1. Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure.

    Angewandte Chemie. International edition in Eng... 55(33):9557 (2016) PMID 27357747

    Rapid antimicrobial susceptibility testing (AST) would decrease misuse and overuse of antibiotics. The "holy grail" of AST is a phenotype-based test that can be performed within a doctor visit. Such a test requires the ability to determine a pathogen's susceptibility after only a short antibioti...
  2. Flow-through Capture and in Situ Amplification Can Enable Rapid Detection of a Few Single Molecules of Nucleic Acids from Several Milliliters of Solution.

    Analytical chemistry 88(15):7647 (2016) PMID 27429181

    Detecting nucleic acids (NAs) at zeptomolar concentrations (few molecules per milliliter) currently requires expensive equipment and lengthy processing times to isolate and concentrate the NAs into a volume that is amenable to amplification processes, such as PCR or LAMP. Shortening the time req...
  3. Polymers in the gut compress the colonic mucus hydrogel.

    PNAS 113(26):7041 (2016) PMID 27303035 PMCID PMC4932961

    Colonic mucus is a key biological hydrogel that protects the gut from infection and physical damage and mediates host-microbe interactions and drug delivery. However, little is known about how its structure is influenced by materials it comes into contact with regularly. For example, the gut abo...
  4. Evaluating 3D printing to solve the sample-to-device interface for LRS and POC diagnostics: example of an interlock meter-mix device for metering and lysing clinical urine samples.

    Lab On a Chip 16(10):1852 (2016) PMID 27122199

    This paper evaluates the potential of 3D printing, a semi-automated additive prototyping technology, as a means to design and prototype a sample-to-device interface, amenable to diagnostics in limited-resource settings, where speed, accuracy and user-friendly design are critical components. As a...
  5. High-Throughput Single-Cell Cultivation on Microfluidic Streak Plates.

    Applied and Environmental Microbiology 82(7):2210 (2016) PMID 26850294 PMCID PMC4807504

    This paper describes the microfluidic streak plate (MSP), a facile method for high-throughput microbial cell separation and cultivation in nanoliter sessile droplets. The MSP method builds upon the conventional streak plate technique by using microfluidic devices to generate nanoliter droplets t...
  6. Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones.

    ACS Nano 10(3):3102 (2016) PMID 26900709 PMCID PMC4819493

    Digital single-molecule technologies are expanding diagnostic capabilities, enabling the ultrasensitive quantification of targets, such as viral load in HIV and hepatitis C infections, by directly counting single molecules. Replacing fluorescent readout with a robust visual readout that can be c...
  7. Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP.

    Nucleic Acids Research 44(2):e10 (2016) PMID 26358811 PMCID PMC4737171

    In this paper, we asked if it is possible to identify the best primers and reaction conditions based on improvements in reaction speed when optimizing isothermal reactions. We used digital single-molecule, real-time analyses of both speed and efficiency of isothermal amplification reactions, whi...
  8. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis.

    Cell 161(2):264 (2015) PMID 25860609 PMCID PMC4393509

    The gastrointestinal (GI) tract contains much of the body's serotonin (5-hydroxytryptamine, 5-HT), but mechanisms controlling the metabolism of gut-derived 5-HT remain unclear. Here, we demonstrate that the microbiota plays a critical role in regulating host 5-HT. Indigenous spore-forming bacter...
  9. A biochemical network can control formation of a synthetic material by sensing numerous specific stimuli.

    Scientific reports 5:10274 (2015) PMID 25975772 PMCID PMC4432564

    Developing bio-compatible smart materials that assemble in response to environmental cues requires strategies that can discriminate multiple specific stimuli in a complex milieu. Synthetic materials have yet to achieve this level of sensitivity, which would emulate the highly evolved and tailore...
  10. The pumping lid: investigating multi-material 3D printing for equipment-free, programmable generation of positive and negative pressures for microfluidic applications.

    Lab On a Chip 14(24):4616 (2014) PMID 25231706

    Equipment-free pumping is a challenging problem and an active area of research in microfluidics, with applications for both laboratory and limited-resource settings. This paper describes the pumping lid method, a strategy to achieve equipment-free pumping by controlled generation of pressure. Pr...
  11. Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering.

    Nature Nanotechnology 9(12):969 (2014) PMID 25466541 PMCID PMC4472305

    Rapid progress in identifying disease biomarkers has increased the importance of creating high-performance detection technologies. Over the last decade, the design of many detection platforms has focused on either the nano or micro length scale. Here, we review recent strategies that combine nan...
  12. Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness.

    Nature 514(7524):638 (2014) PMID 25274297 PMCID PMC4214913

    Systemic infection induces conserved physiological responses that include both resistance and 'tolerance of infection' mechanisms. Temporary anorexia associated with an infection is often beneficial, reallocating energy from food foraging towards resistance to infection or depriving pathogens of...
  13. Digital, ultrasensitive, end-point protein measurements with large dynamic range via Brownian trapping with drift.

    Journal of the American Chemical Society 136(42):14662 (2014) PMID 25289692

    This communication shows that the concept of Brownian trapping with drift can be applied to improve quantitative molecular measurements. It has the potential to combine the robustness of end-point spatially resolved readouts, the ultrasensitivity of digital single-molecule measurements, and the ...
  14. Digital biology and chemistry.

    Lab On a Chip 14(17):3225 (2014) PMID 24889331

    This account examines developments in "digital" biology and chemistry within the context of microfluidics, from a personal perspective. Using microfluidics as a frame of reference, we identify two areas of research within digital biology and chemistry that are of special interest: (i) the study ...
  15. Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips.

    Integrative Biology 6(8):796 (2014) PMID 24953827 PMCID PMC4131746

    Isolating microbes carrying genes of interest from environmental samples is important for applications in biology and medicine. However, this involves the use of genetic assays that often require lysis of microbial cells, which is not compatible with the goal of obtaining live cells for isolatio...
  16. Measuring fate and rate of single-molecule competition of amplification and restriction digestion, and its use for rapid genotyping tested with hepatitis C viral RNA.

    Angewandte Chemie. International edition in Eng... 53(31):8088 (2014) PMID 24889060 PMCID PMC4116457

    We experimentally monitored, at the single-molecule level, the competition among reverse transcription, exponential amplification (RT-LAMP), and linear degradation (restriction enzymes) starting with hepatitis C viral RNA molecules. We found significant heterogeneity in the rate of single-molecu...
  17. Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa.

    PNAS 111(27):9768 (2014) PMID 24965364 PMCID PMC4103313

    This paper describes a microfluidics-based workflow for genetically targeted isolation and cultivation of microorganisms from complex clinical samples. Data sets from high-throughput sequencing suggest the existence of previously unidentified bacterial taxa and functional genes with high biomedi...
  18. A microfluidic device for dry sample preservation in remote settings.

    Lab On a Chip 13(22):4331 (2013) PMID 24056744 PMCID PMC3851311

    This paper describes a microfluidic device for dry preservation of biological specimens at room temperature that incorporates chemical stabilization matrices. Long-term stabilization of samples is crucial for remote medical analysis, biosurveillance, and archiving, but the current paradigm for t...
  19. Increased robustness of single-molecule counting with microfluidics, digital isothermal amplification, and a mobile phone versus real-time kinetic measurements.

    Analytical chemistry 85(22):11129 (2013) PMID 24199852 PMCID PMC3924768

    Quantitative bioanalytical measurements are commonly performed in a kinetic format and are known to not be robust to perturbation that affects the kinetics itself or the measurement of kinetics. We hypothesized that the same measurements performed in a "digital" (single-molecule) format would sh...
  20. Chemical analog-to-digital signal conversion based on robust threshold chemistry and its evaluation in the context of microfluidics-based quantitative assays.

    Journal of the American Chemical Society 135(39):14775 (2013) PMID 24060606 PMCID PMC3860884

    In this article, we describe a nonlinear threshold chemistry based on enzymatic inhibition and demonstrate how it can be coupled with microfluidics to convert a chemical concentration (analog input) into patterns of ON or OFF reaction outcomes (chemical digital readout). Quantification of small ...