Generation of ribosome imprinted polymers for sensitive detection of translational responses

Whilst the profiling of the transcriptome and proteome even of single-cells becomes feasible, the analysis of the translatome, which refers to all messenger RNAs (mRNAs) engaged with ribosomes for protein synthesis, is still an elaborate procedure requiring millions of cells. Herein, we report the generation and use of "smart materials", namely molecularly imprinted polymers (MIPs) to facilitate the isolation of ribosomes and translated mRNAs from merely 1,000 cells. In particular, we show that a hydrogel-based ribosome imprinted polymer could recover ribosomes and associated mRNAs from human, simian and mice cellular extracts, but did not selectively enrich yeast ribosomes, thereby demonstrating selectivity. Furthermore, ribosome imprinted polymers enabled the sensitive measurement of an mRNA translational regulatory event, requiring 1,000-fold less cells than current methodologies. These results provide first evidence for the suitability of MIPs to selectively recover ribonucleoprotein complexes such as ribosomes, founding a novel means for sensitive detection of gene regulation.

Single-Cell Transcriptional Analysis

Despite being a relatively recent technological development, single-cell transcriptional analysis through high-throughput sequencing has already been used in hundreds of fruitful studies to make exciting new biological discoveries that would otherwise be challenging or even impossible. Consequently, this has fueled a virtuous cycle of even greater interest in the field and compelled development of further improved technical methodologies and approaches. Thanks to the combined efforts of the research community, including the fields of biochemistry and molecular biology, technology and instrumentation, data science, computational biology, and bioinformatics, the single-cell RNA-sequencing field is advancing at a pace that is both astounding and unprecedented. In this review, we provide a broad introduction to this revolutionary technology by presenting the state-of-the-art in sample preparation methodologies, technology platforms, and computational analysis methods, while highlighting the key considerations for designing, executing, and interpreting a study using single-cell RNA sequencing.

Long-term preservation of Tetraselmis indica (Chlorodendrophyceae, Chlorophyta) for flow cytometric analysis: Influence of fixative and storage temperature

Immediate enumeration of phytoplankton is seldom possible. Therefore, fixation and subsequent storage are required for delayed analysis. This study investigated the influence of glutaraldehyde (GA) concentrations (0.25%, 0.5%, and 1%) and storage temperatures (-80°C_LN2, -80°C, -20°C, and 5°C) on Tetraselmis indica for flow cytometric analysis. Cell recovery, granularity, and membrane permeability were independent of GA concentration whereas cell size and chlorophyll autofluorescence were concentration dependent. After an initial cell loss (16-19%), no cell loss was observed when samples were stored at 5°C. Cell recovery was not influenced by storage temperature until 4months but later samples preserved at -80°C_LN2, -80°C, and -20°C resulted in ~41% cell loss. Although maximum cell recovery with minimal effect on cell integrity was obtained at 5°C, autofluorescence was retained better at -80°C_LN2 and -80°C. This suggests that in addition to fixative, the choice of storage temperature is equally important. Thus for long-term preservation, especially to retain autofluorescence, the use of lower concentration (0.25%) of GA when stored at a lower temperature (-80°C_LN2 and -80°C) while a higher concentration (1%) of GA when stored at a higher temperature (5°C) is recommended.

Taking control over microbial populations: Current approaches for exploiting biological noise in bioprocesses

Phenotypic plasticity of microbial cells has attracted much attention and several research efforts have been dedicated to the description of methods aiming at characterizing phenotypic heterogeneity and its impact on microbial populations. However, different approaches have also been suggested in order to take benefit from noise in a bioprocess perspective, e.g. by increasing the robustness or productivity of a microbial population. This review is dedicated to outline these controlling methods. A common issue, that has still to be addressed, is the experimental identification and the mathematical expression of noise. Indeed, the effective interfacing of microbial physiology with external parameters that can be used for controlling physiology depends on the acquisition of reliable signals. Latest technologies, like single cell microfluidics and advanced flow cytometric approaches, enable linking physiology, noise, heterogeneity in productive microbes with environmental cues and hence allow correctly mapping and predicting biological behavior via mathematical representations. However, like in the field of electronics, signals are perpetually subjected to noise. If appropriately interpreted, this noise can give an additional insight into the behavior of the individual cells within a microbial population of interest. This review focuses on recent progress made at describing, treating and exploiting biological noise in the context of microbial populations used in various bioprocess applications.

Proteomics of FACS-sorted heterogeneous Corynebacterium glutamicum populations

The metabolic status of individual cells in microbial cultures can differ, being relevant for biotechnology, environmental and medical microbiology. However, it is hardly understood in molecular detail due to limitations of current analytical tools. Here, we demonstrate that FACS in combination with proteomics can be used to sort and analyze cell populations based on their metabolic state. A previously established GFP reporter system was used to detect and sort single Corynebacterium glutamicum cells based on the concentration of branched chain amino acids (BCAA) using FACS. A proteomics workflow optimized for small cell numbers was used to quantitatively compare proteomes of a ΔaceE mutant, lacking functional pyruvate dehydrogenase (PD), and the wild type. About 800 proteins could be quantified from 1,000,000 cells. In the ΔaceE mutant BCAA production was coordinated with upregulation of the glyoxylate cycle and TCA cycle to counter the lack of acetyl CoA resulting from the deletion of aceE.

BIOLOGICAL SIGNIFICANCE

Metabolic pathways in C. glutamicum WT and ΔaceE, devoid of functional pyruvate dehydrogenase, were compared to understand proteome changes that contribute to the high production of branched chain amino acids (BCAA) in the ΔaceE strain. The data complements previous metabolome studies and corroborates the role of malate provided by the glyoxylate cycle and increased activity of glycolysis and pyruvate carboxylase reaction to replenish the TCA cycle. A slight increase in acetohydroxyacid synthase (ILV subunit B) substantiates the previously reported increased pyruvate pool in C. glutamicumΔaceE, and the benefit of additional ilv gene cluster overexpression for BCAA production.

Hydrogel Droplet Microfluidics for High-Throughput Single Molecule/Cell Analysis

Heterogeneity among individual molecules and cells has posed significant challenges to traditional bulk assays, due to the assumption of average behavior, which would lose important biological information in heterogeneity and result in a misleading interpretation. Single molecule/cell analysis has become an important and emerging field in biological and biomedical research for insights into heterogeneity between large populations at high resolution. Compared with the ensemble bulk method, single molecule/cell analysis explores the information on time trajectories, conformational states, and interactions of individual molecules/cells, all key factors in the study of chemical and biological reaction pathways. Various powerful techniques have been developed for single molecule/cell analysis, including flow cytometry, atomic force microscopy, optical and magnetic tweezers, single-molecule fluorescence spectroscopy, and so forth. However, some of them have the low-throughput issue that has to analyze single molecules/cells one by one. Flow cytometry is a widely used high-throughput technique for single cell analysis but lacks the ability for intercellular interaction study and local environment control. Droplet microfluidics becomes attractive for single molecule/cell manipulation because single molecules/cells can be individually encased in monodisperse microdroplets, allowing high-throughput analysis and manipulation with precise control of the local environment. Moreover, hydrogels, cross-linked polymer networks that swell in the presence of water, have been introduced into droplet microfluidic systems as hydrogel droplet microfluidics. By replacing an aqueous phase with a monomer or polymer solution, hydrogel droplets can be generated on microfluidic chips for encapsulation of single molecules/cells according to the Poisson distribution. The sol-gel transition property endows the hydrogel droplets with new functionalities and diversified applications in single molecule/cell analysis. The hydrogel can act as a 3D cell culture matrix to mimic the extracellular environment for long-term single cell culture, which allows further heterogeneity study in proliferation, drug screening, and metastasis at the single-cell level. The sol-gel transition allows reactions in solution to be performed rapidly and efficiently with product storage in the gel for flexible downstream manipulation and analysis. More importantly, controllable sol-gel regulation provides a new way to maintain phenotype-genotype linkages in the hydrogel matrix for high throughput molecular evolution. In this Account, we will review the hydrogel droplet generation on microfluidics, single molecule/cell encapsulation in hydrogel droplets, as well as the progress made by our group and others in the application of hydrogel droplet microfluidics for single molecule/cell analysis, including single cell culture, single molecule/cell detection, single cell sequencing, and molecular evolution.

A microfluidic device for the delivery of enzymes into cells by liposome fusion

Liposomes are versatile carriers of drugs or biomolecules and are ideally suited to transport molecules into cells. However, mechanistic studies to understand and improve the fusion of liposomes with cell membranes and endosomes are difficult. Here, we report a method that allows for stable coimmobilization of liposomes and living cells, thereby bringing the membranes into close contact, which is essential for membrane fusion. The small unilamellar liposomes are tethered to the surface by a linker so that no modification of the liposome membrane for cell binding is required. The cells are positioned above the liposomes by posts that are integrated into the microfluidic device, and a pH drop induces the fusion of the cell-liposome membranes. Both membrane fusion and release of molecules into the cytosol are visualized by fluorescence dequenching assays. Furthermore, we proved the efficient delivery of the enzyme β-galactosidase into the cells when a fusogenic liposome composition was used. The device could be used for fusion studies but is also a versatile means for cell transfection.

Ultrafast laser-scanning time-stretch imaging at visible wavelengths

Optical time-stretch imaging enables the continuous capture of non-repetitive events in real time at a line-scan rate of tens of MHz-a distinct advantage for the ultrafast dynamics monitoring and high-throughput screening that are widely needed in biological microscopy. However, its potential is limited by the technical challenge of achieving significant pulse stretching (that is, high temporal dispersion) and low optical loss, which are the critical factors influencing imaging quality, in the visible spectrum demanded in many of these applications. We present a new pulse-stretching technique, termed free-space angular-chirp-enhanced delay (FACED), with three distinguishing features absent in the prevailing dispersive-fiber-based implementations: (1) it generates substantial, reconfigurable temporal dispersion in free space (>1 ns nm-1) with low intrinsic loss (<6 dB) at visible wavelengths; (2) its wavelength-invariant pulse-stretching operation introduces a new paradigm in time-stretch imaging, which can now be implemented both with and without spectral encoding; and (3) pulse stretching in FACED inherently provides an ultrafast all-optical laser-beam scanning mechanism at a line-scan rate of tens of MHz. Using FACED, we demonstrate not only ultrafast laser-scanning time-stretch imaging with superior bright-field image quality compared with previous work but also, for the first time, MHz fluorescence and colorized time-stretch microscopy. Our results show that this technique could enable a wider scope of applications in high-speed and high-throughput biological microscopy that were once out of reach.

Spinning micropipette liquid emulsion generator for single cell whole genome amplification

Many on-chip approaches that use flow-focusing to pinch the continuous aqueous phase into droplets have become the most popular methods that provide monodisperse emulsion droplets. However, not every lab can easily adapt a microfluidic workflow into their familiar protocols. We develop an off-chip approach, spinning micro-pipette liquid emulsion (SiMPLE) generator, to produce highly stable monodisperse water-in-oil emulsions using a moving micropipette to disperse the aqueous phase in an oil-filled microcentrifuge tube. This method provides a simple way to produce picoliter-size droplets in situ with no dead volume during emulsification. With SiMPLE, single-cell emulsion whole genome amplification was performed to demonstrate that this novel method can seamlessly be integrated with experimental operations and supplies that most researchers are familiar with. The SiMPLE generator has effectively lowered the technical difficulties in applications relying on emulsion droplets.

Multiplex cell microarrays for high-throughput screening

Microarray technology was developed in the early 1990s to measure the transcription levels of thousands of genes in parallel. The basic premise of high-density arraying has since been expanded to create cell microarrays. Cells on chip are powerful experimental tools for high-throughput and multiplex screening of samples or cellular functions. Miniaturization increases assay throughput while reducing both reagent consumption and cell population heterogeneity effect, making these systems attractive for a wide range of assays, from drug discovery to toxicology, stem cell research and therapy. It is usual to functionalize the surface of a substrate to design cell microarrays. One form of cell microarrays, the transfected cell microarray, wherein plasmid DNA or siRNA spotted on the surface of a substrate is reverse-transfected locally into adherent cells, has become a standard tool for parallel cell-based analysis. With the advent of technology, cells can also be directly spotted onto functionalized surfaces using robotic fluid-dispensing devices or printed directly on bio-ink material. We are providing herein an overview of the latest developments in optical cell microarrays allowing high-throughput and high-content analysis.

The application of microfluidic-based technologies in the cycle of metabolic engineering

The process of metabolic engineering consists of multiple cycles of design, build, test and learn, which is typically laborious and time-consuming. To increase the efficiency and the rate of success of strain engineering, novel instrumentation must be applied. Microfluidics, the control of liquid flow in microstructures, has enabled flexible, accurate, automatic, and high-throughput manipulation of cells in liquid at picoliter to nanoliter scale. These attributes hold great promise in advancing metabolic engineering in terms of the phases of design, build, test and learn. To promote the application of microfluidic-based technologies in strain improvement, this review addressed the potentials of microfluidics and the related approaches in DNA assembly, transformation, strain screening, genotyping and phenotyping, and highlighted their adaptations for single-cell analysis. As a result, this facilitates in-depth understanding of the metabolic network, which in turn promote efficient optimization in the following cycles of strain engineering. Taken together, microfluidic-based technologies enable on-chip workflow, and could greatly accelerate the turnaround of metabolic engineering.

Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine Experiments

Background

Microfluidic lab-on-chip technology combined with live-cell imaging has enabled the observation of single cells in their spatio-temporal context. The mother machine (MM) cultivation system is particularly attractive for the long-term investigation of rod-shaped bacteria since it facilitates continuous cultivation and observation of individual cells over many generations in a highly parallelized manner. To date, the lack of fully automated image analysis software limits the practical applicability of the MM as a phenotypic screening tool.

Results

We present an image analysis pipeline for the automated processing of MM time lapse image stacks. The pipeline supports all analysis steps, i.e., image registration, orientation correction, channel/cell detection, cell tracking, and result visualization. Tailored algorithms account for the specialized MM layout to enable a robust automated analysis. Image data generated in a two-day growth study (≈ 90 GB) is analyzed in ≈ 30 min with negligible differences in growth rate between automated and manual evaluation quality. The proposed methods are implemented in the software molyso (MOther machine AnaLYsis SOftware) that provides a new profiling tool to analyze unbiasedly hitherto inaccessible large-scale MM image stacks.

Conclusion

Presented is the software molyso, a ready-to-use open source software (BSD-licensed) for the unsupervised analysis of MM time-lapse image stacks. molyso source code and user manual are available at https://github.com/modsim/molyso.

Development of Droplet Microfluidics Enabling High-Throughput Single-Cell Analysis

This article reviews recent developments in droplet microfluidics enabling high-throughput single-cell analysis. Five key aspects in this field are included in this review: (1) prototype demonstration of single-cell encapsulation in microfluidic droplets; (2) technical improvements of single-cell encapsulation in microfluidic droplets; (3) microfluidic droplets enabling single-cell proteomic analysis; (4) microfluidic droplets enabling single-cell genomic analysis; and (5) integrated microfluidic droplet systems enabling single-cell screening. We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on key performances of throughput, multifunctionality, and absolute quantification.

Optofluidic time-stretch imaging - an emerging tool for high-throughput imaging flow cytometry

Optical imaging is arguably the most effective tool to visualize living cells with high spatiotemporal resolution and in a nearly noninvasive manner. Driven by this capability, state-of-the-art cellular assay techniques have increasingly been adopting optical imaging for classifying different cell types/stages, and thus dissecting the respective cellular functions. However, it is still a daunting task to image and characterize cell-to-cell variability within an enormous and heterogeneous population - an unmet need in single-cell analysis, which is now widely advocated in modern biology and clinical diagnostics. The challenge stems from the fact that current optical imaging technologies still lack the practical speed and sensitivity for measuring thousands to millions of cells down to the single-cell precision. Adopting the wisdom in high-speed fiber-optics communication, optical time-stretch imaging has emerged as a completely new optical imaging concept which is now proven for ultrahigh-throughput optofluidic single-cell imaging, at least 1-2 orders-of-magnitude higher (up to ∼100 000 cells per second) compared to the existing imaging flow cytometers. It also uniquely enables quantification of intrinsic biophysical markers of individual cells - a largely unexploited class of single-cell signatures that is known to be correlated with the overwhelmingly investigated biochemical markers. With the aim of reaching a wider spectrum of experts specializing in cellular assay developments and applications, this paper highlights the essential basics of optical time-stretch imaging, followed by reviewing the recent developments and applications of optofluidic time-stretch imaging. We will also discuss the current challenges of this technology, in terms of providing new insights in basic biology and enriching the clinical diagnostic toolsets.

Integrated Droplet-Based Microextraction with ESI-MS for Removal of Matrix Interference in Single-Cell Analysis

Integrating droplet-based microfluidics with mass spectrometry is essential to high-throughput and multiple analysis of single cells. Nevertheless, matrix effects such as the interference of culture medium and intracellular components influence the sensitivity and the accuracy of results in single-cell analysis. To resolve this problem, we developed a method that integrated droplet-based microextraction with single-cell mass spectrometry. Specific extraction solvent was used to selectively obtain intracellular components of interest and remove interference of other components. Using this method, UDP-Glc-NAc, GSH, GSSG, AMP, ADP and ATP were successfully detected in single MCF-7 cells. We also applied the method to study the change of unicellular metabolites in the biological process of dysfunctional oxidative phosphorylation. The method could not only realize matrix-free, selective and sensitive detection of metabolites in single cells, but also have the capability for reliable and high-throughput single-cell analysis.

Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses

The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. In this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses.

High spatial and temporal resolution cell manipulation techniques in microchannels

Reviewing latest developments on lab on chips for enhanced control of cells’ experiments.

Fluorescence-based tools for single-cell approaches in food microbiology

The better understanding of the functioning of microbial communities is a challenging and crucial issue in the field of food microbiology, as it constitutes a prerequisite to the optimization of positive and technological microbial population functioning, as well as for the better control of pathogen contamination of food. Heterogeneity appears now as an intrinsic and multi-origin feature of microbial populations and is a major determinant of their beneficial or detrimental functional properties. The understanding of the molecular and cellular mechanisms behind the behavior of bacteria in microbial communities requires therefore observations at the single-cell level in order to overcome "averaging" effects inherent to traditional global approaches. Recent advances in the development of fluorescence-based approaches dedicated to single-cell analysis provide the opportunity to study microbial communities with an unprecedented level of resolution and to obtain detailed insights on the cell structure, metabolism activity, multicellular behavior and bacterial interactions in complex communities. These methods are now increasingly applied in the field of food microbiology in different areas ranging from research laboratories to industry. In this perspective, we reviewed the main fluorescence-based tools used for single-cell approaches and their concrete applications with specific focus on food microbiology.

Analysis of metabolites in single cells-what is the best micro-platform?

This review covers new innovations and developments in the field of single-cell level analysis of metabolites, involving the role of microfluidic and microarray platforms to manipulate and handle the cells prior their detection. Microfluidic and microarray platforms have shown great promise. The latest developments demonstrate their potential to identify a particular cell or even an ensemble of cells (sharing a common property or phenotype) that co-exist in a much larger cell population. The reason for this is the capability of these platforms to perform several complex analytical processes, such as: cleanup, sorting, derivatization, separation, and detection, with great robustness, speed, and reduced sample/reagent consumption. Here, we present several examples that illustrate the rapid strides that have been made for the routine analysis of metabolites by coupling different microfluidics and microarrays devices to a wide range of analytical detectors (e.g. fluorescent microscopy, electrochemical, and mass spectrometry). Herein, we also present selected examples detailing the use of microfluidics and microarrays in the visualization of the natural occurring cell-to-cell heterogeneity in isogenic populations, in particular during the response to external cues. The possibility to accurate monitor the cell-to-cell heterogeneity based on different levels of key metabolites is of clinical relevance, since cell-to-cell heterogeneity can influence, for example, the outcome of a drug treatment.

Distinguishing the rates of gene activation from phenotypic variations

Background

Stochastic genetic switching driven by intrinsic noise is an important process in gene expression. When the rates of gene activation/inactivation are relatively slow, fast, or medium compared with the synthesis/degradation rates of mRNAs and proteins, the variability of protein and mRNA levels may exhibit very different dynamical patterns. It is desirable to provide a systematic approach to identify their key dynamical features in different regimes, aiming at distinguishing which regime a considered gene regulatory network is in from their phenotypic variations.

Results

We studied a gene expression model with positive feedbacks when genetic switching rates vary over a wide range. With the goal of providing a method to distinguish the regime of the switching rates, we first focus on understanding the essential dynamics of gene expression system in different cases. In the regime of slow switching rates, we found that the effective dynamics can be reduced to independent evolutions on two separate layers corresponding to gene activation and inactivation states, and the transitions between two layers are rare events, after which the system goes mainly along deterministic ODE trajectories on a particular layer to reach new steady states. The energy landscape in this regime can be well approximated by using Gaussian mixture model. In the regime of intermediate switching rates, we analyzed the mean switching time to investigate the stability of the system in different parameter ranges. We also discussed the case of fast switching rates from the viewpoint of transition state theory. Based on the obtained results, we made a proposal to distinguish these three regimes in a simulation experiment. We identified the intermediate regime from the fact that the strength of cellular memory is lower than the other two cases, and the fast and slow regimes can be distinguished by their different perturbation-response behavior with respect to the switching rates perturbations.

Conclusions

We proposed a simulation experiment to distinguish the slow, intermediate and fast regimes, which is the main point of our paper. In order to achieve this goal, we systematically studied the essential dynamics of gene expression system when the switching rates are in different regimes. Our theoretical understanding provides new insights on the gene expression experiments.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-015-0172-0) contains supplementary material, which is available to authorized users.

Single-Cell Analysis of [18F]Fluorodeoxyglucose Uptake by Droplet Radiofluidics

Radiolabels can be used to detect small biomolecules with high sensitivity and specificity without interfering with the biochemical activity of the labeled molecule. For instance, the radiolabeled glucose analogue, [18F]fluorodeoxyglucose (FDG), is routinely used in positron emission tomography (PET) scans for cancer diagnosis, staging, and monitoring. However, despite their widespread usage, conventional radionuclide techniques are unable to measure the variability and modulation of FDG uptake in single cells. We present here a novel microfluidic technique, dubbed droplet radiofluidics, that can measure radiotracer uptake for single cells encapsulated into an array of microdroplets. The advantages of this approach are multiple. First, droplets can be quickly and easily positioned in a predetermined pattern for optimal imaging throughput. Second, droplet encapsulation reduces cell efflux as a confounding factor, because any effluxed radionuclide is trapped in the droplet. Last, multiplexed measurements can be performed using fluorescent labels. In this new approach, intracellular radiotracers are imaged on a conventional fluorescence microscope by capturing individual flashes of visible light that are produced as individual positrons, emitted during radioactive decay, traverse a scintillator plate placed below the cells. This method is used to measure the cell-to-cell heterogeneity in the uptake of tracers such as FDG in cell lines and cultured primary cells. The capacity of the platform to perform multiplexed measurements was demonstrated by measuring differential FDG uptake in single cells subjected to different incubation conditions and expressing different types of glucose transporters. This method opens many new avenues of research in basic cell biology and human disease by capturing the full range of stochastic variations in highly heterogeneous cell populations in a repeatable and high-throughput manner.

Carbon nanoelectrodes for single-cell probing

Carbon nanoelectrodes with tip diameters ranging from tens to hundreds of nanometers are fabricated by pyrolitic deposition of carbon films along the entire inner surfaces of pulled-glass pipettes. The pulled end of each glass pipette is then etched to expose a desired length (typically, a few micrometers) of carbon pipe. The carbon film provides an electrically conductive path from the nanoscopic carbon tip to the distal, macroscopic end of the pipette, bridging between the nanoscale tip and the macroscale handle, without a need for assembly. We used our nanoelectrodes to penetrate into individual cells and cell nuclei and measured the variations in the electrode impedance upon cell and nucleus penetration as well as the electrode impedance as a function of cell penetration depth. Theoretical predictions based on a simple circuit model were in good agreement with experimental data.

Technical bias of microcultivation environments on single-cell physiology

Microscale cultivation systems are important tools to elucidate cellular dynamics beyond the population average and understand the functional architecture of single cells. However, there is scant knowledge about the bias of different microcultivation technologies on cellular functions. We therefore performed a systematic cross-platform comparison of three different microscale cultivation systems commonly harnessed in single-cell analysis: microfluidic non-contact cell traps driven by negative dielectrophoresis, microfluidic monolayer growth chambers, and semi-solid agarose pads. We assessed the specific single-cell growth rates, division rates and morphological characteristics of single Corynebacterium glutamicum cells and microcolonies as a bacterial model organism with medical and biotechnological relevance under standardized growth conditions. Strikingly, the specific single-cell and microcolony growth rates, μmax, were robust and conserved for several cell generations with all three microcultivation technologies, whereas the division rates of cells grown on agarose pads deviated by up to 50% from those of cells cultivated in negative dielectrophoresis traps and monolayer growth chambers. Furthermore, morphological characteristics like cell lengths and division symmetries of individual cells were affected when the cells were grown on agarose pads. This indicated a significant impact of solid cultivation supports on cellular traits. The results demonstrate the impact of microcultivation technology on microbial physiology for the first time and show the need for a careful selection and design of the microcultivation technology in order to allow unbiased analysis of cellular behavior.

Advantages and Challenges of Relaxor-PbTiO3 Ferroelectric Crystals for Electroacoustic Transducers- A Review

Relaxor-PbTiO3 (PT) based ferroelectric crystals with the perovskite structure have been investigated over the last few decades due to their ultrahigh piezoelectric coefficients (d33 > 1500 pC/N) and electromechanical coupling factors (k33 > 90%), far outperforming state-of-the-art ferroelectric polycrystalline Pb(Zr,Ti)O3 ceramics, and are at the forefront of advanced electroacoustic applications. In this review, the performance merits of relaxor-PT crystals in various electroacoustic devices are presented from a piezoelectric material viewpoint. Opportunities come from not only the ultrahigh properties, specifically coupling and piezoelectric coefficients, but through novel vibration modes and crystallographic/domain engineering. Figure of merits (FOMs) of crystals with various compositions and phases were established for various applications, including medical ultrasonic transducers, underwater transducers, acoustic sensors and tweezers. For each device application, recent developments in relaxor-PT ferroelectric crystals were surveyed and compared with state-of-the-art polycrystalline piezoelectrics, with an emphasis on their strong anisotropic features and crystallographic uniqueness, including engineered domain - property relationships. This review starts with an introduction on electroacoustic transducers and the history of piezoelectric materials. The development of the high performance relaxor-PT single crystals, with a focus on their uniqueness in transducer applications, is then discussed. In the third part, various FOMs of piezoelectric materials for a wide range of ultrasound applications, including diagnostic ultrasound, therapeutic ultrasound, underwater acoustic and passive sensors, tactile sensors and acoustic tweezers, are evaluated to provide a thorough understanding of the materials' behavior under operational conditions. Structure-property-performance relationships are then established. Finally, the impacts and challenges of relaxor-PT crystals are summarized to guide on-going and future research in the development of relaxor-PT crystals for the next generation electroacoustic transducers.

The Effect of Layer-by-Layer Assembly Coating on the Proliferation and Differentiation of Neural Stem Cells

Nanocoating of a single-cell with biocompatible materials creates a defined microenvironment for cell differentiation and proliferation, as well as a model for studies in cell biology. In addition, the acidic environment in the tissue of stroke victims necessitates drug release upon pH stimuli. Here, we report the encapsulation of single neural stem cells (NSCs) using a layer-by-layer (LbL) self-assembly technique with polyelectrolytes gelatin and alginate. Analysis of the NSCs showed that the LbL encapsulation would not affect the viability, proliferation, or differentiation of the cells. When insulin-like growth factor-1 (IGF-1) was loaded on the coating material alginate, its release from alginate into the medium presented in a time-dependent and pH-dependent way. IGF-1 significantly enhanced the proliferation of the encapsulated NSCs, demonstrating a drug-carrier function of the LbL single-cell nanocoating. It provided a potential treatment strategy for nervous system disorders such as stroke.

Analysis of fast protein phosphorylation kinetics in single cells on a microfluidic chip

In the present study, we developed a microfluidic large-scale integration (mLSI) platform for the temporal and chemical control of cell cultures to study fast kinetics of protein phosphorylation. For in situ protein analysis the mLSI chip integrates the Proximity Ligation Assay (PLA). To investigate cell-signaling events with a time resolution of a few seconds we first engineered and optimized the fluidic layout of the chip with 128 individual addressable cell culture chambers. The functionality of the cell culture operations and PLA is demonstrated by the determination of the minimum cell sample size for obtaining robust quantitative PLA signals at the single-cell level. We show that at least 350 cells per assay condition are required to statistically evaluate single cell PLA data. In the following we used the PLA chip with over 500 hundred cells per condition to record sequential phosphorylation reactions of the canonical protein kinase within the Akt pathway, which is activated in various human cancer types. This was achieved by stimulating mouse fibroblast cell cultures with either the platelet-derived growth factor (PDGF) or insulin-like growth factor (IGF-1). Fluidic cell stimulation pulses of 5 seconds were followed by precisely time shifted cell fixation pulses to obtain a temporal resolution of 10 seconds. PLA was then performed on all fixed arrays of cell cultures to extract the characteristic phosphorylation times at the single cell level for either the PDGF, or IGF-1 receptor and the Akt and GSK3β kinases. Characteristic phosphorylation times for the receptors were between 13 and 35 seconds, whereas for downstream kinases between 25 and 200 seconds. Thus we could reveal a molecular order of the phosphorylation reactions during the signal transduction through the Akt pathway. In dependence of the stimulus we found a temporal difference for the characteristic phosphorylation time of 20 and 150 seconds for the Ser-473 and Thr-308 residues on the Akt kinase, respectively. Temporal alteration of sequential phosphorylation reactions on Akt has been proposed as molecular mechanism to differentiate between stimuli and biophysically determined in the present study.

Stochastic particle barcoding for single-cell tracking and multiparametric analysis

This study presents stochastic particle barcoding (SPB), a method for tracking cell identity across bioanalytical platforms. In this approach, single cells or small collections of cells are co-encapsulated within an enzymatically-degradable hydrogel block along with a random collection of fluorescent beads, whose number, color, and position encode the identity of the cell, enabling samples to be transferred in bulk between single-cell assay platforms without losing the identity of individual cells. The application of SPB is demonstrated for transferring cells from a subnanoliter protein secretion/phenotyping array platform into a microtiter plate, with re-identification accuracies in the plate assay of 96±2%. Encapsulated cells are recovered by digesting the hydrogel, allowing subsequent genotyping and phenotyping of cell lysates. Finally, a model scaling is developed to illustrate how different parameters affect the accuracy of SPB and to motivate scaling of the method to thousands of unique blocks.

Comprehensive chemical secretory measurement of single cells trapped in a micro-droplet array with mass spectrometry

By trapping individual single cells in a micro-well, molecules secreted by a single cell can be analyzed using mass spectrometry.

Single-cell printing based on impedance detection

Label-free isolation of single cells is essential for the growing field of single-cell analysis. Here, we present a device which prints single living cells encapsulated in free-flying picoliter droplets. It combines inkjet printing and impedance flow cytometry. Droplet volume can be controlled in the range of 500 pl-800 pl by piezo actuator displacement. Two sets of parallel facing electrodes in a 50 μm × 55 μm channel are applied to measure the presence and velocity of a single cell in real-time. Polystyrene beads with <5% variation in diameter generated signal variations of 12%-17% coefficients of variation. Single bead efficiency (i.e., printing events with single beads vs. total number of printing events) was 73% ± 11% at a throughput of approximately 9 events/min. Viability of printed HeLa cells and human primary fibroblasts was demonstrated by culturing cells for at least eight days.

Emerging microengineered tools for functional analysis and phenotyping of blood cells

The available techniques for assessing blood cell functions are limited considering the various types of blood cell and their diverse functions. In the past decade, rapid advances in microengineering have enabled an array of blood cell functional measurements that are difficult or impossible to achieve using conventional bulk platforms. Such miniaturized blood cell assay platforms also provide the attractive capabilities of reducing chemical consumption, cost, and assay time, as well as exciting opportunities for device integration, automation, and assay standardization. This review summarizes these contemporary microengineered tools and discusses their promising potential for constructing accurate in vitro models and rapid clinical diagnosis using minimal amounts of whole-blood samples.

Plant single-cell and single-cell-type metabolomics

In conjunction with genomics, transcriptomics, and proteomics, plant metabolomics is providing large data sets that are paving the way towards a comprehensive and holistic understanding of plant growth, development, defense, and productivity. However, dilution effects from organ- and tissue-based sampling of metabolomes have limited our understanding of the intricate regulation of metabolic pathways and networks at the cellular level. Recent advances in metabolomics methodologies, along with the post-genomic expansion of bioinformatics knowledge and functional genomics tools, have allowed the gathering of enriched information on individual cells and single cell types. Here we review progress, current status, opportunities, and challenges presented by single cell-based metabolomics research in plants.

A new toolbox for assessing single cells

Unprecedented access to the biology of single cells is now feasible, enabled by recent technological advancements that allow us to manipulate and measure sparse samples and achieve a new level of resolution in space and time. This review focuses on advances in tools to study single cells for specific areas of biology. We examine both mature and nascent techniques to study single cells at the genomics, transcriptomics, and proteomics level. In addition, we provide an overview of tools that are well suited for following biological responses to defined perturbations with single-cell resolution. Techniques to analyze and manipulate single cells through soluble and chemical ligands, the microenvironment, and cell-cell interactions are provided. For each of these topics, we highlight the biological motivation, applications, methods, recent advances, and opportunities for improvement. The toolbox presented in this review can function as a starting point for the design of single-cell experiments.

Lab-on-chip device for single cell trapping and analysis

Traditional cell assay gives us an average result of multiple cells and it is assumed that the resultant is the outcome of all cells in population. However, single cell studies have revealed that individual cells of same type may differ dramatically and these differences may have important role to play in cells functionality. Such information can be obscured in only studying cell population experimental approach. To uncover biological principles and ultimately to improve the detection and treatment of disease, new approaches are highly required to single cell analysis. We propose to fabricate a lab on chip device to study high throughput single cell nanotoxicity analysis. The chip incorporates independently addressable active microwell electrodes for cell manipulation and analysis. We employed positive-dielectrophoresis approach to quickly and efficiently capture single cells in each wells with having control over individual microwells. We examined change in impedance properties to verify cell capture in microwell and its health and present a novel model of single cell assay for nanotoxicity, and drug testing.