User-Loaded SlipChip for Equipment-Free Multiplexed Nanoliter-Scale Experiments

This paper describes a microfluidic approach to perform multiplexed nanoliter-scale experiments by combining a sample with multiple different reagents, each at multiple mixing ratios. This approach employs a user-loaded, equipment-free SlipChip. The mixing ratios, characterized by diluting a fluorescent dye, could be controlled by the volume of each of the combined wells. The SlipChip design was validated on an ∼12 nL scale by screening the conditions for crystallization of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei against 48 different reagents; each reagent was tested at 11 different mixing ratios, for a total of 528 crystallization trials. The total consumption of the protein sample was ∼10 μL. Conditions for crystallization were successfully identified. The crystallization experiments were successfully scaled up in well plates using the conditions identified in the SlipChip. Crystals were characterized by X-ray diffraction and provided a protein structure in a different space group and at a higher resolution than the structure obtained by conventional methods. In this work, this user-loaded SlipChip has been shown to reliably handle fluids of diverse physicochemical properties, such as viscosities and surface tensions. Quantitative measurements of fluorescent intensities and high-resolution imaging were straighforward to perform in these glass SlipChips. Surface chemistry was controlled using fluorinated lubricating fluid, analogous to the fluorinated carrier fluid used in plug-based crystallization. Thus, we expect this approach to be valuable in a number of areas beyond protein crystallization, especially those areas where droplet-based microfluidic systems have demonstrated successes, including measurements of enzyme kinetics and blood coagulation, cell-based assays, and chemical reactions

User-Loaded SlipChip for Equipment-Free Multiplexed Nanoliter-Scale Experiments

This paper describes a microfluidic approach to perform multiplexed nanoliter-scale experiments by combining a sample with multiple different reagents, each at multiple mixing ratios. This approach employs a user-loaded, equipment-free SlipChip. The mixing ratios, characterized by diluting a fluorescent dye, could be controlled by the volume of each of the combined wells. The SlipChip design was validated on an ∼12 nL scale by screening the conditions for crystallization of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei against 48 different reagents; each reagent was tested at 11 different mixing ratios, for a total of 528 crystallization trials. The total consumption of the protein sample was ∼10 μL. Conditions for crystallization were successfully identified. The crystallization experiments were successfully scaled up in well plates using the conditions identified in the SlipChip. Crystals were characterized by X-ray diffraction and provided a protein structure in a different space group and at a higher resolution than the structure obtained by conventional methods. In this work, this user-loaded SlipChip has been shown to reliably handle fluids of diverse physicochemical properties, such as viscosities and surface tensions. Quantitative measurements of fluorescent intensities and high-resolution imaging were straighforward to perform in these glass SlipChips. Surface chemistry was controlled using fluorinated lubricating fluid, analogous to the fluorinated carrier fluid used in plug-based crystallization. Thus, we expect this approach to be valuable in a number of areas beyond protein crystallization, especially those areas where droplet-based microfluidic systems have demonstrated successes, including measurements of enzyme kinetics and blood coagulation, cell-based assays, and chemical reactions

Multiparameter Screening on SlipChip Used for Nanoliter Protein Crystallization Combining Free Interface Diffusion and Microbatch Methods

This paper describes two SlipChip-based approaches to protein crystallization: a SlipChip-based free interface diffusion (FID) method and a SlipChip-based composite method that simultaneously performs microbatch and FID crystallization methods in a single device. The FID SlipChip was designed to screen multiple reagents, each at multiple diffusion equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis, against 48 different reagents at five different equilibration times each, consuming 12 μL of each protein for a total of 480 experiments using three SlipChips. The composite SlipChip was designed to screen multiple reagents, each at multiple mixing ratios and multiple equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis. To prevent cross-contamination while keeping the solution in the neck channels for FID stable, the plates of the SlipChip were etched with a pattern of nanowells. This nanopattern was used to increase the contact angle of aqueous solutions on the surface of the silanized glass. The composite SlipChip increased the number of successful crystallization conditions and identified more conditions for crystallization than separate FID and microbatch screenings. Crystallization experiments were scaled up in well plates using conditions identified during the SlipChip screenings, and X-ray diffraction data were obtained to yield the protein structure of dihydrofolate reductase/thymidylate synthase at 1.95 Å resolution. This free-interface diffusion approach provides a convenient and high-throughput method of setting up gradients in microfluidic devices and may find additional applications in cell-based assays

User-Loaded SlipChip for Equipment-Free Multiplexed Nanoliter-Scale Experiments

This paper describes a microfluidic approach to perform multiplexed nanoliter-scale experiments by combining a sample with multiple different reagents, each at multiple mixing ratios. This approach employs a user-loaded, equipment-free SlipChip. The mixing ratios, characterized by diluting a fluorescent dye, could be controlled by the volume of each of the combined wells. The SlipChip design was validated on an ∼12 nL scale by screening the conditions for crystallization of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei against 48 different reagents; each reagent was tested at 11 different mixing ratios, for a total of 528 crystallization trials. The total consumption of the protein sample was ∼10 μL. Conditions for crystallization were successfully identified. The crystallization experiments were successfully scaled up in well plates using the conditions identified in the SlipChip. Crystals were characterized by X-ray diffraction and provided a protein structure in a different space group and at a higher resolution than the structure obtained by conventional methods. In this work, this user-loaded SlipChip has been shown to reliably handle fluids of diverse physicochemical properties, such as viscosities and surface tensions. Quantitative measurements of fluorescent intensities and high-resolution imaging were straighforward to perform in these glass SlipChips. Surface chemistry was controlled using fluorinated lubricating fluid, analogous to the fluorinated carrier fluid used in plug-based crystallization. Thus, we expect this approach to be valuable in a number of areas beyond protein crystallization, especially those areas where droplet-based microfluidic systems have demonstrated successes, including measurements of enzyme kinetics and blood coagulation, cell-based assays, and chemical reactions

Multiparameter Screening on SlipChip Used for Nanoliter Protein Crystallization Combining Free Interface Diffusion and Microbatch Methods

This paper describes two SlipChip-based approaches to protein crystallization: a SlipChip-based free interface diffusion (FID) method and a SlipChip-based composite method that simultaneously performs microbatch and FID crystallization methods in a single device. The FID SlipChip was designed to screen multiple reagents, each at multiple diffusion equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis, against 48 different reagents at five different equilibration times each, consuming 12 μL of each protein for a total of 480 experiments using three SlipChips. The composite SlipChip was designed to screen multiple reagents, each at multiple mixing ratios and multiple equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis. To prevent cross-contamination while keeping the solution in the neck channels for FID stable, the plates of the SlipChip were etched with a pattern of nanowells. This nanopattern was used to increase the contact angle of aqueous solutions on the surface of the silanized glass. The composite SlipChip increased the number of successful crystallization conditions and identified more conditions for crystallization than separate FID and microbatch screenings. Crystallization experiments were scaled up in well plates using conditions identified during the SlipChip screenings, and X-ray diffraction data were obtained to yield the protein structure of dihydrofolate reductase/thymidylate synthase at 1.95 Å resolution. This free-interface diffusion approach provides a convenient and high-throughput method of setting up gradients in microfluidic devices and may find additional applications in cell-based assays

Cross-Interface Emulsification for Generating Size-Tunable Droplets

We report cross-interface emulsification (XiE), a simple method for the generation of monodisperse droplets of controllable volumes from picoliter to nanoliter. A device is set up in which a fused-silica capillary is vibrating across the surface of the continuous phase (mineral oil) in a reservoir, and the flow of the dispersed phase (aqueous solution) in the capillary is segmented into monodisperse droplets at the air/oil interface. We find that the volume of droplets is mainly dominated by the flow rate and vibrating frequency and not significantly influenced by other factors, such as the viscosity of the continuous phase and dispersed phase, the inner diameter of the capillary (20–100 μm), or the shape of the tip (tapered or flat). These features reflect high robustness, flexibility, and precision of XiE for on-demand volume control of droplets. The droplets automatically assemble into planar monolayer droplet arrays (PMDA) in flat-bottomed microwells of 96-well plates, offering excellent convenience for imaging of droplets. As a representative application, we carry out digital loop-mediated isothermal amplification using PMDAs with multivolume droplets for the absolute quantification of nucleic acids. Our results demonstrate that XiE is simple and controllable for the production of monodisperse size-tunable droplets, and it offers opportunities for common laboratories, even without microfabrication facilities, to perform digital quantification, single cell analysis, and other biochemical assays with high throughput

Cross-Interface Emulsification for Generating Size-Tunable Droplets

We report cross-interface emulsification (XiE), a simple method for the generation of monodisperse droplets of controllable volumes from picoliter to nanoliter. A device is set up in which a fused-silica capillary is vibrating across the surface of the continuous phase (mineral oil) in a reservoir, and the flow of the dispersed phase (aqueous solution) in the capillary is segmented into monodisperse droplets at the air/oil interface. We find that the volume of droplets is mainly dominated by the flow rate and vibrating frequency and not significantly influenced by other factors, such as the viscosity of the continuous phase and dispersed phase, the inner diameter of the capillary (20–100 μm), or the shape of the tip (tapered or flat). These features reflect high robustness, flexibility, and precision of XiE for on-demand volume control of droplets. The droplets automatically assemble into planar monolayer droplet arrays (PMDA) in flat-bottomed microwells of 96-well plates, offering excellent convenience for imaging of droplets. As a representative application, we carry out digital loop-mediated isothermal amplification using PMDAs with multivolume droplets for the absolute quantification of nucleic acids. Our results demonstrate that XiE is simple and controllable for the production of monodisperse size-tunable droplets, and it offers opportunities for common laboratories, even without microfabrication facilities, to perform digital quantification, single cell analysis, and other biochemical assays with high throughput

Cross-Interface Emulsification for Generating Size-Tunable Droplets

We report cross-interface emulsification (XiE), a simple method for the generation of monodisperse droplets of controllable volumes from picoliter to nanoliter. A device is set up in which a fused-silica capillary is vibrating across the surface of the continuous phase (mineral oil) in a reservoir, and the flow of the dispersed phase (aqueous solution) in the capillary is segmented into monodisperse droplets at the air/oil interface. We find that the volume of droplets is mainly dominated by the flow rate and vibrating frequency and not significantly influenced by other factors, such as the viscosity of the continuous phase and dispersed phase, the inner diameter of the capillary (20–100 μm), or the shape of the tip (tapered or flat). These features reflect high robustness, flexibility, and precision of XiE for on-demand volume control of droplets. The droplets automatically assemble into planar monolayer droplet arrays (PMDA) in flat-bottomed microwells of 96-well plates, offering excellent convenience for imaging of droplets. As a representative application, we carry out digital loop-mediated isothermal amplification using PMDAs with multivolume droplets for the absolute quantification of nucleic acids. Our results demonstrate that XiE is simple and controllable for the production of monodisperse size-tunable droplets, and it offers opportunities for common laboratories, even without microfabrication facilities, to perform digital quantification, single cell analysis, and other biochemical assays with high throughput

μMET: A Novel Reusable Microfluidic Chip for Precision Microbial Enumeration Tests

This work describes μMET, a novel microfluidic device for precise microbial enumeration tests (MET), essential in pharmaceutical, cosmetic, and food industries for ensuring microbiological safety standards. The μMET chip, comprising two hydrophobic glass plates, features a 15-μm deep μMET chamber enhanced by nanopillars and air supply units, facilitating both immediate and growth-dependent MET. Experimental results, with E. coli as a model bacterium, demonstrate that μMET provides counting linearity that outperforms traditional hemocytometers. The chip’s design mitigates challenges like evaporation and ensures high-resolution imaging, making it a cost-effective and reusable alternative to conventional methods. Notably, bright-field μMET eliminates the need for fluorescent staining, streamlining operations with deep-learning algorithms for bacterial counts. Furthermore, we have developed a high-parallel μMET chip featuring 16 counting chambers, enhancing throughput and accommodating immediate and growth-dependent MET approaches. Its innovative design and adaptability render the μMET chip as a valuable tool for microbiology, medicine, and industry applications

Niche and ecosystem preference of earliest diverging fungi in soils

Within the supergroup Rotosphaeromycetes, or “Holomycota”/“Nucletmycea”, there are several well-recognised unicellular clades in the earliest diverging fungi (EDF). However, we know little about their occurrence. Here, we investigated EDF in the rhizosphere and bulk soils from cropland, forest, orchard, and wetland ecosystems around the Beijing-Hebei area, China, to illustrate their niche and ecosystem preference. More than 500 new operational taxonomic units (OTUs) of EDF were detected based on the 18S rRNA genes. Microsporida and Aphelida constitute dominant groups, whereas Rozellosporida was quite rare. Although the EDF community was site-specific, the soil chemical characteristics, vegetation, and other eukaryotic microorganisms were the key factors driving the occurrence of EDF. Moreover, the stochastic process consisted the most of the EDF community assembly.</p