Research

From Heterogeneous Samples to Single Cell Analysis: Separation and Encapsulation in Microfluidic Droplets

In our recent work, we published a paper titled “Integrated microfluidic platform for inertial separation and encapsulation of single cells in droplets”. In this study, we address a key challenge in modern biomedical research: the reliable analysis of individual cells within heterogeneous samples, where even cells of the same type exhibit intrinsic cell-to-cell variability. Single-cell analysis is therefore essential for understanding cellular heterogeneity, rare cell populations, and diverse biological functions and disease processes. However, conventional methods often rely on complex, multi-step workflows that can result in sample loss (particularly problematic for rare cells), contamination, and low efficiency.

To overcome these limitations, we developed an integrated microfluidic platform that combines inertial cell separation with precise single-cell encapsulation in droplets, enabling a seamless and high-throughput workflow for single-cell studies. The core innovation of this platform lies in the integration of two complementary microfluidic mechanisms.

The inertial separation module continuously focuses and separates cells based on size, generating a well-ordered cell stream. Subsequently, the droplet-based encapsulation module efficiently traps individual target cells within uniform microdroplets, creating isolated microenvironments suitable for downstream biological analysis. This platform achieves high encapsulation fidelity, ensuring that droplets contain either single cells or remain empty in a statistically controlled manner. Such precision is essential for applications including single-cell genomics and digital molecular assays.

Overall, this integrated platform opens new possibilities for a wide range of applications, including single-cell genomic and transcriptomic analysis, digital LAMP and digital PCR, rare cell detection in cancer and infectious diseases, and high-throughput screening of cellular responses to drugs or environmental stimuli.

You can find this research article at the following link:

https://doi.org/10.1039/D6LC00085A

When Tiny Beads Survive the Gut: A Closer Look at Smart Delivery Systems

Imagine swallowing a tiny capsule that doesn’t just carry a payload, but protects it, responds to your digestive system, and releases its contents only when the environment is right. This is the idea behind our work on core-shell hydrogel beads with emulsion cores, designed to behave like intelligent micro-carriers inside the gastrointestinal tract (GI).

In this study, “Stability and release characteristics of core‐shell beads with emulsion core under gastrointestinal conditions”, we explored how these structured microbeads behave as they move through the complex environments of digestion, from the acidic stomach to the more neutral and enzyme-rich intestines. The GI tract is a highly challenging environment for delivering sensitive ingredients such as probiotics, enzymes, or bioactive compounds. Acidic pH, enzymes, and varying ionic conditions can easily degrade or deactivate them before they reach their target site.

To address this, we developed core-shell beads: The core is an oil-in-water emulsion that can encapsulate hydrophobic or sensitive compounds. The shell is a protective hydrogel matrix that acts as a physical and chemical barrier. Together, this structure works like a microscopic “double shield,” combining protection and controlled release functionality.

We investigated how these beads respond under simulated gastrointestinal conditions, mimicking three key stages:

• Mouth phase: neutral pH

• Gastric phase: highly acidic environment with strong enzymatic activity

• Intestinal phase: neutral to slightly alkaline conditions with bile salts and enzymes

The key advantage of this system becomes most apparent in the intestinal phase. At this stage, the beads gradually begin to degrade, enabling the controlled release of the encapsulated emulsion core. This highlights an important aspect of the system: it is not only designed for protection, but also for spatiotemporal control of release. The objective is to ensure that delivery occurs at the site where absorption is most effective.

Overall, this work contributes to the broader field of advanced delivery systems for food, nutraceutical, and biomedical applications, where precise control over protection and release is essential for improving functionality and efficacy.

You can find this research article at the following link:

https://doi.org/10.1002/anbr.202500106

Turning DNA into Countable Beads: A New Era of Digital PCR

Imagine being able to count individual DNA molecules one by one, like counting grains of sand on a vast beach, so precisely that even a single copy of a gene can be detected and quantified. This is the power behind digital PCR, and our recent work takes a step forward in making it more robust, flexible, and easier to use through microfluidic technology.

In our study, titled “Microfluidic encapsulation of DNAs in liquid beads for digital PCR application”, we developed a microfluidic platform that transforms bulk DNA samples into thousands to millions of tiny, uniform liquid beads. Each bead acts as an independent microreactor, capable of holding either zero, one, or a few DNA molecules.

Traditional PCR methods measure DNA in bulk, which can sometimes mask subtle but important differences in concentration. Digital PCR, on the other hand, breaks the sample into many small compartments so that amplification happens at the single-molecule level. This allows for absolute quantification of DNA without relying on calibration curves. However, a major challenge is how to reliably generate large numbers of uniform, stable compartments that can survive thermal cycling without merging or losing their contents.

We addressed this challenge using a microfluidic encapsulation strategy. First, highly uniform DNA-containing droplets are generated under controlled flow conditions. These droplets are then further encapsulated to form core-shell liquid beads, where a protective outer shell surrounds the liquid core. The shell plays a critical role: it prevents coalescence, minimises evaporation, and protects the reaction contents from external contamination. At the same time, the shell remains optically transparent, allowing real-time observation and analysis of the reactions inside.

To validate the performance of this platform, we applied it to microbial DNA testing, demonstrating its capability to detect and quantify low concentrations of target DNA with high sensitivity and reliability. By analyzing partitioned reactions across thousands of beads, we confirmed accurate digital quantification and consistent amplification behavior, highlighting the robustness of the system for biological samples.

This approach offers several important advantages:

• High uniformity: Microfluidics enables precise control over bead size, improving quantitative accuracy. 

• Low reagent consumption: Reactions are miniaturized, reducing cost and sample requirements. 

• Improved stability: Encapsulation protects DNA and reagents from cross-contamination and evaporation. 

• True digital quantification: After PCR, beads are simply counted as positive or negative, enabling absolute DNA quantification. 

This technology opens new possibilities for genetic analysis in medical diagnostics, environmental monitoring, and biotechnology.

You can find this research article at the following link:

https://doi.org/10.1039/D3AN00868A