Automated Raman based cell sorting with 3D microfluidics

Raman-Activated, Interactive Sorting of Isotope-Labeled Bacteria

Due to its high spatial resolution, Raman microspectroscopy allows for the analysis of single microbial cells. Since Raman spectroscopy analyzes the whole cell content, this method is phenotypic and can therefore be used to evaluate cellular changes. In particular, labeling with stable isotopes (SIPs) enables the versatile use and observation of different metabolic states in microbes. Nevertheless, static measurements can only analyze the present situation and do not allow for further downstream evaluations. Therefore, a combination of Raman analysis and cell sorting is necessary to provide the possibility for further research on selected bacteria in a sample. Here, a new microfluidic approach for Raman-activated continuous-flow sorting of bacteria using an optical setup for image-based particle sorting with synchronous acquisition and analysis of Raman spectra for making the sorting decision is demonstrated, showing that active cells can be successfully sorted by means of this microfluidic chip.

Raman cell sorting for single-cell research

Cells constitute the fundamental units of living organisms. Investigating individual differences at the single-cell level facilitates an understanding of cell differentiation, development, gene expression, and cellular characteristics, unveiling the underlying laws governing life activities in depth. In recent years, the integration of single-cell manipulation and recognition technologies into detection and sorting systems has emerged as a powerful tool for advancing single-cell research. Raman cell sorting technology has garnered attention owing to its non-labeling, non-destructive detection features and the capability to analyze samples containing water. In addition, this technology can provide live cells for subsequent genomics analysis and gene sequencing. This paper emphasizes the importance of single-cell research, describes the single-cell research methods that currently exist, including single-cell manipulation and single-cell identification techniques, and highlights the advantages of Raman spectroscopy in the field of single-cell analysis by comparing it with the fluorescence-activated cell sorting (FACS) technique. It describes various existing Raman cell sorting techniques and introduces their respective advantages and disadvantages. The above techniques were compared and analyzed, considering a variety of factors. The current bottlenecks include weak single-cell spontaneous Raman signals and the requirement for a prolonged total cell exposure time, significantly constraining Raman cell sorting technology's detection speed, efficiency, and throughput. This paper provides an overview of current methods for enhancing weak spontaneous Raman signals and their associated advantages and disadvantages. Finally, the paper outlines the detailed information related to the Raman cell sorting technology mentioned in this paper and discusses the development trends and direction of Raman cell sorting.

Raman spectroscopy-based microfluidic platforms: A promising tool for detection of foodborne pathogens in food products

Rapid and sensitive detection of foodborne pathogens in food products is paramount for ensuring food safety and public health. In the ongoing effort to tackle this issue, detection methods are continually researched and upgraded to achieve rapidity, sensitivity, portability, and cost-effectiveness. This review addresses the critical need for improved technique by focusing on Raman spectroscopy-based microfluidic platforms, which have shown potential in revolutionizing the field of foodborne pathogen analysis offering point-of-care diagnosis and multiplex detection. The key problem lies in the persistent threat of compromised food quality and public health due to inadequate pathogen detection. The review elucidates the various trapping strategies employed in a microfluidic platform, including optical trapping, electrical trapping, mechanical trapping, and acoustic trapping for the capture of microbial cells. Subsequently, the review delves into the key aspects of the application of microbial detection in food products, highlighting recent advances and challenges in the field. The integrated technique allows point-of-care application assessment, which is an attractive quality for in-line and real-time detection of foodborne pathogens. However, the application of the technique in food products is limited and requires further research to combat the complexity of the food matrix, reduced costs of production, and ensure real-time use for diverse pathogens. Ultimately, this review aims to propel advancements in microbial detection, thus promoting enhanced food safety through state-of-the-art technologies.

Ultrasensitive discrimination of volatile organic compounds using a microfluidic silicon SERS artificial intelligence chip

Current gaseous sensors hardly discriminate trace volatile organic compounds at the ppt level. Herein, we present an integrated platform for simultaneously enabling rapid preconcentration, reliable surface-enhanced Raman scattering, (SERS) detection and automatic identification of trace aldehydes at the ppt level. For rapid preconcentration, we demonstrate that the nozzle-like microfluidic concentrator allows the enrichment of rare gaseous analytes by five-fold in only 0.01 ms. The enriched gas is subsequently captured and detected by an integrated silicon-based SERS chip, which is made of zeolitic imidazolate framework-8 coated silver nanoparticles grown in situ on a silicon wafer. After SERS measurement, a fully connected deep neural network is built to extract faint features in the spectral dataset and discriminate volatile organic compound classes. We demonstrate that six kinds of gaseous aldehydes at 100 ppt could be detected and classified with an identification accuracy of ∼80.9% by using this platform.

High-throughput single-cell sorting by stimulated Raman-activated cell ejection

Single-cell sorting is essential to explore cellular heterogeneity in biology and medicine. Recently developed Raman-activated cell sorting (RACS) circumvents the limitations of fluorescence-activated cell sorting, such as the cytotoxicity of labels. However, the sorting throughputs of all forms of RACS are limited by the intrinsically small cross-section of spontaneous Raman scattering. Here, we report a stimulated Raman-activated cell ejection (S-RACE) platform that enables high-throughput single-cell sorting based on high-resolution multi-channel stimulated Raman chemical imaging, in situ image decomposition, and laser-induced cell ejection. The performance of this platform was illustrated by sorting a mixture of 1 μm polymer beads, where 95% yield, 98% purity, and 14 events per second throughput were achieved. Notably, our platform allows live cell ejection, allowing for the growth of single colonies of bacteria and fungi after sorting. To further illustrate the chemical selectivity, lipid-rich Rhodotorula glutinis cells were successfully sorted from a mixture with Saccharomyces cerevisiae, confirmed by downstream quantitative PCR. Furthermore, by integrating a closed-loop feedback control circuit into the system, we realized real-time single-cell imaging and sorting, and applied this method to precisely eject regions of interest from a rat brain tissue section. The reported S-RACE platform opens exciting opportunities for a wide range of single-cell applications in biology and medicine.

High-performance microchip electrophoresis separations of preterm birth biomarkers using 3D printed microfluidic devices

We employed digital light processing-stereolithography 3D printing to create microfluidic devices with different designs for microchip electrophoresis (µCE). Short or long straight channel, and two- or four-turn serpentine channel microfluidic devices with separation channel lengths of 1.3, 3.1, 3.0, and 4.7 cm, respectively, all with a cross injector design, were fabricated. We measured current as a function of time and voltage to determine a separation time window and conditions for the onset of Joule heating in these designs. Separations in these devices were evaluated by performing µCE and measuring theoretical plate counts for electric field strengths near and above the onset of Joule heating, with fluorescently labeled glycine and phenylalanine as model analytes. We further demonstrated µCE of peptides and proteins related to preterm birth risk, showing increased peak capacity and resolution compared to previous results with 3D printed microdevices. These results mark an important step forward in the use of 3D printed microfluidic devices for rapid bioanalysis by µCE.

Versatile, facile and low-cost single-cell isolation, culture and sequencing by optical tweezer-assisted pool-screening

Real-time image-based sorting of target cells in a precisely indexed manner is desirable for sequencing or cultivating individual human or microbial cells directly from clinical or environmental samples; however, the versatility of existing methods is limited as they are usually not broadly applicable to all cell sizes. Here, an optical tweezer-assisted pool-screening and single-cell isolation (OPSI) system is established for precise, indexed isolation of individual bacterial, yeast or human-cancer cells. A controllable static flow field that acts as a cell pool is achieved in a microfluidics chip, to enable precise and ready screening of cells of 1 to 40 μm in size by bright-field, fluorescence, or Raman imaging. The target cell is then captured by a 1064 nm optical tweezer and deposited as one-cell-harboring nanoliter microdroplets in a one-cell-one-tube manner. For bacterial, yeast and human cells, OPSI achieves a >99.7% target-cell sorting purity and a 10-fold elevated speed of 10-20 cells per min. Moreover, OPSI-based one-cell RNA-seq of human cancer cells yields high quality and reproducible single-cell transcriptome profiles. The versatility, facileness, flexibility, modularized design, and low cost of OPSI suggest its broad applications for image-based sorting of target cells.

Upgraded User-Friendly Image-Activated Microfluidic Cell Sorter Using an Optimized and Fast Deep Learning Algorithm

Image-based cell sorting is essential in biological and biomedical research. The sorted cells can be used for downstream analysis to expand our knowledge of cell-to-cell differences. We previously demonstrated a user-friendly image-activated microfluidic cell sorting technique using an optimized and fast deep learning algorithm. Real-time isolation of cells was carried out using this technique with an inverted microscope. In this study, we devised a recently upgraded sorting system. The cell sorting techniques shown on the microscope were implemented as a real system. Several new features were added to make it easier for the users to conduct the real-time sorting of cells or particles. The newly added features are as follows: (1) a high-resolution linear piezo-stage is used to obtain in-focus images of the fast-flowing cells; (2) an LED strobe light was incorporated to minimize the motion blur of fast-flowing cells; and (3) a vertical syringe pump setup was used to prevent the cell sedimentation. The sorting performance of the upgraded system was demonstrated through the real-time sorting of fluorescent polystyrene beads. The sorter achieved a 99.4% sorting purity for 15 μm and 10 μm beads with an average throughput of 22.1 events per second (eps).

ANN-Based Instantaneous Simulation of Particle Trajectories in Microfluidics

Microfluidics has shown great potential in cell analysis, where the flowing path in the microfluidic device is important for the final study results. However, the design process is time-consuming and labor-intensive. Therefore, we proposed an ANN method with three dense layers to analyze particle trajectories at the critical intersections and then put them together with the particle trajectories in straight channels. The results showed that the ANN prediction results are highly consistent with COMSOL simulation results, indicating the applicability of the proposed ANN method. In addition, this method not only shortened the simulation time but also lowered the computational expense, providing a useful tool for researchers who want to receive instant simulation results of particle trajectories.

3D in-plane integrated micro reflectors enhancing signal capture in lab on a chip applications

The integration of micro-optics in lab on a chip (LOCs) devices is crucial both for increasing the solid angle of acquisition and reducing the optical losses, aiming at improving the signal-to-noise ratio (SNR). In this work, we present the thriving combination of femtosecond laser irradiation followed by chemical etching (FLICE) technique with CO₂ laser polishing and inkjet printing to fabricate in-plane, 3D off-axis reflectors, featuring ultra-high optical quality (RMS ∼3 nm), fully integrated on fused silica substrates. Such micro-optic elements can be used both in the excitation path, focusing an incoming beam in 3D, and in the acquisition branch, harvesting the optical signal coming from a specific point in space. The flexibility of the manufacturing process allows the realization of micro-optics with several sizes, shapes and their integration with photonic circuits and microfluidic networks.

Microfluidics and surface-enhanced Raman spectroscopy, a win-win combination?

With the continuous development in nanoscience and nanotechnology, analytical techniques like surface-enhanced Raman spectroscopy (SERS) render structural and chemical information of a variety of analyte molecules in ultra-low concentration. Although this technique is making significant progress in various fields, the reproducibility of SERS measurements and sensitivity towards small molecules are still daunting challenges. In this regard, microfluidic surface-enhanced Raman spectroscopy (MF-SERS) is well on its way to join the toolbox of analytical chemists. This review article explains how MF-SERS is becoming a powerful tool in analytical chemistry. We critically present the developments in SERS substrates for microfluidic devices and how these substrates in microfluidic channels can improve the SERS sensitivity, reproducibility, and detection limit. We then introduce the building materials for microfluidic platforms and their types such as droplet, centrifugal, and digital microfluidics. Finally, we enumerate some challenges and future directions in microfluidic SERS. Overall, this article showcases the potential and versatility of microfluidic SERS in overcoming the inherent issues in the SERS technique and also discusses the advantage of adding SERS to the arsenal of microfluidics.

Advances in droplet microfluidics for SERS and Raman analysis

Raman spectroscopy can realize qualitative and quantitative characterization, and surface-enhanced Raman spectroscopy (SERS) can further enhance its detection sensitivity. In combination with droplet microfluidics, some significant but insurmountable limitations of SERS and Raman spectroscopy can be overcome to some extent, thus improving their detection capability and extending their application. During the past decade, these systems have constantly developed and demonstrated a great potential in more applications, but there is no new review systematically summarizing the droplet microfluidics-based Raman and SERS analysis system since the first related review was published in 2011. Thus, there is a great need for a new review to summarize the advances. In this review, we focus on droplet microfluidics-based Raman and SERS analysis, and summarize two mainstream research directions on this topic up to now. The one is SERS or Raman detection in the moving droplet microreactors, including analysis of molecules, single cells and chemical reaction processes. The other one is SERS active microparticle fabrication via microfluidic droplet templates covering polymer matrix and photonic crystal microparticles. We also comment on the advantages, disadvantage and correlation resolution of droplet microfluidics for SERS or Raman. Finally, we summarize these systems and illustrate our perspectives for future research directions in this field.

Constructing a Defined Starter for Multispecies Vinegar Fermentation via Evaluating the Vitality and Dominance of Functional Microbes in Autochthonous Starter

Mature vinegar culture has usually been used as a type of autochthonous starter for rapidly initiate initiating the next batch of acetic acid fermentation (AAF) and maintaining the batch-to-batch uniformity of AAF in the production of traditional cereal vinegar. However, the vitality and dominance of functional microbes in autochthonous starters remain unclear, which hinders further improvement of fermentation yield and production. Here, based on metagenomic (MG), metatranscriptomic (MT), and 16S rRNA gene sequencings, 11 bacterial operational taxonomic units (OTUs) with significant metabolic activity (MT/MG ratio >1) and dominance (relative abundance >1%) were targeted in the autochthonous vinegar starter, all of which were assigned to 4 species (Acetobacter pasteurianus, Lactobacillus acetotolerans, L. helveticus, Acetilactobacillus jinshanensis). Then, we evaluated the successions and interactions of these 11 bacterial OTUs at different AAF stages. Last, a defined starter was constructed with 4 core species isolated from the autochthonous starter (A. pasteurianus, L. acetotolerans, L. helveticus, Ac. jinshanensis). The defined starter culture could rapidly initiate the AAF in a sterile or unsterilized environment and similar dynamics of metabolites (ethanol, titratable acidity, acetic acid, lactic acid, and volatile compounds) and environmental indexes (temperature, pH) of fermentation were observed as compared with that of autochthonous starter (P > 0.05). This work provides a method to construct a defined microbiota from a complex system while preserving its metabolic function. IMPORTANCE Complex microorganisms are beneficial to the flavor formation in natural food fermentation, but they also pose challenges to the mass production of standardized products. It is attractive to construct a defined starter to rapidly initiate fermentation process and significantly improve fermentation yield. This study provides a comprehensive understanding of vital and dominant species in the autochthonous vinegar starter via multi-omics, and designs a defined microbial community for the efficient fermentation of cereal vinegar.

Plasmonic Optical Tweezers for Particle Manipulation: Principles, Methods, and Applications

Inspired by the idea of combining conventional optical tweezers with plasmonic nanostructures, a technique named plasmonic optical tweezers (POT) has been widely explored from fundamental principles to applications. With the ability to break the diffraction barrier and enhance the localized electromagnetic field, POT techniques are especially effective for high spatial-resolution manipulation of nanoscale or even subnanoscale objects, from small bioparticles to atoms. In addition, POT can be easily integrated with other techniques such as lab-on-chip devices, which results in a very promising alternative technique for high-throughput single-bioparticle sensing or imaging. Despite its label-free, high-precision, and high-spatial-resolution nature, it also suffers from some limitations. One of the main obstacles is that the plasmonic nanostructures are located over the surfaces of a substrate, which makes the manipulation of bioparticles turn from a three-dimensional problem to a nearly two-dimensional problem. Meanwhile, the operation zone is limited to a predefined area. Therefore, the target objects must be delivered to the operation zone near the plasmonic structures. This review summarizes the state-of-the-art target delivery methods for the POT-based particle manipulating technique, along with its applications in single-bioparticle analysis/imaging, high-throughput bioparticle purifying, and single-atom manipulation. Future developmental perspectives of POT techniques are also discussed.

Microfluidics for microalgal biotechnology

Microalgae have expanded their roles as renewable and sustainable feedstocks for biofuel, smart nutrition, biopharmaceutical, cosmeceutical, biosensing, and space technologies. They accumulate valuable biochemical compounds from protein, carbohydrate, and lipid groups, including pigments and carotenoids. Microalgal biomass, which can be adopted for multivalorization under biorefinery settings, allows not only the production of various biofuels but also other value-added biotechnological products. However, state-of-the-art technologies are required to optimize yield, quality, and the economical aspects of both upstream and downstream processes. As such, the need to use microfluidic-based devices for both fundamental research and industrial applications of microalgae, arises due to their microscale sizes and dilute cultures. Microfluidics-based devices are superior to their competitors through their ability to perform multiple functions such as sorting and analyzing small amounts of samples (nanoliter to picoliter) with higher sensitivities. Here, we review emerging applications of microfluidic technologies on microalgal processes in cell sorting, cultivation, harvesting, and applications in biofuels, biosensing, drug delivery, and nutrition.

One-Dimensional Flow of Bacteria on an Electrode Rail by Dielectrophoresis: Toward Single-Cell-Based Analysis

Many applications in biotechnology and medicine, among other disciplines, require the rapid enumeration of bacteria, preferably using miniaturized portable devices. Microfluidic technology is expected to solve this miniaturization issue. In the enumeration of bacteria in microfluidic devices, the technique of aligning bacteria in a single line prior to counting is the key to an accurate count at single-bacterium resolution. Here, we describe the numerical and experimental evaluation of a device utilizing a dielectrophoretic force to array bacteria in a single line, allowing their facile numeration. The device comprises a channel to flow bacteria, two counter electrodes, and a capture electrode several microns or less in width for arranging bacteria in a single line. When the capture electrode is narrower than the diameter of a bacterium, the entrapment efficiency of the one-dimensional array is 80% or more within 2 s. Furthermore, since some cell-sorting applications require bacteria to move against the liquid flow, we demonstrated that bacteria can move in a single line in the off-axial direction tilted 30° from the flow direction. Our findings provide the basis for designing miniature, portable devices for evaluating bacteria with single-cell accuracy.