I would like to thank my mentors, Drs. The work in this thesis would never have been completed without your guidance and hard work. 115 Figure 4.6 The geometry with key parameters for simulation of acoustic simulation of. a) isometric view including the sorting area liquid on top, underlying 3D printing material and a piezoelectric transducer sticking on the bottom.
Introduction
- Waterborne bacterial pathogen diseases: Problems and needs
- Bacterial pathogen detection and analysis methods
- Microfluidic toolbox
- Towards minimal instrumentation
- Thesis overview
For bacterial analysis with clinical relevance, antibiotic susceptibility tests (AST) are usually performed to guide antibiotic prescribing (Syal et al., 2017). Comprehensive reviews of biosensors for waterborne microbial pathogen detection are available (Justino et al., 2017; Kumar et al., 2018).
Multiphysics simulation in microfluidic pathogen detection
Designing a 3D-printed microfluidic device for efficient PCR determination of
- Abstract
- Introduction
- Materials and methods
- Flow simulation
- Chip design, fabrication and characterization
- Cell cultures and natural water samples
- PMA pretreatment on the prototype chip
- PCR assays
- Results and discussions
- Simulation of PMA-sample mixing by SAR mixers
- Chip fabrication
- Performance of on-chip PMA pretreatment
- Conclusions
- Acknowledgements
- Supplementary Information
Due to poor water and sanitation conditions, outbreaks of waterborne diseases claim millions of lives each year in many developing and conflict countries (eg the cholera epidemics in Yemen and Haiti) (Ashbolt, 2004; Gleick, 2002). The SAR mixers aid in diffusion by “folding” the joined streams, as shown in Figure 2.2a (Glatzel et al., 2008).
Understanding DNA extraction performance of electrochemical lysis
- Introduction
- Device design and DNA extraction performance
- Understanding ECL performance through pH profile simulation
- Simulation methods
For all 4 model bacteria the highest ΔCT values of the ECL were in the range of and were observed with 1 min of ECL treatment. As indicated by the calculated flow field shown in Figure 2.7a, gas evolution helps to mix the solution in the simulated cathodic chamber. The liquid in the upper volume is noticeably accelerated and would promote convective transport of OH ions.
The results also highlight that there is a higher pH at the cathode surface than in the bulk electrolyte. The liquid in the cathodic chamber was modeled as a mm3 block, with the electrode surface and cation exchange membrane represented by the two sides of 5 x 50 mm2.
Validating cell distribution on an asymmetric membrane for integrated digital
- Asymmetric membrane for digital cell detection directly from
- Validating the random particle distribution assumption
- Simulation methods
After filtration, optimized assay reagents were introduced into an asymmetric membrane for rapid and isothermal amplification of target nucleic acids from single bacteria within each pore. To verify this assumption, we performed finite element analysis using COMSOL to simulate fluid flow and particle trajectories through the asymmetric membrane. The results suggest that the cells are theoretically evenly distributed across the asymmetric membrane, so that cells have an equal chance to divide into each micropore during filtration.
The fluid regime above the asymmetric membrane was modeled to resemble the geometry inside the membrane fitter used in the experiments. The asymmetric membrane is modeled as two liquid separator layers, each with a thickness of 25 µm and a diameter of 13 mm.
A hydrogel bead-based platform for linking single-cell phenotypic analysis
Abstract
Introduction
For example, temperature manipulation or UV irradiation can affect the phenotype and genotype of encapsulated cells (Ikehata & Ono, 2011), and alginate is a known PCR inhibitor (Wadowsky et al., 1994). PEG cross-linked by a thiol-Michael addition reaction between the bioinert acrylate and thiol groups has been tried in bulk analyzes and is one of the most promising solutions (Huang et al., 2018; . Xu et al., 2016), but it is still being developed for our specific purpose. Herein, we report a novel PEG hydrogel bead-based platform for coupling single-cell phenotypic analysis and in situ molecular detection (Figure 3.1a-b).
To solve the challenge of the fast thiol-Michael addition gelling chemistry, we developed a disposable centrifugal droplet generation device (Figure 3.1c). A hydrogel bead (Gelbeads) based cell analysis platform was developed for (a) single cell phenotypic analysis and (b) digital molecular sensing including PCR and LAMP.
Results
- Development of the disposable droplet generation device
- Gelbead generation and thermal stability characterization
- Gelbeads for cell viability phenotyping
- Gelbead digital PCR (gdPCR)
- Gelbeads digital LAMP (gdLAMP)
- Reagent exchange for in situ PCR following viability phenotyping
The sizes were investigated for droplets and Gelbeads before and after common heating protocols for PCR and LAMP respectively (see methods, Figure 3.3b). As shown in Figure 3.4a, the observed number of encapsulated cells was close to the theoretical distribution. It was observed that Gelbeads appear to be much brighter than the droplets were before incubation (Figure 3.7); this may have been due to additional reduction of resazurin by thiol group (Neufeld et al., 2018).
This was supposedly due to the fact that LAMP produces a much larger amount of amplification products than PCR (Notomi et al., 2000). The negatively charged amplified DNA may have affected the interfacial tension when adsorbed to the interface. However, it was still observed that positive Gelbeads tended to stick together next to each other (Figure 3.6a).
Discussion
Because the cells are encapsulated in individual compartments, the viability phenotype can be observed independently of the intercellular cooperation common to bacterial cells under stress (Lee et al., 2010; Yurtsev et al., 2016).
Materials and methods
- PEG crosslinking and characterizations
- Development of the disposable droplet generation device
- Gelbead generation and thermal stability characterization
- Bacterial cell culture and DNA preparation
- Gelbeads for cell viability phenotyping
- Gelbead digital PCR (gdPCR) assay
- Gelbead digital LAMP (gdLAMP) assay
- Combined phenotyping and gdPCR for antibiotic resistance analysis83
The oil phase was added to the bottom of the microcentrifuge tube and the aqueous reaction mixture was added to the Luer-lock on the needle. To optimize gdPCR, the same concentration of template DNA (600-fold dilution from . grown) was added for gdPCR assays and ddPCR control. Droplets or gel beads were generated in BioRad droplet generation oil and then extracted into PCR tubes for thermocycling.
The droplets or gel beads were then extracted into PCR tubes for 30 min of heating at 65 °C, followed by 5 min of polymerase deactivation at 80 °C. A concentrated PCR reagent mixture was added to the drained gel beads at twice their estimated volume.
Acknowledgements
For analysis of bright Gelbeads fraction, the data for each pixel was the intensity ratio between TXR channel and FITC channel. For generation of droplets and Gelbeads as well as thermal stability characterizations, the images were analyzed for individual compartment diameters. For gdPCR, gdLAMP and phenotyping assays, in addition to size analysis, the images were also analyzed for the number of positive and negative compartments by setting a light-dark threshold.
Using the ratio of negative compartments to total compartments, the input concentration of DNA or cells was estimated with a Poisson distribution (Pinheiro et al., 2012). For the images from the phenotypic assays, since the distinction between dark and light gel beads was difficult to visually inspect, a Gaussian fit was used to advise the threshold (Figure 3.8).
Supplementary notes
- Characterization of PEG hydrogel crosslinking
- Droplet generation performance and sources of error
- Microscope objective choice
- Overcoming challenges of PCR reagent infusion for Gelbeads
- In situ PCR results
Therefore, it is expected that the actual CV of the generated droplets or Gelbeads should be lower than reported. In this case, the fluorescence exhibited by negative spaces was too low to be distinguished from the oil phase under 1.25× objective. The overnight freezing of Gelbeads in water was intended to expand the pores through ice crystal formation, which has been used to prepare macroporous hydrogel for biomedical applications (Oxley et al., 1993).
It was also observed that after phase transfers, even without freeze-thaw treatment, the diameter of the Gelbead increased approx. from 160 µm to 220 µm. However, the actual volume of the raised Gelbeads must be carefully estimated while preparing the concentrated PCR reagent mixture so that the final component concentrations can be accurately obtained.
Supplementary illustrations
- Tables
- Figures
The phenotyped Gelbeads were subject to reagent exchange, which involved (c) breaking the emulsion with PFO, (d) facilitating phase separation by centrifugation, (e) removing all the liquid and adding water to freeze overnight, (f) draining the water with pipette, (g) incubate with concentrated PCR reagents, and (i) wash the Gelbeads with BioRad oil and resuspend for PCR. j) Example fluorescence image of the Gelbeads further analyzed by in situ gdPCR. A fluorescence image was analyzed in the software (Leica Application Suite X) accompanied by the fluorescence microscope. a) The fluorescence image with 10 bright and dark Gelbeads surrounded as regions of interest (ROIs) to be analyzed. The ROIs were selected as pairwise neighboring bright and dark Gelbeads to limit the interference of the focusing effect.
The average mean fluorescence intensity of the bright Gelbeads was 40% higher than the dark ones. Highly sensitive and quantitative detection of rare pathogens through agarose droplet microfluidic emulsion PCR at the single-cell level.
Sorting hydrogel beads with a gravity driven fluorescence activated acoustic
- Abstract
- Introduction
- Results and discussion
- Design and prototype of MiniFABS
- Bead spacing in MiniFABS
- Acoustic actuation in MiniFABS
- Conclusions
- Experimental section
- Numerical simulation for gravity-driven bead movement
- Numerical simulation for acoustic actuation in the sorting region
- Prototype fabrication
- Acknowledgements
The reagent exchange capacity of the interconnected hydrogel network promises in situ downstream analysis (Zhu et al., 2019). Hydrogel beads suspended in heavier fluorinated oil are held at the bottom of the microfluidic tube. For the liquid in the grading region and the solid of the 3D printing base material, the acoustic pressure induced by the piezoelectric transducer was simulated at different frequencies including 40 kHz, 113 kHz and 1.65 MHz as shown in Figure 4.4a-c.
The geometry of the sorting region fluid, the underlying 3D printing material and a piezoelectric transducer at the bottom, as shown in Figure 4.6a. The multiphysics module then solves the scalar wave equation and the Helmholtz equation with pressure acoustics, frequency domain module for the geometry of the fluid.
Prospective development and applications
DropTube: Integrated centrifugal device for in-field pathogen analysis
- Introduction
- Integration of functional structures in DropTube
- DropTube for serovar-specific quantitative detection
- DropTube for AMR characterization
These proteins act as a chloride channel on the membrane of human epithelial cells in many organs (Pier et al., 1998). Enrichment by culture is slow and is highly likely to be limited by background microbiota (Abirami et al., 2016; Lim et al., 2015). While keeping the cells intact for molecular analysis, it is possible to perform serovar-selective enrichment by specific recognition of certain cell membrane proteins by aptamer-coated magnetic beads or antibody-coated porous materials (Davies & . Wray, 1997; Jyoti et al., 2011).
Typhi (resistant to the first-line antibiotics amoxicillin, chloramphenicol and cotrimoxazole) has rapidly gained dominance over other clades since its first isolation in the 1970s (Crump, 2015; . Feasey et al., 2015; Olarte & Galindo, 1973; , 2016). Subsequently, reagents will be exchanged prior to molecular detection of RNA production to indicate the live/dead status of the cells.
Gelbead-based AMR evolution kinetics study
- Mutation induced fast emergence and evolution of AMR
- Provisional study workflow
The sample containing the cells will be split into droplets of hydrogel with a targeted antibiotic, which we will soon incubate. The bacteria and the antibiotic will be incubated at the same time, and a small part of the cells will be imaged. Significant SNPs (ideally, one that appears to be directly associated with resistance and one that appears to be irrelevant) will be selected as targets for PCR assays.
The primers that amplify the genes containing the SNP will either be found in literature or designed using BLAST. For the experiments, during the co-incubation of bacteria and the antibiotic, cell samples will be extracted and washed before entering the single cell analysis workflow.
Conclusions and Outlooks
An aliquot of the control was extracted using the same commercial DNA extraction kit as the control. This may be primarily due to DNA damage during the ECL process (e.g., local high pH, which will be discussed later through simulation in this study), as we rule out PCR inhibition caused by electrolyzed cathodic discharges. The concentration of target bacteria in a sample can be obtained by direct counting of positive pores and calibrated using a Poisson distribution.
Therefore, the ionic strength of environmental water samples can have a significant impact on the performance of SAP microspheres. The 3D printed filter divided the tube into two chambers and the water samples are confined to the upper chamber prior to centrifugation by the filter due to the surface tension of the sample.
