serovars of L. monocytogenes can be distinguished from each other. The electrokinetic and dielectrophoretic mobilities of each serovar was determined through a combination of electrokinetic velocity and dielectrophoretic trapping assessments, in conjunction with finite element multi-physics modeling. A mathematical model of the data, which defines the various factors of dielectrophoretic trapping, is utilized and verified based on the behavior of L. monocytogenes in the microchannel. The trapping condition for the serovars were evaluated as 2.8±0.2×10⁹, 2.2±0.2×10⁹, and 2.2±0.3×10⁹Vm^-2 and the electrokinetic mobility was assessed to be 19±0.7, 17±0.7, and for the L. monocytogenes serovars 1/2a, 1/2b, and 4b, respectively.

Single-cell electro-phenotyping for rapid assessment of Clostridium difficile heterogeneity under vancomycin treatment at sub-MIC (minimum inhibitory concentration) levels

Current methods for measurement of antibiotic susceptibility of pathogenic bacteria are highly reliant on microbial culture, which is time consuming (requires > 16 hours), especially at near minimum inhibitory concentration (MIC) levels of the antibiotic. We present the use of single-cell electrophysiology-based microbiological analysis for rapid phenotypic identification of antibiotic susceptibility at near-MIC levels, without the need for microbial culture. Clostridium difficile (C. difficile) is the single most common cause of antibiotic-induced enteric infection and disease recurrence is common after antibiotic treatments to suppress the pathogen. Herein, we show that de-activation of C. difficile after MIC-level vancomycin treatment, as validated by microbiological growth assays, can be ascertained rapidly by measuring alterations to the microbial cytoplasmic conductivity that is gauged by the level of positive dielectrophoresis (pDEP) and the frequency spectra for co-field electro-rotation (ROT). Furthermore, this single-cell electrophysiology technique can rapidly identify and quantify the live C. difficile subpopulation after vancomycin treatment at sub-MIC levels, whereas methods based on measurement of the secreted metabolite toxin or the microbiological growth rate can identify this persistent C. difficile subpopulation only after 24 hours of microbial culture, without any ability to quantify the subpopulation. The application of multiplexed versions of this technique is envisioned for antibiotic susceptibility screening.

Frequency-selective electrokinetic enrichment of biomolecules in physiological media based on electrical double-layer polarization

Proteomic biomarkers of interest to the early diagnosis of diseases and infections are present at trace levels versus interfering species. Hence, their selective enrichment is needed within bio-assays for speeding binding kinetics with receptors and for reducing signal interferences. While DC fields can separate biomolecules based on their electrokinetic mobilities, they are unable to selectively enrich biomarkers versus interfering species, which may possess like-charges. We present the utilization of AC electrokinetics to enable frequency-selective enrichment of nanocolloidal biomolecules, based on the characteristic time constant for polarization of their electrical double-layer, since surface conduction in their ion cloud depends on colloidal size, shape and surface charge. In this manner, using DC-offset AC fields, differences in frequency dispersion for negative dielectrophoresis are balanced against electrophoresis in a nanoslit channel to enable the selective enrichment of prostate specific antigen (PSA) versus anti-mouse immunoglobulin antibodies that cause signal interferences to immunoassays. Through coupling enrichment to capture by receptors on graphene-modified surfaces, we demonstrate the elimination of false positives caused by anti-mouse immunoglobulin antibodies to the PSA immunoassay.

Label-Free Quantification of Intracellular Mitochondrial Dynamics Using Dielectrophoresis

Mitochondrial dynamics play an important role within several pathological conditions, including cancer and neurological diseases. For the purpose of identifying therapies that target aberrant regulation of the mitochondrial dynamics machinery and characterizing the regulating signaling pathways, there is a need for label-free means to detect the dynamic alterations in mitochondrial morphology. We present the use of dielectrophoresis for label-free quantification of intracellular mitochondrial modifications that alter cytoplasmic conductivity, and these changes are benchmarked against label-based image analysis of the mitochondrial network. This is validated by quantifying the mitochondrial alterations that are carried out by entirely independent means on two different cell lines: human embryonic kidney cells and mouse embryonic fibroblasts. In both cell lines, the inhibition of mitochondrial fission that leads to a mitochondrial structure of higher connectivity is shown to substantially enhance conductivity of the cell interior, as apparent from the significantly higher positive dielectrophoresis levels in the 0.5-15 MHz range. Using single-cell velocity tracking, we show ∼10-fold higher positive dielectrophoresis levels at 0.5 MHz for cells with a highly connected versus those with a highly fragmented mitochondrial structure, suggesting the feasibility for frequency-selective dielectrophoretic isolation of cells to aid the discovery process for development of therapeutics targeting the mitochondrial machinery.

Tracking Inhibitory Alterations during Interstrain Clostridium difficile Interactions by Monitoring Cell Envelope Capacitance

Global threats arising from the increasing use of antibiotics coupled with the high recurrence rates of Clostridium difficile (C. difficile) infections (CDI) after standard antibiotic treatments highlight the role of commensal probiotic microorganisms, including nontoxigenic C. difficile (NTCD) strains in preventing CDI due to highly toxigenic C. difficile (HTCD) strains. However, optimization of the inhibitory permutations due to commensal interactions in the microbiota requires probes capable of monitoring phenotypic alterations to C. difficile cells. Herein, by monitoring the field screening behavior of the C. difficile cell envelope with respect to cytoplasmic polarization, we demonstrate that inhibition of the host-cell colonization ability of HTCD due to the S-layer alterations occurring after its co-culture with NTCD can be quantitatively tracked on the basis of the capacitance of the cell envelope of co-cultured HTCD. Furthermore, it is shown that effective inhibition requires the dynamic contact of HTCD cells with freshly secreted extracellular factors from NTCD because contact with the cell-free supernatant causes only mild inhibition. We envision a rapid method for screening the inhibitory permutations to arrest C. difficile colonization by routinely probing alterations in the HTCD dielectrophoretic frequency response due to variations in the capacitance of its cell envelope.

Increasing local density and purity of molecules/bacteria on a sensing surface from diluted blood using 3D hybrid electrokinetics

We present a long-range and selective nanocolloid/molecular/bacteria concentrator based on 3D hybrid AC electrokinetics (ACEK) that includes AC dielectrophoresis (DEP) and biased AC electroosmosis (ACEO). Through a convergency comb-shaped electrode design, this long-range ACEO allows the effective transport of a high number of targets into the centre of the detection zone. In the proposed 3D hybrid electrokinetics model, 3D ACEO provides long-range transportation, and the 3D DEP provides an effective separation mechanism. Thus, detection targets ranging from nanoscale to micrometers could be selectively concentrated long-range from diluted blood. The proposed design was used for selectively concentrating nanocolloids and bacteria in the diluted blood sample, respectively. Compared to a 3D short-range dipolar electrode configuration, the detection limit of long-range 3D convergency tripolar electrode configuration is one order of magnitude higher. The result also shows that the 3D hybrid ACEK demonstrated a higher purity of any plane above the electrode, which compared positively to the same design of a 2D hybrid ACEK. The concentration factor of the proposed 3D hybrid electrokinetics device increased by several orders of local density and raised the local purity at least 6 orders (from 0.05% to greater than 99.9%). The chip is capable of making a DNA/protein/bacterial aggregate characterized by high local density and purity for further molecular and bacteria detection/analysis.

Nanoslit design for ion conductivity gradient enhanced dielectrophoresis for ultrafast biomarker enrichment in physiological media

Selective and rapid enrichment of biomolecules is of great interest for biomarker discovery, protein crystallization, and in biosensing for speeding assay kinetics and reducing signal interferences. The current state of the art is based on DC electrokinetics, wherein localized ion depletion at the microchannel to nanochannel interface is used to enhance electric fields, and the resulting biomarker electromigration is balanced against electro-osmosis in the microchannel to cause high degrees of biomarker enrichment. However, biomarker enrichment is not selective, and the levels fall off within physiological media of high conductivity, due to a reduction in ion concentration polarization and electro-osmosis effects. Herein, we present a methodology for coupling AC electrokinetics with ion concentration polarization effects in nanoslits under DC fields, for enabling ultrafast biomarker enrichment in physiological media. Using AC fields at the critical frequency necessary for negative dielectrophoresis of the biomarker of interest, along with a critical offset DC field to create proximal ion accumulation and depletion regions along the perm-selective region inside a nanoslit, we enhance the localized field and field gradient to enable biomarker enrichment over a wide spatial extent along the nanoslit length. While enrichment under DC electrokinetics relies solely on ion depletion to enhance fields, this AC electrokinetic mechanism utilizes ion depletion as well as ion accumulation regions to enhance the field and its gradient. Hence, biomarker enrichment continues to be substantial in spite of the steady drop in nanostructure perm-selectivity within physiological media.

Real-time dielectrophoretic signaling and image quantification methods for evaluating electrokinetic properties of nanoparticles

Real‐time image signaling and quantification methods are described that allow easy‐to‐use, fast extraction of the electrical properties of nanoparticles. Positive dielectrophoretic (pDEP) collection rate analysis enables the dielectric properties of very small samples of nanoparticles to be accurately quantified. Advancing earlier work involving dual‐cycle pulsed pDEP 1 collection experiments, we report the development of a statistical image quantification method that significantly advances the evaluation of nanoparticle dielectric properties. Compared with traditional methods that require information about the geometry of the electrode array to be entered for semiautomated quantification 2, the new statistical approach described does not require a priori knowledge of device geometry. The efficacy of the statistical method is experimentally demonstrated using 200 nm diameter latex nanospheres, suspended in low conductivity medium, that are attracted by pDEP onto planar castellated electrode arrays with 5‐micron‐sized features. The method is shown to yield estimates for the nanoparticle conductivity and surface conductance, σp=25.8 mS/m and KS=1.29 nS, that concur closely with those obtained using traditional geometric methods previously reported 1. Consequently, the statistical method is accurate, fast, robust, supervisor‐free, and useful for determining nanoparticle electrokinetic parameters.

A simple electrokinetic protein preconcentrator utilizing nano-interstices

This work proposes a simple method for creating nanofluidic channels for protein preconcentration through self-assembled gold nanoparticles (AuNPs) using the exclusion-enrichment effect. A depletion force is elicited in nano-interstices among self-assembled AuNPs due to the overlap of electrical double layers (EDLs); therefore, proteins quickly accumulate. The experimental results show that the generation of depletion forces is correlated with the size of the AuNPs. The self-assembled monolayer of AuNPs (13 nm in diameter) can successfully preconcentrate proteins through effective EDL overlapping. This approach provides a new process to produce nanochannels that does not require high-voltage or time-consuming fabrication.

Ultrafast immunoassays by coupling dielectrophoretic biomarker enrichment in nanoslit channel with electrochemical detection on graphene

Heterogeneous immunoassays usually require long incubation times to promote specific target binding and several wash steps to eliminate non-specific binding. Hence, signal saturation is rarely achieved at detection limit levels of analyte, leading to significant errors in analyte quantification due to extreme sensitivity of the signals to incubation time and methodology. The poor binding kinetics of immunoassays at detection limit levels can be alleviated through creating an enriched analyte plug in the vicinity of immobilized capture probes to enable signal saturation at higher levels and at earlier times, due to higher analyte association and its faster replenishment at the binding surface. Herein, we achieve this by coupling frequency-selective dielectrophoretic molecular dam enrichment of the target biomarker in physiological media to capture probes immobilized on graphene-modified surfaces in a nanoslit to enable ultrafast immunoassays with near-instantaneous (<2 minutes) signal saturation at dilute biomarker levels (picomolar) within ultra-low sample volumes (picoliters). This methodology is applied to the detection of Prostate Specific Antigen (PSA) diluted in serum samples, followed by validation against a standard two-step immunoassay using three de-identified patient samples. Based on the ability of dielectrophoretic molecular dam analyte enrichment methods to enable the detection of PSA at 1-5 pg mL(-1) levels within a minute, and the relative insensitivity of the signals to incubation time after the first two minutes, we envision its application for improving the sensitivity of immunoassays and their accuracy at detection limit levels.

An on-demand nanofluidic concentrator

Preconcentration of biomolecules by electrokinetic trapping at the nano/microfluidic interface has been extensively studied due to its significant efficiency. Conventionally, sample preconcentration takes place in continuous flow and therefore suffers from diffusion and dispersion. Encapsulation of the preconcentrated sample into isolated droplets offers a superior way to preserve the sample concentration for further analysis. Nevertheless, the rationale for an optimal design to obviate the sample dilution prior to encapsulation is still lacking. Herein, we propose a pressure-assisted strategy for positioning the concentrated sample plug directly at the ejecting nozzle, which greatly eliminates the concentration decline during sample ejection. A distinctive mechanism for this plug localization was elucidated by two-dimensional numerical simulations. Based on the simulation results, we developed an on-demand nanofluidic concentrator in which the nanochannels were facilely generated through lithography-free nanocracking on a polystyrene substrate. By wisely implementing an on-demand droplet generation module, our system can adaptively encapsulate the highly concentrated sample and effectively enhance the long-term stability. We experimentally demonstrated the preconcentration of a fluorescently labelled biomolecule, bovine serum albumin (BSA), by using an amplification factor of 10(4). We showed that, by adjusting the applied voltage, accumulation time, and pulsed pressure imposed on the control microchannel, our system can generate a droplet of the desired volume with a target sample concentration at a prescribed time. This study not only provides insights into the previously unidentified role of assisted pressure in sample positioning, but also offers an avenue for varied requirements in low-abundance biomolecule detection and analysis.