Design and performance of microfluidic devices for viscoelastic-controlled encapsulation

ZoBell, Claude E. (University of California, La Jolla), and Andre B. Cobet. Filament formation by Escherichia coli at increased hydrostatic pressures. J. Bacteriol. 87:710-719. 1964.-The reproduction as well as the growth of Escherichia coli is retarded by hydrostatic pressures ranging from 200 to 500 atm. Reproduction was indicated by an increase in the number of cells determined by plating on EMB Agar as well as by direct microscopic counts. Growth, which is not necessarily synonymous with reproduction, was indicated by increase in dry weight and protein content of the bacterial biomass. At increased pressures, cells of three different strains of E. coli tended to form long filaments. Whereas most normal cells of E. coli that developed at 1 atm were only about 2 mu long, the mean length of those that developed at 475 atm was 2.93 mu for strain R(4), 3.99 mu for strain S, and 5.82 mu for strain B cells. Nearly 90% of the bacterial biomass produced at 475 atm by strain B was found in filaments exceeding 5 mu in length; 74.7 and 16.4% of the biomass produced at 475 atm by strains S and R(4), respectively, occurred in such filaments. Strain R(4) formed fewer and shorter (5 to 35 mu) filaments than did the other two strains, whose filaments ranged in length from 5 to >100 mu. The bacterial biomass produced at all pressures had approximately the same content of protein and nucleic acids. But at increased pressures appreciably more ribonucleic acid (RNA) and proportionately less deoxyribonucleic acid (DNA) was found per unit of biomass. Whereas the RNA content per cell increased with cell length, the amount of DNA was nearly the same in long filaments formed at increased pressure as in cells of normal length formed at 1 atm. The inverse relationship between the concentration of DNA and cell length in all three strains of E. coli suggests that the failure of DNA to replicate at increased pressure may be responsible for a repression of cell division and consequent filament formation.

Short periods of incubation in medium containing nalidixic acid or hydroxyurea, followed by a return to normal growth conditions, induced filament formation in Escherichia coli B (fil(+)) and AB1899NM (lon(-)) but not in B/r (fil(-)) and AB1157 (lon(+)). These drugs reversibly stopped deoxyribonucleic acid (DNA) synthesis with little or no effect on ribonucleic acid (RNA) synthesis or mass increase. The initial imbalance caused by incubation in these drugs was the same for B and B/r as was macromolecular synthesis following a return to normal growth conditions. DNA degradation caused by nalidixic acid was measured and found to be the same for B and B/r. Hydroxyurea caused no DNA degradation in these two strains. Survival curves as determined under various conditions by colony formation suggested that the property of filament formation was responsible for the extrasensitivity of fil(+) and lon(-) strains to either nalidixic acid or hydroxyurea. E. coli B was more sensitive to either drug than was B/r or B(s-1). Pantoyl lactone or liquid holding treatment aided division and colony formation of nalidixic acid-treated B but had no effect on B/r. Likewise, the filament-former AB1899NM was more sensitive to nalidixic acid than was the non-filament-former AB1157. The sensitivity of B/r and B(s-1) to nalidixic acid was nearly the same except at longer times in nalidixic acid, when B(s-1) appeared more resistant. Even though nalidixic acid, hydroxyurea, and ultraviolet light may produce quite different molecular alterations in E. coli, they all cause a metabolic imbalance resulting in a lowered ratio of DNA to RNA and protein. We propose that it is this imbalance per se rather than any specific primary chemical or photochemical alterations which leads to filament formation by some genetically susceptible bacterial strains such as lon(-) and fil(+).

Recently, two-phase flow in microfluidics has attracted much attention because of its importance in generating droplets or bubbles that can be used as building blocks for material synthesis and biological applications. However, there are many unresolved issues in understanding droplet and bubble generation processes, especially when complex fluids are involved. In this study, we investigated elastic effects on bubble generation processes in a flow-focusing geometry and the shapes of the produced bubbles flowing through a microchannel. We used dilute polymer solutions with nearly constant shear viscosities so that the shear-thinning effects on bubble generation could be precluded. We observed that a very small amount of polymer (poly(ethylene oxide) at ~O(10) ppm) significantly affects bubble generation. When the polymer was added to a Newtonian fluid, the fluctuation in bubble size increased notably, which was attributed to the chaotic flow dynamics in the flow-focusing region. In addition, it was demonstrated that the bubbles were thinner along the minor axis in the viscoelastic fluid than they were in the Newtonian fluid. We expect that the current results will contribute to understanding the dynamics of two-phase flow in microchannels and the design and operation of the microfluidic devices to generate microbubbles.

Whole genome sequencing (WGS) is a promising strategy to unravel variants or genes responsible for human diseases and traits. However, there is a lack of robust platforms for a comprehensive downstream analysis. In the present study, we first proposed three novel algorithms, sequence gap-filled gene feature annotation, bit-block encoded genotypes and sectional fast access to text lines to address three fundamental problems. The three algorithms then formed the infrastructure of a robust parallel computing framework, KGGSeq, for integrating downstream analysis functions for whole genome sequencing data. KGGSeq has been equipped with a comprehensive set of analysis functions for quality control, filtration, annotation, pathogenic prediction and statistical tests. In the tests with whole genome sequencing data from 1000 Genomes Project, KGGSeq annotated several thousand more reliable non-synonymous variants than other widely used tools (e.g. ANNOVAR and SNPEff). It took only around half an hour on a small server with 10 CPUs to access genotypes of ∼60 million variants of 2504 subjects, while a popular alternative tool required around one day. KGGSeq's bit-block genotype format used 1.5% or less space to flexibly represent phased or unphased genotypes with multiple alleles and achieved a speed of over 1000 times faster to calculate genotypic correlation.

Circulating tumor cells (CTCs) are regarded as a strong biomarker which includes clinically valuable information. However, CTCs are very rare and require precise separation and detection for effective clinical applications. Furthermore, downstream analysis has become necessary to identify the distinct sub-population of CTCs that causes metastasis. Here, we report a flow-restricted microfluidic trap array capable of deterministic single-cell capture of CTCs. The extent of flow restriction, correlating with the device geometry, was then optimized using a highly invasive breast cancer cell line (LM2 MDA-MB-231) to achieve 97% capture efficiency with a single-cell capture rate of 99%. Single-cell capture of CTCs from mice with full-blown metastasis was also demonstrated. The single-CTC capturing ability of the flow-restricted trap array not only showed cell enumerating ability but also high prospects for application in future automated downstream analysis.

Microfluidic-based sorting systems are an integral part of many biological applications, where sorting of cells, microorganisms, and particles is of interest. In this paper, a computational fluid dynamics model is established to expand investigations on a hybrid microparticle sorting method, which combines inertia-magnetic focusing and hydrodynamic separation, known as multiplex inertia-magnetic fractionation (MIMF). This microfluidic device consists of two regions, i.e. a narrow microchannel with a magnet on its side for inertial and magnetophoretic focusing of particles and a downstream wide hydrodynamic expansion zone for particles’ separation and imaging. A Lagrangian–Eulerian framework was adopted to simulate particle trajectories using the ANSYS-Fluent discrete phase modeling (DPM) approach. Acting forces that were considered to predict particle trajectories included the drag, inertial lift, Saffman lift, gravitational, and magnetophoretic forces. User-defined functions were used for inertial lift and magnetophoretic forces that are not built-in relations in the ANSYS-Fluent DPM. Numerical results were verified and validated against the experimental data for MIMF of 5 and 11 µm magnetic particles at flow rates of 0.5–5 mL/h. Particles fractionation throughput and purity in the expansion region could be predicted with errors of 6% and 2%, respectfully. The validated model was then used to perform a numerical parametric study on the unknown effects of magnetization, particle size, higher flow rates, and fluid viscosity on MIMF. The presented numerical approach can be used as a tool for future experimental design of inertia-magnetophoretic microfluidic particle sorting devices.

BackgroundIn recent years, Single-cell RNA sequencing (scRNA-seq) is increasingly accessible to researchers of many fields. However, interpreting its data demands proficiency in multiple programming languages and bioinformatic skills, which limited researchers, without such expertise, exploring information from scRNA-seq data. Therefore, there is a tremendous need to develop easy-to-use software, covering all the aspects of scRNA-seq data analysis.ResultsWe proposed a clear analysis framework for scRNA-seq data, which emphasized the fundamental and crucial roles of cell identity annotation, abstracting the analysis process into three stages: upstream analysis, cell annotation and downstream analysis. The framework can equip researchers with a comprehensive understanding of the analysis procedure and facilitate effective data interpretation. Leveraging the developed framework, we engineered Shaoxia, an analysis platform designed to democratize scRNA-seq analysis by accelerating processing through high-performance computing capabilities and offering a user-friendly interface accessible even to wet-lab researchers without programming expertise.ConclusionShaoxia stands as a powerful and user-friendly open-source software for automated scRNA-seq analysis, offering comprehensive functionality for streamlined functional genomics studies. Shaoxia is freely accessible at http://www.shaoxia.cloud, and its source code is publicly available at https://github.com/WiedenWei/shaoxia.

The clustered regularly interspaced short palindromic repeats (CRISPR) system is widely used for various biological applications, including genome editing. We developed engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR to isolate target genomic regions from cells for their biochemical characterization. In this study, we developed 'invitro enChIP' using recombinant CRISPR ribonucleoproteins (RNPs) to isolate target genomic regions. in vitro enChIP has the great advantage over conventional enChIP of not requiring expression of CRISPR complexes in cells. We first showed that invitro enChIP using recombinant CRISPR RNPs can be used to isolate target DNA from mixtures of purified DNA in a sequence-specific manner. In addition, we showed that this technology can be used to efficiently isolate target genomic regions, while retaining their intracellular molecular interactions, with negligible contamination from irrelevant genomic regions. Thus, invitro enChIP technology is of potential use for sequence-specific isolation of DNA, as well as for identification of molecules interacting with genomic regions of interest invivo in combination with downstream analysis.

The synthesis and characterization of new engineered structured inorganic nanomaterials is essential in bioanalytical research and requires for multidisciplinary analytical platforms.

In this paper, we present a theoretical study on irreversible electroporation of multiple blood cells in a continuous flow microfluidic device for high throughput applications. Irreversible electroporation is the cell lysis process in which the application of electric field permanently permeabilizes the cell membrane, allowing the intercellular content to eject out for downstream genetic analysis. The device geometry can be manipulated for fluid transport and irreversible electroporation. Our study concentrates on the effect of voltage, flow velocity, geometry and the location of cells inside the device for efficient irreversible electroporation. Our results show that by controlling the applied voltage, cells can be irreversibly electroporated. The flow velocity influences irreversible electroporation. If the flow velocity is greater than the resident velocity of the cell, the pores on the membrane will reseal thereby resulting in reversible electroporation. The nanofluidic channels increase the duration of electroporation as the larger cells cannot pass through them.

Deterministic lateral displacement (DLD) is a microfluidic technique for size fractionation of particles/cells in continuous flow with a great potential for biological and clinical applications. Growing interest of DLD devices in enabling high-throughput operation for practical applications, such as circulating tumor cell (CTC) separation, necessitates employing higher flow rates, leading to operation at moderate to high Reynolds number (Re) regimes. Recently, it has been shown that symmetric airfoil shaped pillars with neutral angle-of-attack (AoA) can be used for high-throughput design of DLD devices due to their mitigation of vortex effects and preservation of flow symmetry under high Re conditions. While high-Re operation with symmetric airfoil shaped pillars has been established, the effect of AoAs on the DLD performance has not been investigated. In this paper, we have characterized the airfoil DLD device with various AoAs. The transport behavior of microparticles has been observed and analyzed with various AoAs in realistic high-Re. Furthermore, we have modeled the flow fields and anisotropy in a representative airfoil pillar array, for both positive and negative AoA configurations. Unlike the conventional DLD device, lateral displacement has been suppressed with +5° and + 15° AoA configurations regardless of particle sizes. On the other hand, stronger lateral displacement has been seen with -5° and - 15° AoAs. This can be attributed to growing flow anisotropy as Re climbs, and significant expansion or compression of streamlines between airfoils with AoAs. The findings in this study can be utilized for the design and optimization of airfoil DLD microfluidic devices with various AoAs.

Within recent years, the analysis of single biological cells has emerged as key topic in cell-biology research. Studying cells and cellular functions within large cell populations is still common practice in the life-sciences, but is hampered by several limitations. True access to a cell's physiology, phenotype and genotype can often only be achieved on a single cell level. The European research project “Platform for Advanced Single Cell Analysis” (PASCA) focuses on developing an approach towards inkjet-like printing of single cells. A fully automated prototype instrument for printing of single living cells has been developed, and its potential use is currently being investigated in various biological applications. The various elements of project design, management, and implementation developed within this project to support the commercial exploitation and dissemination of the project results will be discussed. Based on the dedicated project structure of involving external non-funded participants from the beginning of the project and extending it to the preparation of a prototype related market study, various activities aimed at commercializing the project results are presented. We present the lessons learned from those activities alongside the technical results achieved with the PASCA prototype instruments and the perspectives for future commercialization.

Gliomas are the most common and malignant intracranial tumors in adults. Recent studies have revealed the significance of functional genomics for glioma pathophysiological studies and treatments. However, access to comprehensive genomic data and analytical platforms is often limited. Here, we developed the Chinese Glioma Genome Atlas (CGGA), a user-friendly data portal for the storage and interactive exploration of cross-omics data, including nearly 2000 primary and recurrent glioma samples from Chinese cohort. Currently, open access is provided to whole-exome sequencing data (286 samples), mRNA sequencing (1018 samples) and microarray data (301 samples), DNA methylation microarray data (159 samples), and microRNA microarray data (198 samples), and to detailed clinical information (age, gender, chemoradiotherapy status, WHO grade, histological type, critical molecular pathological information, and survival data). In addition, we have developed several tools for users to analyze the mutation profiles, mRNA/microRNA expression, and DNA methylation profiles, and to perform survival and gene correlation analyses of specific glioma subtypes. This database removes the barriers for researchers, providing rapid and convenient access to high‐quality functional genomic data resources for biological studies and clinical applications. CGGA is available at http://www.cgga.org.cn.

In this article, a theoretical investigation is analyzing the effects of the complaint wall properties, the slip conditions, the space porosity, and the transverse magnetic field on the magnetohydrodynamic peristaltic transport of viscous compressible flow carrying out some rigid spherical suspension particles flowing through space porous medium in a horizontal elastic rectangular channel. The flexible channel walls are taken as a sinusoidal wave. The expressions describing the peristaltic transport are mathematically analyzed using the perturbation technique with a small amplitude wave ratio. The analytical study describes the influence of various wall parameters such as damping force, wall tension, and wall elasticity and flow parameters as compressibility parameter, slip parameter, suspension parameter, Reynolds number, space porosity, and magnetic field parameter on the net axial velocity. The reversal flow occurs at the channel core and boundaries due to the slip and the magnetic field effects. Biological, geophysical, and industrial fluid dynamics applications are important models for the peristaltic transport described in this work.

BackgroundNeural stem cells are motile and proliferative cells that undergo mitosis, dividing to produce daughter cells and ultimately generating differentiated neurons and glia. Understanding the mechanisms controlling neural stem cell proliferation and differentiation will play a key role in the emerging fields of regenerative medicine and cancer therapeutics. Stem cell studies in vitro from 2-D image data are well established. Visualizing and analyzing large three dimensional images of intact tissue is a challenging task. It becomes more difficult as the dimensionality of the image data increases to include time and additional fluorescence channels. There is a pressing need for 5-D image analysis and visualization tools to study cellular dynamics in the intact niche and to quantify the role that environmental factors play in determining cell fate.ResultsWe present an application that integrates visualization and quantitative analysis of 5-D (x,y,z,t,channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and cancer biology. Our application automatically segments, tracks, and lineages the image sequence data and then allows the user to view and edit the results of automated algorithms in a stereoscopic 3-D window while simultaneously viewing the stem cell lineage tree in a 2-D window. Using the GPU to store and render the image sequence data enables a hybrid computational approach. An inference-based approach utilizing user-provided edits to automatically correct related mistakes executes interactively on the system CPU while the GPU handles 3-D visualization tasks.ConclusionsBy exploiting commodity computer gaming hardware, we have developed an application that can be run in the laboratory to facilitate rapid iteration through biological experiments. We combine unsupervised image analysis algorithms with an interactive visualization of the results. Our validation interface allows for each data set to be corrected to 100% accuracy, ensuring that downstream data analysis is accurate and verifiable. Our tool is the first to combine all of these aspects, leveraging the synergies obtained by utilizing validation information from stereo visualization to improve the low level image processing tasks.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-15-328) contains supplementary material, which is available to authorized users.