Quantitative phase imaging by gradient retardance optical microscopy

Quantitative phase imaging (QPI) has become a vital tool in bioimaging, offering precise measurements of wavefront distortion and, thus, of key cellular metabolism metrics, such as dry mass and density. However, only a few QPI applications have been demonstrated in optically thick specimens, where scattering increases background and reduces contrast. Building upon the concept of structured illumination interferometry, we introduce Gradient Retardance Optical Microscopy (GROM) for QPI of both thin and thick samples. GROM transforms any standard Differential Interference Contrast (DIC) microscope into a QPI platform by incorporating a liquid crystal retarder into the illumination path, enabling independent phase-shifting of the DIC microscope's sheared beams. GROM greatly simplifies related configurations, reduces costs, and eradicates energy losses in parallel imaging modalities, such as fluorescence. We successfully tested GROM on a diverse range of specimens, from microbes and red blood cells to optically thick (~ 300 μm) plant roots without fixation or clearing.

Scattered-light-sheet microscopy with sub-cellular resolving power

Since its first demonstration over 100 years ago, scattering-based light-sheet microscopy has recently re-emerged as a key modality in label-free tissue imaging and cellular morphometry; however, scattering-based light-sheet imaging with subcellular resolution remains an unmet target. This is because related approaches inevitably superimpose speckle or granular intensity modulation on to the native subcellular features. Here, we addressed this challenge by deploying a time-averaged pseudo-thermalized light-sheet illumination. While this approach increased the lateral dimensions of the illumination sheet, we achieved subcellular resolving power after image deconvolution. We validated this approach by imaging cytosolic carbon depots in yeast and bacteria with increased specificity, no staining, and ultralow irradiance levels. Overall, we expect this scattering-based light-sheet microscopy approach will advance single, live cell imaging by conferring low-irradiance and label-free operation towards eradicating phototoxicity.

Correction: Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations

[This corrects the article DOI: 10.1371/journal.pgen.1008458.].

Video-rate Raman-based metabolic imaging by Airy light-sheet illumination and photon-sparse detection

Despite its massive potential, Raman imaging represents just a modest fraction of all research and clinical microscopy to date. This is due to the ultralow Raman scattering cross-sections of most biomolecules that impose low-light or photon-sparse conditions. Bioimaging under such conditions is suboptimal, as it either results in ultralow frame rates or requires increased levels of irradiance. Here, we overcome this tradeoff by introducing Raman imaging that operates at both video rates and 1,000-fold lower irradiance than state-of-the-art methods. To accomplish this, we deployed a judicially designed Airy light-sheet microscope to efficiently image large specimen regions. Further, we implemented subphoton per pixel image acquisition and reconstruction to confront issues arising from photon sparsity at just millisecond integrations. We demonstrate the versatility of our approach by imaging a variety of samples, including the three-dimensional (3D) metabolic activity of single microbial cells and the underlying cell-to-cell variability. To image such small-scale targets, we again harnessed photon sparsity to increase magnification without a field-of-view penalty, thus, overcoming another key limitation in modern light-sheet microscopy.

Airy light-sheet Raman imaging

Light-sheet fluorescence microscopy has greatly improved the speed and overall photostability of optically sectioning cellular and multi-cellular specimens. Similar gains have also been conferred by light-sheet Raman imaging; these schemes, however, rely on diffraction limited Gaussian beams that hinder the uniformity and size of the imaging field-of-view, and, as such, the resulting throughput rates. Here, we demonstrate that a digitally scanned Airy beam increases the Raman imaging throughput rates by more than an order of magnitude than conventional diffraction-limited beams. Overall, this, spectrometer-less, approach enabled 3D imaging of microparticles with high contrast and 1 µm axial resolution at 300 msec integration times per plane and orders of magnitude lower irradiation density than coherent Raman imaging schemes. We detail the apparatus and its performance, as well as its compatibility with fluorescence light-sheet and quantitative-phase imaging towards rapid and low phototoxicity multimodal imaging.

Deep learning classification of lipid droplets in quantitative phase images

We report the application of supervised machine learning to the automated classification of lipid droplets in label-free, quantitative-phase images. By comparing various machine learning methods commonly used in biomedical imaging and remote sensing, we found convolutional neural networks to outperform others, both quantitatively and qualitatively. We describe our imaging approach, all implemented machine learning methods, and their performance with respect to computational efficiency, required training resources, and relative method performance measured across multiple metrics. Overall, our results indicate that quantitative-phase imaging coupled to machine learning enables accurate lipid droplet classification in single living cells. As such, the present paradigm presents an excellent alternative of the more common fluorescent and Raman imaging modalities by enabling label-free, ultra-low phototoxicity, and deeper insight into the thermodynamics of metabolism of single cells.

Microbial metabolic noise

From the time a cell was first placed under the microscope, it became apparent that identifying two clonal cells that "look" identical is extremely challenging. Since then, cell-to-cell differences in shape, size, and protein content have been carefully examined, informing us of the ultimate limits that hinder two cells from occupying an identical phenotypic state. Here, we present recent experimental and computational evidence that similar limits emerge also in cellular metabolism. These limits pertain to stochastic metabolic dynamics and, thus, cell-to-cell metabolic variability, including the resulting adapting benefits. We review these phenomena with a focus on microbial metabolism and conclude with a brief outlook on the potential relationship between metabolic noise and adaptive evolution. This article is categorized under: Metabolic Diseases > Computational Models Metabolic Diseases > Biomedical Engineering.

Integrative quantitative-phase and airy light-sheet imaging

Light-sheet microscopy enables considerable speed and phototoxicity gains, while quantitative-phase imaging confers label-free recognition of cells and organelles, and quantifies their number-density that, thermodynamically, is more representative of metabolism than size. Here, we report the fusion of these two imaging modalities onto a standard inverted microscope that retains compatibility with microfluidics and open-source software for image acquisition and processing. An accelerating Airy-beam light-sheet critically enabled imaging areas that were greater by more than one order of magnitude than a Gaussian beam illumination and matched exactly those of quantitative-phase imaging. Using this integrative imaging system, we performed a demonstrative multivariate investigation of live-cells in microfluidics that unmasked that cellular noise can affect the compartmental localization of metabolic reactions. We detail the design, assembly, and performance of the integrative imaging system, and discuss potential applications in biotechnology and evolutionary biology.

Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations

While microbiologists often make the simplifying assumption that genotype determines phenotype in a given environment, it is becoming increasingly apparent that phenotypic heterogeneity (in which one genotype generates multiple phenotypes simultaneously even in a uniform environment) is common in many microbial populations. The importance of phenotypic heterogeneity has been demonstrated in a number of model systems involving binary phenotypic states (e.g., growth/non-growth); however, less is known about systems involving phenotype distributions that are continuous across an environmental gradient, and how those distributions change when the environment changes. Here, we describe a novel instance of phenotypic diversity in tolerance to a metabolic toxin within wild-type populations of Methylobacterium extorquens, a ubiquitous phyllosphere methylotroph capable of growing on the methanol periodically released from plant leaves. The first intermediate in methanol metabolism is formaldehyde, a potent cellular toxin that is lethal in high concentrations. We have found that at moderate concentrations, formaldehyde tolerance in M. extorquens is heterogeneous, with a cell's minimum tolerance level ranging between 0 mM and 8 mM. Tolerant cells have a distinct gene expression profile from non-tolerant cells. This form of heterogeneity is continuous in terms of threshold (the formaldehyde concentration where growth ceases), yet binary in outcome (at a given formaldehyde concentration, cells either grow normally or die, with no intermediate phenotype), and it is not associated with any detectable genetic mutations. Moreover, tolerance distributions within the population are dynamic, changing over time in response to growth conditions. We characterized this phenomenon using bulk liquid culture experiments, colony growth tracking, flow cytometry, single-cell time-lapse microscopy, transcriptomics, and genome resequencing. Finally, we used mathematical modeling to better understand the processes by which cells change phenotype, and found evidence for both stochastic, bidirectional phenotypic diversification and responsive, directed phenotypic shifts, depending on the growth substrate and the presence of toxin.

Scientists tend to appreciate microbes for their simplicity and predictability: a population of genetically identical cells inhabiting a uniform environment is expected to behave in a uniform way. However, counter-examples to this assumption are frequently being discovered, forcing a re-examination of the relationship between genotype and phenotype. In most such examples, bacterial cells are found to split into two discrete populations, for instance growing and non-growing. Here, we report the discovery of a novel example of microbial phenotypic heterogeneity in which cells are distributed along a gradient of phenotypes, ranging from low to high tolerance of a toxic chemical. Furthermore, we demonstrate that the distribution of phenotypes changes in different growth conditions, and we use mathematical modeling to show that cells may change their phenotype either randomly or in a particular direction in response to the environment. Our work expands our understanding of how a bacterial cell's genome, family history, and environment all contribute to its behavior, with implications for the diverse situations in which we care to understand the growth of any single-celled populations.

Eliciting the impacts of cellular noise on metabolic trade-offs by quantitative mass imaging

Optimal metabolic trade-offs between growth and productivity are key constraints in strain optimization by metabolic engineering; however, how cellular noise impacts these trade-offs and drives the emergence of subpopulations with distinct resource allocation strategies, remains largely unknown. Here, we introduce a single-cell strategy for quantifying the trade-offs between triacylglycerol production and growth in the oleaginous microorganism Yarrowia lipolytica. The strategy relies on high-throughput quantitative-phase imaging and, enabled by nanoscale secondary ion mass spectrometry analyses and dedicated image processing, allows us to image how resources are partitioned between growth and productivity. Enhanced precision over population-averaging biotechnologies and conventional microscopy demonstrates how cellular noise impacts growth and productivity differently. As such, subpopulations with distinct metabolic trade-offs emerge, with notable impacts on strain performance and robustness. By quantifying the self-degradation of cytosolic macromolecules under nutrient-limiting conditions, we discover the cell-to-cell heterogeneity in protein and fatty-acid recycling, unmasking a potential bet-hedging strategy under starvation.

An unexpected phase transformation of ceria nanoparticles in aqueous media

Cerium oxide Nanoparticles (CNPs) are of significant interest to the scientific community due to their wide spread applications in a variety of fields. It is proposed that size dependent variations in the extent of Ce3+ and Ce4+ oxidation states of cerium in CNPs determines the performance of CNPs in application environments. To obtain greater molecular and structural understanding of chemical state transformations previously reported for ceria ≈ 3 nm nanoparticles (CNPs) in response to changing ambient conditions, microXRD and Raman measurements were carried out for various solution conditions. The particles were observed to undergo a reversible transformation from a defective ceria structure to a non-ceria amorphous oxy-hydroxide/peroxide phase in response to the addition of 30% hydrogen peroxide. For CNPs made up of ~8 nm crystallites, a partial transformation was observed and no transformation was observed for CNPs made up of ~ 40 nm crystallites. This observation of differences in size dependent transition behavior may help explain the benefits of using smaller CNPs in applications requiring regenerative behavior.

Solvent immersion imprint lithography: A high-performance, semi-automated procedure

We expand upon our recent, fundamental report on solvent immersion imprint lithography (SIIL) and describe a semi-automated and high-performance procedure for prototyping polymer microfluidics and optofluidics. The SIIL procedure minimizes manual intervention through a cost-effective (∼$200) and easy-to-assemble apparatus. We analyze the procedure's performance specifically for Poly (methyl methacrylate) microsystems and report repeatable polymer imprinting, bonding, and 3D functionalization in less than 5 min, down to 8 μm resolutions and 1:1 aspect ratios. In comparison to commercial approaches, the modified SIIL procedure enables substantial cost reductions, a 100-fold reduction in imprinting force requirements, as well as a more than 10-fold increase in bonding strength. We attribute these advantages to the directed polymer dissolution that strictly localizes at the polymer-solvent interface, as uniquely offered by SIIL. The described procedure opens new desktop prototyping opportunities, particularly for non-expert users performing live-cell imaging, flow-through catalysis, and on-chip gas detection.

Exploiting Bioprocessing Fluctuations to Elicit the Mechanistics of De Novo Lipogenesis in Yarrowia lipolytica

Despite substantial achievements in elucidating the metabolic pathways of lipogenesis, a mechanistic representation of lipid accumulation and degradation has not been fully attained to-date. Recent evidence suggests that lipid accumulation can occur through increases of either the cytosolic copy-number of lipid droplets (LDs), or the LDs size. However, the prevailing phenotype, or how such mechanisms pertain to lipid degradation remain poorly understood. To address this shortcoming, we employed the-recently discovered-innate bioprocessing fluctuations in Yarrowia lipolytica, and performed single-cell fluctuation analysis using optical microscopy and microfluidics that generate a quasi-time invariant microenvironment. We report that lipid accumulation at early stationary phase in rich medium is substantially more likely to occur through variations in the LDs copy-number, rather than the LDs size. Critically, these mechanistics are also preserved during lipid degradation, as well as upon exposure to a protein translation inhibitor. The latter condition additionally induced a lipid accumulation phase, accompanied by the downregulation of lipid catabolism. Our results enable an in-depth mechanistic understanding of lipid biogenesis, and expand longitudinal single-cell fluctuation analyses from gene regulation to metabolism.

Origins of Cell-to-Cell Bioprocessing Diversity and Implications of the Extracellular Environment Revealed at the Single-Cell Level

Bioprocess limitations imposed by microbial cell-to-cell phenotypic diversity remain poorly understood. To address this, we investigated the origins of such culture diversity during lipid production and assessed the impact of the fermentation microenvironment. We measured the single-cell lipid production dynamics in a time-invariant microfluidic environment and discovered that production is not monotonic, but rather sporadic with time. To characterize this, we introduce bioprocessing noise and identify its epigenetic origins. We linked such intracellular production fluctuations with cell-to-cell productivity diversity in culture. This unmasked the phenotypic diversity amplification by the culture microenvironment, a critical parameter in strain engineering as well as metabolic disease treatment.

Modular Polymer Biosensors by Solvent Immersion Imprint Lithography

We recently demonstrated Solvent Immersion Imprint Lithography (SIIL), a rapid benchtop microsystem prototyping technique, including polymer functionalization, imprinting and bonding. Here, we focus on the realization of planar polymer sensors using SIIL through simple solvent immersion without imprinting. We describe SIIL's impregnation characteristics, including an inherent mechanism that not only achieves practical doping concentrations, but their unexpected 2-fold enhancement compared to the immersion solution. Subsequently, we developed and characterized optical sensors for detecting molecular O₂. To this end, a substantially high dynamic range is reported, including its control through the immersion duration, a manifestation of SIIL's modularity. Overall, SIIL exhibits the potential of improving the operating characteristics of polymer sensors, while significantly accelerating their prototyping, as it requires a few seconds of processing and no need for substrates or dedicated instrumentation. These are critical for O₂ sensing as probed by way of example here, as well as any polymer permeable reactant.

Review of methods to probe single cell metabolism and bioenergetics

Single cell investigations have enabled unexpected discoveries, such as the existence of biological noise and phenotypic switching in infection, metabolism and treatment. Herein, we review methods that enable such single cell investigations specific to metabolism and bioenergetics. Firstly, we discuss how to isolate and immobilize individuals from a cell suspension, including both permanent and reversible approaches. We also highlight specific advances in microbiology for its implications in metabolic engineering. Methods for probing single cell physiology and metabolism are subsequently reviewed. The primary focus therein is on dynamic and high-content profiling strategies based on label-free and fluorescence microspectroscopy and microscopy. Non-dynamic approaches, such as mass spectrometry and nuclear magnetic resonance, are also briefly discussed.

Solvent immersion imprint lithography

We present Solvent Immersion Imprint Lithography (SIIL), a technique for polymer functionalization and microsystem prototyping. SIIL is based on polymer immersion in commonly available solvents. This was experimentally and computationally analyzed, uniquely enabling two practical aspects. The first is imprinting and bonding deep features that span the 1 to 100 μm range, which are unattainable with existing solvent-based methods. The second is a functionalization scheme characterized by a well-controlled, 3D distribution of chemical moieties. SIIL is validated by developing microfluidics with embedded 3D oxygen sensors and microbioreactors for quantitative metabolic studies of a thermophile anaerobe microbial culture. Polystyrene (PS) was employed in the aforementioned applications; however all soluble polymers - including inorganic ones - can be employed with SIIL under no instrumentation requirements and typical processing times of less than two minutes.

Optofluidic-tunable color filters and spectroscopy based on liquid-crystal microflows

The integration of color filters with microfluidics has attracted substantial attention in recent years, for on-chip absorption, fluorescence, or Raman analysis. We describe such tunable filters based on the micro-flow of liquid crystals. The filter operation is based on the wavelength-dependent liquid crystal birefringence that can be tuned by modifying the flow velocity field in the microchannel. The latter is possible both temporally and spatially by varying the inlet pressure and the channel geometry, respectively. We explored the use of these optofluidic filters for on-chip absorption spectroscopy in poly(dimethylsiloxane) microfluidic systems; by integrating the distance-dependent color filter with a dye-filled micro-channel, the absorption spectrum of a dye could be measured. Liquid crystal microflows substantially simplify the optofluidic integration, actuation and tuning of color filters for lab-on-a-chip spectroscopic applications.

Electro-switchable polydimethylsiloxane-based optofluidics

We report on the fabrication and characterization of a new generation of electro-switchable optofluidic devices based on flexible substrates, combined with the extraordinary properties of reconfigurable soft-materials. A conductive polydimethylsiloxane microstructure has been first sputtered with an Indium Tin Oxide (ITO) layer and then functionalized with an amorphous film of SiO(x). Then, the "layer" by "layer" microstructure has been infiltrated with an anisotropic and reconfigurable fluid (Nematic Liquid Crystal, NLC). The sample has been characterized in terms of morphological, optical and electro-optical properties: the soft-conductive microstructure exhibits a uniform and regular morphology, even after testing with mechanical stretching and deformations. Combination of the conductive ITO with the functionalization film (which has been employed for inducing in-plane alignment of NLC molecules) enables us to carry out a series of optical and electro-optical experiments; these confirm excellent properties in terms of a reconfigurable device and a diffractive element as well.

Elastomer based tunable optofluidic devices

The synergetic integration of photonics and microfluidics has enabled a wide range of optofluidic devices that can be tuned based on various physical mechanisms. One such tuning mechanism can be realized based on the elasticity of polydimethylsiloxane (PDMS). The mechanical tuning of these optofluidic devices was achieved by modifying the geometry of the device upon applying internal or external forces. External or internal forces can deform the elastomeric components that in turn can alter the optical properties of the device or directly induce flow. In this review, we discuss recent progress in tunable optofluidic devices, where tunability is enabled by the elasticity of the construction material. Different subtypes of such tuning methods will be summarized, namely tuning based on bulk or membrane deformations, and pneumatic actuation.

Precision intracellular delivery based on optofluidic polymersome rupture

We present an optical approach for intracellular delivery of molecules contained within oxidation-sensitive polymersomes. The photosensitizer ethyl eosin is associated with the polymersome membrane to oxidatively increase the hydrophilicity of the hydrophobic block under optical excitation. This optofluidic interaction induces rapid polymersome rupture and payload release via the reorganization of the aggregate structure into smaller diameter vesicles and micelles. When the particles are endocytosed by phagocytes, such as RAW macrophages and dendritic cells, the polymersomes' payload escapes the endosome and is released in the cell cytosol within a few seconds of illumination. The released payload is rapidly distributed throughout the cytosol within milliseconds. The presented optofluidic method enables fast delivery and distribution throughout the cytosol of individual cells, comparable to photochemical internalization, but a factor of 100 faster than similar carrier mediated delivery methods (e.g., liposomes, polymersomes, or nanoparticles). Due to the ability to simultaneously induce payload delivery and endosomal escape, this approach can find applications in detailed characterizations of intra- and intercellular processes. As an example in quantitative cell biology, a peptide antigen was delivered in dendritic cells and MHC I presentation kinetics were measured at the single cell and single complex level.

Silicon oxide deposition for enhanced optical switching in polydimethylsiloxane-liquid crystal hybrids

We report an optical switch based on a diffraction grating by combining PDMS microstructures with a photo-responsive Nematic Liquid Crystal (NLC). The grating was realized via replica molding and was subsequently coated with a thin SiO layer. SiO induced a full planar alignment of the liquid crystal. The induced parallel alignment of the LC reduces the response time of the structure by approximately an order of magnitude compared to the same structures without SiO. We explored the effect of the pump intensity on the transmission properties and time response of the switch and identified a strong dependence on the probe polarization, due to the full planar alignment in this structure. The aforementioned inclusion of the SiO layer enables enhanced performance of optical devices based on the fusion of nematogens with soft and flexible substrates.

Enhancing single molecule imaging in optofluidics and microfluidics

Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking.

Fluidic fibre dye lasers

We report the demonstration of compact fluidic fibre lasers based on capillary tubes and photonic crystal fibres, featuring single channel and multiple laterally integrated fluidic lasers respectively. Their preparation was based on capillary action and lasing occurred without the need for external mirrors or lithographically defined microstructures. The fibre lasers were found to be tunable by varying the chromophore density in the liquid core and a functional wavelength selectivity mechanism inherent in both types of lasers provided a long free spectral range that does not correspond to the length of the fibres. The enhanced mode spacing is attributed to a Vernier resonant effect.

Diode pumped distributed Bragg reflector lasers based on a dye-to-polymer energy transfer blend

We report the demonstration of a compact, all-solid-state polymer laser system comprising of a Gallium Nitride (GaN) semiconductor diode laser as the pump source. The polymer laser was configured as a surface emitting, distributed Bragg reflector laser (DBR), based on a novel energy transfer blend of Coumarin 102 and the conjugated polymer poly(2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylene vinylene). In this configuration, diode pumping was possible both due to the improved quality of the resonators and the improved harvesting of the diode laser light.