Microwell fluoride assay screening for enzymatic defluorination

There is intense interest in removing fluorinated compounds from the environment, environments are most efficiently remediated by microbial enzymes, and defluorinating enzymes are readily monitored by fluoride determination. Fluorine is the most electronegative element. Consequently, all mechanisms of enzymatic C-F bond cleavage produce fluoride anion, F-. Therefore, methods for the determination of fluoride are critical for C-F enzymology and apply to any fluorinated organic compounds, including PFAS, or per- and polyfluorinated alkyl substances. The biodegradation of most PFAS chemicals is rare or unknown. Accordingly, identifying new enzymes, or re-engineering the known defluorinases, will require rapid and sensitive methods for measuring fluoride in aqueous media. Most studies currently use ion chromatography or fluoride specific electrodes which are relatively sensitive but low throughput. The methods here describe refashioning a drinking water test to efficiently determine fluoride in enzyme and cell culture reaction mixtures. The method is based on lanthanum alizarin complexone binding of fluoride. Reworking the method to a microtiter well plate format allows detection of as little as 4 nmol of fluoride in 200 μL of assay buffer. The method is amenable to color imaging, spectrophotometric plate reading and automated liquid handling to expedite assays with thousands of enzymes and/or substrates for discovering and improving enzymatic defluorination.

Digital PCR using a simple PDMS microfluidic chip and standard laboratory equipment

Digital PCR (dPCR) enables sensitive and precise quantification of template nucleic acid without calibration. However, dPCR is not yet in widespread use, probably due to the need for expensive specialized instruments. In this paper, we describe a dPCR system using a simple microfluidic chip and common laboratory tools. The microfluidic chip consists of two parts: a PDMS part with 24,840 × 0.25 nL microwells and a PDMS-coated flat glass plate. Human RNase P gene was adopted as the model template. Commercial products of human genomic DNA and real-time PCR reagents were mixed to make a PCR mixture. The PCR mixture was confined to the microwells by the PDMS degas-driven liquid control technique. The thermal cycling was performed on a common well-type thermal cycler with a minor modification. During the thermal cycling, evaporation of the PCR mixture was prevented with a handmade water holder. In the fluorescence image, bright (positive) microwells and dim (negative) ones were clearly discriminated. The number of the positive microwells was counted using software, and was used for estimation of the template concentration in the sample based on the theory of the Poisson distribution. The estimated concentrations well agreed with the input template concentrations in the range from 1.32 copies/µL to 13 200 copies/µL. The techniques presented in this paper will pave the way for facile dPCR in a broad range of laboratories without the need for expensive instruments.

Back to the future: optimised microwell culture of individual human preimplantation stage embryos

Although in vitro culture of human embryos is a crucial step in assisted reproduction, the lack of focused research hampers worldwide standardisation and consistent outcomes. Only 1.2% of research papers published in five leading journals in human reproduction in 2019 focused on in vitro culture conditions, creating the impression that the optimisation process has approached its limits. On the other hand, in vitro culture of mammalian embryos is based on old principles, while there is no consensus on basic issues as density, time, medium change, gas atmosphere and small technical details including the way of drop preparation. This opinion paper aims to highlight and analyse the slow advancement in this field and stimulate research for simple and affordable solutions to meet the current requirements. A possible way for advancement is discussed in detail. Selection of embryos with the highest developmental competence requires individual culture and modification of the widely used "drop under oil" approach. Current use of three-dimensional surfaces instead of large flat bottoms is restricted to time-lapse systems, but these wells are designed for optical clarity, not for the needs of embryos. The size and shape of the original microwells (Well of the Well; WOW) offer a practical and straightforward solution to combine the benefits of communal and individual incubation and improve the overall quality of cultured embryos.

A microfluidic microwell device operated by the automated microfluidic control system for surface-enhanced Raman scattering-based antimicrobial susceptibility testing

Bloodstream infection (BSI) is a serious public health issue worldwide. Timely and effective antibiotics for controlling infection are crucial towards patient outcomes. However, the current culture-based methods of identifying bacteria and antimicrobial susceptibility testing (AST) remain labor-intensive and time-consuming, and are unable to provide early support to physicians in critical hours. To improve the effectiveness of early antibiotic therapy, Surface-enhanced Raman scattering (SERS) technology, has been used in bacterial detection and AST based on its high specificity and label-free features. To simplify sample preparation steps in SERS-AST, we proposed an automated microfluidic control system to integrate all required procedures into a single device. Our preliminary results demonstrated the system can achieve on-chip reagent replacement, bacteria trapping, and buffer exchange. Finally, in-situ SERS-AST was performed within 3.5 h by loading isolates of ampicilin susceptible and resistant E. coli and clear discrimination of two strains under antibiotic treatment was demonstrated. Overall, our system can standardize and simplify the SERS-AST protocol and implicate parallel bacterial detection. This prototypical integration demonstrates timely microbiological support to optimize early antibiotic therapy for fighting bacteremia.

Back to the future: optimised microwell culture of individual human preimplantation stage embryos

Although in vitro culture of human embryos is a crucial step in assisted reproduction, the lack of focused research hampers worldwide standardisation and consistent outcomes. Only 1.2% of research papers published in five leading journals in human reproduction in 2019 focused on in vitro culture conditions, creating the impression that the optimisation process has approached its limits. On the other hand, in vitro culture of mammalian embryos is based on old principles, while there is no consensus on basic issues as density, time, medium change, gas atmosphere and small technical details including the way of drop preparation. This opinion paper aims to highlight and analyse the slow advancement in this field and stimulate research for simple and affordable solutions to meet the current requirements. A possible way for advancement is discussed in detail. Selection of embryos with the highest developmental competence requires individual culture and modification of the widely used "drop under oil" approach. Current use of three-dimensional surfaces instead of large flat bottoms is restricted to time-lapse systems, but these wells are designed for optical clarity, not for the needs of embryos. The size and shape of the original microwells (Well of the Well; WOW) offer a practical and straightforward solution to combine the benefits of communal and individual incubation and improve the overall quality of cultured embryos.

Well-Based Antibody Arrays

Multiplex immunoassays are important tools in basic research and diagnostics. The ability to accurately quantify the presence of several antigens within an individual sample all at once has been useful in developing a proteomics view of biology. This in turn has enabled the development of disease-associated immunodiagnostic panels for better prognosis and well-being. Moreover, it is well understood that such multiplexing approaches lend themselves to automation, thereby reducing labor while providing the ability to dramatically conserve both reagent and sample all of which will reduce the cost per test. Here we describe various methods to create and use multiplex immunoassays in the wells of microtiter plates or similar formats.

Generation of uniform liver spheroids from human pluripotent stem cells for imaging-based drug toxicity analysis

Recent advances in pluripotent stem cell technology provide an alternative source of human hepatocytes to overcome the limitations of current toxicity tests. However, this approach requires optimization and standardization before it can be used as a fast and reliable toxicity screening system. Here, we designed and tested microwell culture platforms with various diameters. We found that large quantities of uniformly-sized hepatocyte-like cell (HLC) spheroids (3D-uniHLC-Ss) could be efficiently and reproducibly generated in a short period time from a small number of differentiating human pluripotent stem cells (hPSCs). The hPSC-3D-uniHLC-Ss that were produced in 500-μm diameter microwells consistently exhibited high expressions of hepatic marker genes and had no significant signs of cell death. Importantly, a hepatic master gene hepatocyte nuclear factor 4α (HNF4α) was maintained at high levels, and the epithelial-mesenchymal transition was significantly attenuated in hPSC-3D-uniHLC-Ss. Additionally, when compared with 3D-HLC-Ss that were produced in other 3D platforms, hPSC-3D-uniHLC-Ss showed significantly higher hepatic gene expressions and drug-metabolizing activity of the enzyme, CYP3A4. Imaging-based drug toxicity studies demonstrated that hPSC-3D-uniHLC-Ss exhibited enhanced sensitivity to various hepatotoxicants, compared to HLCs, which were differentiated under 2D conditions. Precise prediction of drug-induced hepatotoxicity is a crucial step in the early phases of drug discovery. Thus, the hPSC-3D-uniHLC-Ss produced using our microwell platform could be used as an imaging-based toxicity screening system to predict drug hepatotoxicity.

3D Microwell Platforms for Control of Single Cell 3D Geometry and Intracellular Organization

Introduction

Cell structure and migration is impacted by the mechanical properties and geometry of the cell adhesive environment. Most studies to date investigating the effects of 3D environments on cells have not controlled geometry at the single-cell level, making it difficult to understand the influence of 3D environmental cues on single cells. Here, we developed microwell platforms to investigate the effects of 2D vs. 3D geometries on single-cell F-actin and nuclear organization.

Methods

We used microfabrication techniques to fabricate three polyacrylamide platforms: 3D microwells with a 3D adhesive environment (3D/3D), 3D microwells with 2D adhesive areas at the bottom only (3D/2D), and flat 2D gels with 2D patterned adhesive areas (2D/2D). We measured geometric swelling and Young's modulus of the platforms. We then cultured C2C12 myoblasts on each platform and evaluated the effects of the engineered microenvironments on F-actin structure and nuclear shape.

Results

We tuned the mechanical characteristics of the microfabricated platforms by manipulating the gel formulation. Crosslinker ratio strongly influenced geometric swelling whereas total polymer content primarily affected Young's modulus. When comparing cells in these platforms, we found significant effects on F-actin and nuclear structures. Our analysis showed that a 3D/3D environment was necessary to increase actin and nuclear height. A 3D/2D environment was sufficient to increase actin alignment and nuclear aspect ratio compared to a 2D/2D environment.

Conclusions

Using our novel polyacrylamide platforms, we were able to decouple the effects of 3D confinement and adhesive environment, finding that both influenced actin and nuclear structure.

Intermittent parathyroid hormone (1-34) supplementation of bone marrow stromal cell cultures may inhibit hypertrophy, but at the expense of chondrogenesis

Background

Bone marrow stromal cells (BMSC) have promise in cartilage tissue engineering, but for their potential to be fully realised, the propensity to undergo hypertrophy must be mitigated. The literature contains diverging reports on the effect of parathyroid hormone (PTH) on BMSC differentiation. Cartilage tissue models can be heterogeneous, confounding efforts to improve media formulations.

Methods

Herein, we use a novel microwell platform (the Microwell-mesh) to manufacture hundreds of small-diameter homogeneous micro-pellets and use this high-resolution assay to quantify the influence of constant or intermittent PTH(1–34) medium supplementation on BMSC chondrogenesis and hypertrophy. Micro-pellets were manufactured from 5000 BMSC each and cultured in standard chondrogenic media supplemented with (1) no PTH, (2) intermittent PTH, or (3) constant PTH.

Results

Relative to control chondrogenic cultures, BMSC micro-pellets exposed to intermittent PTH had reduced hypertrophic gene expression following 1 week of culture, but this was accompanied by a loss in chondrogenesis by the second week of culture. Constant PTH treatment was detrimental to chondrogenic culture.

Conclusions

This study provides further clarity on the role of PTH on chondrogenic differentiation in vitro and suggests that while PTH may mitigate BMSC hypertrophy, it does so at the expense of chondrogenesis.

Nx1-Seq (Well Based Single-Cell Analysis System)

Research on the hierarchical nature of cell differentiation and heterogeneity in tissues has been performed by isolating and identifying cells by the use of monoclonal antibodies, cell sorting, microdissection, and functional assays. However, it is difficult to analyze continuous changes in cell differentiation and the identification of cells for which cell markers are unclear. Furthermore, cell populations considered identical were shown to be diverse. Recently, single cell gene expression analysis was performed to help understand the complexity of cell populations. Single-cell analysis can analyze the diversity of individual cell populations as well as the tissue microenvironment, and is extremely useful for research on intercellular interactions in diseases and identifying specific marker genes. Recent advances in technology have made it possible to analyze hundreds of single cells. In this paper, we introduce our newly developed well-based single-cell transcriptome method, which includes other methods.

A microwell culture system that allows group culture and is compatible with human single media

PURPOSE

A microwell culture system that facilitates group culture, such as well-of-the-well (WOW), improves embryonic development in an individual culture. We examined the effect of WOW on embryonic development in vitro with commercially available human single culture media.

METHODS

Using four different commercial human single culture media, in vitro development and imprinted gene expression of bovine embryos cultured in WOW were compared to droplet culture (one zygote per drop). To determine the effects of microwell and group culture on embryonic development, different numbers of embryos were cultured in droplet or WOW. Diffusion simulation of accumulating metabolites was conducted using the finite volume method.

RESULTS

WOW had a positive effect on bovine embryonic development, regardless of the type of single culture media. Imprinted gene expression was not different between droplet- and WOW-derived blastocysts. The microwell and group cultures in WOW showed a significant positive effect on the rate of total blastocysts and the rate of development to the expanded and hatching blastocyst stages. The assumed cumulative metabolite concentration of WOW with one embryo was 1.47 times higher than that of droplet culture with one embryo. Furthermore, the concentration of WOW with three embryos was 1.54 times higher than that of WOW with one embryo.

CONCLUSIONS

In using human single culture media, a microwell culture system that allows group culture could be a powerful clinical tool for improving the success of assisted reproductive technologies.

Hydrogel Printing Based on UV-Induced Projection for Cell-Based Microarray Fabrication

A considerable number of studies have focused on fabrication of hydrogel microstructures due to its wide applications in tissue engineering, drug delivery, and extracellular matrix construction. Here, we introduce a hydrogel printing method based on UV-induced projection via a digital micromirror device (DMD). Arbitrary microstructures could be fabricated within few seconds (<3) by modulating UV projection using DMD as digital dynamic masks instead of a physical mask, which also offers a high degree of flexibility and repeatability. Furthermore, the ability of PEGDA film to hinder cell adhesion makes it possible to control area over which cells attach.

Laser-fabricated cell patterning stencil for single cell analysis

Precise spatial positioning and isolation of mammalian cells is a critical component of many single cell experimental methods and biological engineering applications. Although a variety of cell patterning methods have been demonstrated, many of these methods subject cells to high stress environments, discriminate against certain phenotypes, or are a challenge to implement. Here, we demonstrate a rapid, simple, indiscriminate, and minimally perturbing cell patterning method using a laser fabricated polymer stencil. The stencil fabrication process requires no stencil-substrate alignment, and is readily adaptable to various substrate geometries and experiments.

Isolation of single cells for protein therapeutics using microwell selection and Surface Plasmon Resonance imaging

Here the feasibility is demonstrated that by combining Surface Plasmon Resonance Imaging (SPRi) and self-sorting microwell technology product secretion of individual cells can be monitored. Additionally isolation of the selected cells can be performed by punching the cells from the microwells using coordinates of the positions of microwells obtained with SPRi. Cells of interest can be retrieved sterile from the microwell array for further cultivation.

Early retinal differentiation of human pluripotent stem cells in microwell suspension cultures

Objective

To develop a microwell suspension platform for the adaption of attached stem cell differentiation protocols into mixed suspension culture.

Results

We adapted an adherent protocol for the retinal differentiation of human induced pluripotent stem cells (hiPSCs) using a two-step protocol. Establishing the optimum embryoid body (EB) starting size and shaking speed resulted in the translation of the original adherent process into suspension culture. Embryoid bodies expanded in size as the culture progressed resulting in the expression of characteristic markers of early (Rx, Six and Otx2) and late (Crx, Nrl and Rhodopsin) retinal differentiation. The new process also eliminated the use of matrigel, an animal-derived extracellular matrix coating.

Conclusions

Shaking microwells offer a fast and cost-effective method for proof-of-concept studies to establish whether pluripotent stem cell differentiation processes can be translated into mixed suspension culture.

Electronic supplementary material

The online version of this article (doi:10.1007/s10529-016-2244-7) contains supplementary material, which is available to authorized users.

Advances in digital polymerase chain reaction (dPCR) and its emerging biomedical applications

Since the invention of polymerase chain reaction (PCR) in 1985, PCR has played a significant role in molecular diagnostics for genetic diseases, pathogens, oncogenes and forensic identification. In the past three decades, PCR has evolved from end-point PCR, through real-time PCR, to its current version, which is the absolute quantitive digital PCR (dPCR). In this review, we first discuss the principles of all key steps of dPCR, i.e., sample dispersion, amplification, and quantification, covering commercialized apparatuses and other devices still under lab development. We highlight the advantages and disadvantages of different technologies based on these steps, and discuss the emerging biomedical applications of dPCR. Finally, we provide a glimpse of the existing challenges and future perspectives for dPCR.

Homodimerization of glucocorticoid receptor from single cells investigated using fluorescence correlation spectroscopy and microwells

Glucocorticoid receptor α (GR) binds to the promoter regions of target genes as a homodimer and activates its transcriptional process. Though the homodimerization is thought to be the initial and essential process, the dissociation constant for homodimerization of GR remains controversial. To quantify homodimerization of (enhanced green fluorescence protein) EGFP-(glucocorticoid receptor) GR, the particle brightness in lysates from single cell was estimated for the fraction of homodimeric EGFP-GR using fluorescence correlation spectroscopy and microwells. Fitting the data with a bimolecular reaction model, the dissociation constant was determined. Moreover slow-diffusion complex was observed. These results suggest that EGFP-GR forms not only a monomer-dimer equivalent state but also a large-molecular-weight complex.

The microwell-mesh: A novel device and protocol for the high throughput manufacturing of cartilage microtissues

Microwell platforms are frequently described for the efficient and uniform manufacture of 3-dimensional (3D) multicellular microtissues. Multiple partial or complete medium exchanges can displace microtissues from discrete microwells, and this can result in either the loss of microtissues from culture, or microtissue amalgamation when displaced microtissues fall into common microwells. Herein we describe the first microwell platform that incorporates a mesh to retain microtissues within discrete microwells; the microwell-mesh. We show that bonding a nylon mesh with an appropriate pore size over the microwell openings allows single cells to pass through the mesh into the microwells during the seeding process, but subsequently retains assembled microtissues within discrete microwells. To demonstrate the utility of this platform, we used the microwell-mesh to manufacture hundreds of cartilage microtissues, each formed from 5 × 10(3) bone marrow-derived mesenchymal stem/stromal cells (MSC). The microwell-mesh enabled reliable microtissue retention over 21-day cultures that included multiple full medium exchanges. Cartilage-like matrix formation was more rapid and homogeneous in microtissues than in conventional large diameter control cartilage pellets formed from 2 × 10(5) MSC each. The microwell-mesh platform offers an elegant mechanism to retain microtissues in microwells, and we believe that this improvement will make this platform useful in 3D culture protocols that require multiple medium exchanges, such as those that mimic specific developmental processes or complex sequential drug exposures.