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The papers in this special section focus on biophotonics. This is an emerging and widely growing field of advanced biomedical technologies that has opened up new horizons for extensive transfer of state-of-the-art technologies coming from the areas of quantum electronics, lasers, fiber optics and electro-optics to the life sciences and medicine. This field continues to vastly expand with advanced developments across the entire spectrum of biomedical applications ranging from fundamental laboratory bench studies to clinical patient diagnostics, bioimaging, biosensing and therapeutics. Recently developed innovative biophotonics technologies have made a significant impact on biomedical research and public health, since they provide advanced minimally invasive, cost-effective and rapid techniques for diagnostics, monitoring and treatment of a variety of diseases.

We investigate the internal morphology of smart core-shell microgels by super-resolution fluorescence microscopy exploiting a combination of 3D single molecule localization and structured illumination microscopy utilizing freely diffusing fluorescent dyes. This approach does not require any direct chemical labeling and does not perturb the network structure of these colloidal gels. Hence, it allows us to study the morphology of the particles with very high precision. We found that the structure of the core-forming seed particles is drastically changed by the second synthesis step necessary for making the shell, resulting in a core region with highly increased dye localization density. The present work shows that super-resolution microscopy has great potential with respect to the study of soft colloidal systems.

The availability of cost-effective, highly portable, and easy to use high-resolution live-cell imaging systems could present a significant technological break-through in challenging environments, such as high-level biosafety laboratories or sites where new viral outbreaks are suspected. We describe and demonstrate a cost-effective high-speed fluorescence microscope enabling the live tracking of virus particles across virological synapses that form between infected and uninfected T cells. The dynamics of HIV-1 proteins studied at the cellular level and the formation of virological synapses in living T cells reveals mechanisms by which cell-cell interactions facilitate infection between immune cells. Dual-color 3D fluorescence deconvolution microscopy of HIV-1 particles at frames rates of 100 frames per second allows us to follow the transfer of HIV-1 particles across the T cell virological synapse between living T cells. We also confirm the successful transfer of virus by imaging T cell samples fixed at specific time points during cell-cell virus transfer by super-resolution structured illumination microscopy.

During HIV-1 transmission through T cell virological synapses, the recruitment of the envelope (Env) glycoprotein to the site of cell–cell contact is important for adhesion and for packaging onto nascent virus particles which assemble at the site. Live imaging studies in CD4 T cells have captured the rapid recruitment of the viral structural protein Gag to VSs. We explored the role of endocytic trafficking of Env initiated by a membrane proximal tyrosine motif during HIV transfer into target cells and examined the factors that allow Gag and Env to be transferred together across the synapse. To facilitate tracking of Env in live cells, we adapted an Env tagging method and introduced a biotin acceptor peptide (BAP) into the V4 loop of Env gp120, enabling sensitive fluorescent tracking of V4-biotinylated Env. The BAP-tagged and biotinylated HIVs were replication-competent in cell-free and cell-to-cell infection assays. Live cell fluorescent imaging experiments showed rapid internalized cell surface Env on infected cells. Cell–cell transfer experiments conducted with the Env endocytosis mutant (Y712A) showed increased transfer of Env. Paradoxically, this increase in Env transfer was associated with significantly reduced Gag transfer into target cells, when compared to viral transfer associated with WT Env. This Y712A Env mutant also exhibited an altered Gag/biotin Env fluorescence ratio during transfer that correlated with decreased productive cell-to-cell infection. These results may suggest that the internalization of Env into recycling pools plays an important role in the coordinated transfer of Gag and Env across the VS, which optimizes productive infection in target cells.

The papers in this special issues focus on the emerging field of biophotonics, one of the most extensively growing areas in biomedical technology that integrates state-of-the-art photonics techniques coming from the areas of quantum electronics, lasers, fiber optics and electro-optics to the life sciences and medicine. This field continues to vastly expand with advanced developments across the entire spectrum of biomedical applications ranging from fundamental laboratory studies to clinical patient diagnostics, bioimaging, biosensing and therapeutics. Recently developed innovative biophotonics technologies have made a significant impact on biomedical research and public health, since they provide advanced minimally invasive, cost-effective and rapid techniques for diagnostics, monitoring and treatment of a variety of diseases. Medical devices utilizing minimally invasive biophotonics technology are rapidly finding their way into the mainstream for early disease diagnosis and improved patient acceptance and comfort.

Digital micromirror devices (DMDs) are spatial light modulators that employ the electro-mechanical movement of miniaturized mirrors to steer and thus modulate the light reflected off a mirror array. Their wide availability, low cost and high speed make them a popular choice both in consumer electronics such as video projectors, and scientific applications such as microscopy. High-end fluorescence microscopy systems typically employ laser light sources, which by their nature provide coherent excitation light. In super-resolution microscopy applications that use light modulation, most notably structured illumination microscopy (SIM), the coherent nature of the excitation light becomes a requirement to achieve optimal interference pattern contrast. The universal combination of DMDs and coherent light sources, especially when working with multiple different wavelengths, is unfortunately not straight forward. The substructure of the tilted micromirror array gives rise to a blazed grating, which has to be understood and which must be taken into account when designing a DMD-based illumination system. Here, we present a set of simulation frameworks that explore the use of DMDs in conjunction with coherent light sources, motivated by their application in SIM, but which are generalizable to other light patterning applications. This framework provides all the tools to explore and compute DMD-based diffraction effects and to simulate possible system alignment configurations computationally, which simplifies the system design process and provides guidance for setting up DMD-based microscopes. This article is part of the Theo Murphy meeting ‘Super-resolution structured illumination microscopy (part 1)’.

Planar photonic waveguides enable ultrathin sample illumination in fluorescence microscopy over exceedingly large fields of view. Their fabrication has been based on hard coatings requiring sputter deposition and ion-beam lithography, making volume production cumbersome and thereby limiting their availability. Additionally, they are typically fabricated on top of opaque silicon wafers, which restricts the use to upright microscopes. Here, we present a low-cost photonic waveguide chip based on standard 170 μm thick glass coverslips coated with a micrometer-thin layer of EpoCore, a photoresist polymer with a high refractive index. These chips enable wide-field excitation for fluorescence microscopy and nanoscopy on inverted microscopes using fluorescence detection through the transparent substrate. Channel waveguides with varying widths provide uniform near-field illumination by evanescent waves for fields of view up to the millimeter scale. We demonstrate multicolor fluorescence excitation resulting in high-contrast immunofluorescence and super-resolution imaging with a resolution of approximately 60 nm.

Photoinduced off-switching of organic fluorophores is routinely used in super-resolution microscopy to separate and localize single fluorescent molecules, but the method typically relies on the use of complex imaging buffers. The most common buffers use primary thiols to reversibly reduce excited fluorophores to a non-fluorescent dark state, but these thiols have a limited shelf life and additionally require high illumination intensities in order to efficiently switch the emission of fluorophores. Recently a high-index, thiol-containing imaging buffer emerged which used sodium sulfite as an oxygen scavenger, but the switching properties of sulfite was not reported on. Here, we show that sodium sulfite in common buffer solutions reacts with fluorescent dyes, such as Alexa Fluor 647 and Alexa Fluor 488 under low to medium intensity illumination to form a semi-stable dark state. The duration of this dark state can be tuned by adding glycerol to the buffer. This simplifies the realization of different super-resolution microscopy modalities such as direct Stochastic Reconstruction Microscopy (dSTORM) and Super-resolution Optical Fluctuation Microscopy (SOFI). We characterize sulfite as a switching agent and compare it to the two most common switching agents by imaging cytoskeleton structures such as microtubules and the actin cytoskeleton in human osteosarcoma cells.

Optical nanoscopy is rapidly gaining momentum in the life sciences. Current instruments are, however, often large and expensive, and there is a substantial delay between raw data collection and super-resolved image display. Here, we describe the implementation of a compact, cost-effective, high-speed, structured illumination microscope (SIM), which allows for video-rate super-resolved image reconstructions at imaging rates up to 60 Hz. The instrument is based on a digital micromirror device (DMD) and a global-shutter camera, which enables faster pattern cycles and higher duty cycles than commonly used liquid crystal-based spatial light modulators. In order to utilize a DMD for creating illumination patterns by the coherent superposition of laser beams, we carefully studied its blazed grating effect Through both simulation and experimental determination of system parameters, we identified and optimized its alignment for optimal SIM pattern contrast. Raw image data are collected using inexpensive industry-grade CMOS cameras, while a parallel-computing platform allowed us to reconstruct and visualize living cells in real time. We demonstrate the performance of this system by imaging submicron-sized fluorescent beads diffusing in an aqueous solution, resolving bead-bead interactions in real time. We show that the system is sensitive enough to image intracellular vesicles labeled with fluorescent proteins in fixed cells. We also image dynamic fluctuations of the endoplasmic reticulum (ER), as well as the movement of mitochondria in living osteosarcoma cells, where the cellular organelles are labeled with live cell fluorescent stains.

HIV-1 infection is enhanced by cell-cell adhesions between infected and uninfected T cells called virological synapses (VS). VS are initiated by the interactions of cell-surface HIV-1 envelope glycoprotein (Env) and CD4 on target cells and act as sites of viral assembly and viral transfer between cells. To study the process that recruits and retains HIV-1 Env at the VS, a replication-competent HIV-1 clone carrying an Env-sfGFP fusion protein was designed to enable live tracking of Env within infected cells. Using surface pulse-labeling of Env and fluorescence recovery after photobleaching (FRAP) studies, we observed targeted accumulation and sustained recycling of Env between the endocytic recycling compartment (ERC) and the VS. We observed dynamic exchange of Env at the VS while the viral structural protein, Gag, was largely immobile at the VS. The disparate exchange rates of Gag and Env at the synapse indicate that retention of Env is not likely to be maintained by entrapment into an immobile Gag lattice or through immobilizing interactions with CD4 on the target cell. A FRAP study of an Env endocytosis mutant showed that recycling is required for the rapid exchange of Env at the VS. We conclude that the mechanism of Env accumulation at the VS and incorporation into nascent particles involves continuous internalization and targeted secretion rather than irreversible interactions with the budding virus.

Chip-based optical nanoscopy, relying on single molecule localization microscopy has recently been demonstrated to reach 70 nm lateral resolution over wide fields of view (500 µm x 500 µm). To make this technique more sustainable for live-cell imaging we embedded a photonic chip into a microfluidic support that is able to perfuse and thermalize the samples. In this way specimens are maintained under physiological conditions during the imaging which can be a timeconsuming process. The system consists of a multilayer chip with the size of a glass coverslip (60 mm × 24 mm). The sample is illuminated using waveguides that are fabricated from high refractive index material. The waveguide hosts a chamber (17.3 μl) where cells are seeded and perfused with medium. A thin layer (188 µm) of cyclic olefin polymer (COP) seals the chamber and allows optical image acquisition. A thermalizing solution is perfused from the bottom to accurately warm up/cool down the waveguide in a range of 5°C - 45°C. Thus, samples are kept at the proper temperature. As proof of concept and verification of super-resolution imaging, we imaged fluorescent beads perfused across the coated surface (fibronectin 0.2 mg/ml) of the chip, which is needed to guarantee proper cell-to-substrate adhesion.

Super-resolution fluorescence microscopy has become a powerful tool in cell biology to observe sub-cellular organization and molecular details below the diffraction limit of light. Super-resolution methods are generally classified into three main concepts: stimulated emission depletion (STED), single molecule localization microscopy (SMLM) and structured illumination microscopy (SIM). Here, we highlight the novel concept of modulation-enhanced localization microscopy (meLM) which we designate as the 4th super-resolution method. Recently, a series of modulation-enhanced localization microscopy methods have emerged, namely MINFLUX, SIMPLE, SIMFLUX, ModLoc and ROSE. Although meLM combines key ideas from STED, SIM and SMLM, the main concept of meLM relies on a different idea: isolated emitters are localized by measuring their modulated fluorescence intensities in a precisely shifted structured illumination pattern. To position meLM alongside state-of-the-art super-resolution methods we first highlight the basic principles of existing techniques and show which parts of these principles are utilized by the meLM method. We then present the overall novel super-resolution principle of meLM that can theoretically reach unlimited localization precision whenever illumination patterns are translated by an arbitrarily small distance. L R acknowledges support of a fellowship from 'la Caixa' Foundation (ID 100010434, LCF/BQ/IN18/11660032) and funding from the European Union´s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 713673. V R acknowledges support from the Spanish Ministry of Economy and Competitiveness through the Program 'Centro de Excelencia Severo Ochoa 2013-2017', the CERCA Programme/Generalitat de Catalunya, MINECO's Plan Nacional (BFU2017-86296-P) and support from the CRG Advanced Light Microscopy Facility. S W acknowledges support from the Spanish Ministry of Economy and Competitiveness through the 'Severo Ochoa' program for Centres of Excellence in R&D (SEV-2015-0522), from Fundació Privada Cellex, and from Generalitat de Catalunya through the CERCA program.

In a recent publication [Bergmann et al. Phys. Chem. Chem. Phys., 2018, 20, 5074-5083] we presented a method which enables to investigate the morphology of microgels by superresolution fluorescence microscopy. Here, this method is applied to three microgel species, based on N-isopropylmethacrylamide (NIPMAM), N-n-propylacrylamide (NNPAM) and N-n-propylmethacrylamide (NNPMAM)) with 5, 7.5 and 10 mol% cross-linker, respectively. Super-resolution microscopy reveals differences of the network morphology of the synthesized particles showing the importance of the monomer structure.

Super-resolved structured illumination microscopy (SR-SIM) is among the most rapidly growing fluorescence microscopy techniques that can surpass the optical diffraction limit. The strength of SR-SIM is that it can be readily applied to samples prepared for conventional fluorescence microscopy, requiring no sophisticated sample preparation protocols. As an extension of wide-field fluorescence microscopy, it is inherently capable of multicolor imaging and optical sectioning and, with sufficiently fast implementations, permits live cell imaging. Image reconstruction, however, currently relies on sophisticated computational procedures, susceptible to reconstruction artifacts, requiring trained users to recognize and avoid them. Here, we review the latest developments in SR-SIM research. Starting from a historical overview of the development of SR-SIM, we review how this method can be implemented in various experimental schemes, we provide an overview of the important parameters involved in successful image reconstruction, we summarize recent biological applications, and we provide a brief outlook of the directions in which we believe SR-SIM is headed in the future.

Accepted manuscript version. Published version available at http://doi.org/10.1038/nphoton.2017.55. Present optical nanoscopy techniques use a complex microscope for imaging and a simple glass slide to hold the sample. Here, we demonstrate the inverse: the use of a complex, but mass-producible optical chip, which hosts the sample and provides a waveguide for the illumination source, and a standard low-cost microscope to acquire super-resolved images via two different approaches. Waveguides composed of a material with high refractive-index contrast provide a strong evanescent field that is used for single-molecule switching and fluorescence excitation, thus enabling chip-based single-molecule localization microscopy. Additionally, multimode interference patterns induce spatial fluorescence intensity variations that enable fluctuation-based super-resolution imaging. As chip-based nanoscopy separates the illumination and detection light paths, total-internal-reflection fluorescence excitation is possible over a large field of view, with up to 0.5 mm × 0.5 mm being demonstrated. Using multicolour chip-based nanoscopy, we visualize fenestrations in liver sinusoidal endothelial cells.

Structured illumination microscopy (SIM) is among the most widely used super-resolution fluorescence microscopy techniques for visualizing the dynamics of cellular organelles, such as mitochondria, the endoplasmic reticulum, or the cytoskeleton. In its most wide-spread implementation, SIM relies on the creation of an interference pattern at the diffraction limit using the coherent addition of laser beams created by a diffraction pattern.Spatial light modulators based on liquid crystal displays allow SIM micro-scopes to run at image rates of up to hundreds of super-resolved images per second. Digital micromirror devices are another natural choice for creating interference-based SIM patterns, but are not used to their fullest potential because of the blazed grating effect. This effect arises due to the fixed angles between which the mirrors can be switched, creating a sawtooth arrangement of mirrors and thus leading to a change in the intensity distribution of the diffracted beams. This results in SIM patterns with varying modulation contrast which are prone to reconstruction artifacts.We have carefully studied the blazed grating effect of DMDs by simulations, varying a range of parameters and compared the simulation results with experiments. This allowed us to identify settings which result in very high modulation contrast across all angles and phases required to generate 2-beam SIM pattern. The use of inexpensive industry-grade CMOS cameras as well as low-cost lasers enabled us to construct a cost-effective, high-speed SIM system. Reconstruction of the super-resolved SIM images is achieved on a recently demonstrated parallel-computing platform, which allowed us to visualize living cells with super-resolution at multiple reconstructed frames per second in real time. We demonstrate the versatility of this new platform by imaging cellular organelle dynamics based on live-cell fluorescent stains as well as with fluorescent protein stained samples.

Super-resolution structured illumination microscopy (SR-SIM) can be conducted at video-rate acquisition speeds when combined with high-speed spatial light modulators and sCMOS cameras, rendering it particularly suitable for live cell imaging. If, however, three-dimensional (3D) information is desired, the sequential acquisition of vertical image stacks employed by current setups significantly slows down the acquisition process. In this work we present a multi-plane approach to SR-SIM that overcomes this slowdown via the simultaneous acquisition of multiple object planes, employing a recently introduced multi-plane image splitting prism combined with high-speed SR-SIM illumination. This strategy requires only the introduction of a single optical element and the addition of a second camera to acquire a laterally super-resolved three-dimensional image stack. We demonstrate the performance of multi-plane SR-SIM by applying this instrument to the dynamics of live mitochondrial network.

Super-resolution microscopy (SRM) bypasses the diffraction limit, a physical barrier that restricts the optical resolution to roughly 250 nm and was previously thought to be impenetrable. SRM techniques allow the visualization of subcellular organization with unprecedented detail, but also confront biologists with the challenge of selecting the best-suited approach for their particular research question. Here, we provide guidance on how to use SRM techniques advantageously for investigating cellular structures and dynamics to promote new discoveries.

Coherent Raman scattering (CRS) imaging is a powerful tool in biomedical researches [1], thanks to its label­free chemical-specific contrast and the high spatial resolution. However, the large footprints and high cost of the commonly used solid-state laser sources hinder the translation of CRS microscopy to industries and clinical applications. Recently, a variety of fiber laser designs, including soliton self-frequency shift [2], supercontiuum (SC) generation [3] and fiber optical parametric wavelength conversion [4], have been proposed. However, they usually suffer from high intensity noise or low power density. Here, we show a passively-synchronized pulsed fiber laser source that provides excellent stability, power level and wavelength tunability. Both high quality coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) images are demonstrated.

We present a structured illumination microscopy based point localization estimator (SIMPLE) that achieves a 2-fold increase in single molecule localization precision compared to conventional centroid estimation methods. SIMPLE advances the recently introduced MINFLUX concept by using precisely phase-shifted sinusoidal wave patterns as nanometric rulers for simultaneous particle localization based on photon count variation over a 20 μm field of view. We validate SIMPLE in silico and experimentally on a TIRF-SIM setup using a digital micro-mirror device (DMD) as a spatial light modulator. Funding: “la Caixa” Foundation (ID 100010434, LCF/BQ/IN18/11660032); Marie Skłodowska-Curie Horizon 2020 (713673, 754558, 642157); Spanish Ministry Centro de Excelencia Severo Ochoa (SEV-2015-0522); MINECO’s Plan Nacional (BFU2017-86296-P); Generalitat de Catalunya (CERCA); Fundació Privada Cellex

Single-molecule localization microscopy (SMLM) provides a powerful toolkit to specifically resolve intracellular structures on the nanometer scale, even approaching resolution classically reserved for electron microscopy (EM). Although instruments for SMLM are technically simple to implement, researchers tend to stick to commercial microscopes for SMLM implementations. Here we report the construction and use of a “custom-built” multi-color channel SMLM system to study liver sinusoidal endothelial cells (LSECs) and platelets, which costs significantly less than a commercial system. This microscope allows the introduction of highly affordable and low-maintenance SMLM hardware and methods to laboratories that, for example, lack access to core facilities housing high-end commercial microscopes for SMLM and EM. Using our custom-built microscope and freely available software from image acquisition to analysis, we image LSECs and platelets with lateral resolution down to about 50 nm. Furthermore, we use this microscope to examine the effect of drugs and toxins on cellular morphology.

Endotoxin (lipooligosaccharide, LOS, and lipopolysaccharide, LPS) is the major molecular component of Gram-negative bacteria outer membrane, and very potent pro-inflammatory substance. Visualizing and tracking the distribution of the circulating endotoxin is one of the fundamental approaches to understand the molecular aspects of infection with subsequent inflammatory and immune responses, LPS also being a key player in the molecular dialogue between microbiota and host. While fluorescently labeled LPS has previously been used to track its subcellular localization and colocalization with TLR4 receptor and downstream effectors, our knowledge on lipopolysaccharide (LOS) localization and cellular activity remains almost unexplored. In this study, LOS was labeled with a novel fluorophore, Cy7N, featuring a large Stokes-shifted emission in the deep-red spectrum resulting in lower light scattering and better imaging contrast. The LOS-Cy7N chemical identity was determined by mass spectrometry, and immunoreactivity of the conjugate was evaluated. Interestingly, its application to microscopic imaging showed a faster cell internalization compared to LPS-Alexa488, despite that it is also CD14-dependent and undergoes the same endocytic pathway as LPS toward lysosomal detoxification. Our results suggest the use of the new infrared fluorophore Cy7N for cell imaging of labeled LOS by confocal fluorescence microscopy, and propose that LOS is imported in the cells by mechanisms different from those responsible for LPS uptake.

Super-resolution (SR) fluorescence microscopy is typically carried out on research microscopes equipped with high-NA TIRF objectives and powerful laser light sources. Super-resolution optical fluctuation imaging (SOFI) is a fast SR technique capable of live-cell imaging, that is compatible with many wide-field microscope systems. However, especially when employing fluorescent proteins, a key part of the imaging system is a very sensitive and well calibrated camera sensor. The substantial costs of such systems preclude many research groups from employing SR imaging techniques. Here, we examine to what extent SOFI can be performed using a range of imaging hardware comprising different technologies and costs. In particular, we quantitatively compare the performance of an industry-grade CMOS camera to both state-of-the-art emCCD and sCMOS detectors, with SOFI-specific metrics. We show that SOFI data can be obtained using a cost-efficient industry-grade sensor, both on commercial and home-built microscope systems, though our analysis also readily exposes the merits of the per-pixel corrections performed in scientific cameras.

Alveolar type II (ATII) cells in the peripheral human lung spontaneously differentiate toward ATI cells, thus enabling air‐blood barrier formation. Here, linear Raman and coherent anti‐Stokes Raman scattering (CARS) microscopy are applied to study cell differentiation of freshly isolated ATII cells. The Raman spectra can successfully be correlated with gradual morphological and molecular changes during cell differentiation. Alveolar surfactant rich vesicles in ATII cells are identified based on phospholipid vibrations, while ATI‐like cells are characterized by the absence of vesicular structures. Complementary, CARS microscopy allows for three‐dimensional visualization of lipid vesicles within ATII cells and their secretion, while hyperspectral CARS enables the distinction between cellular proteins and lipids according to their vibrational signatures. This study paves the path for further label‐free investigations of lung cells and the role of the pulmonary surfactant, thus also providing a basis for rational development of future lung therapeutics.

We present a new method to resolve the network morphology of colloidal particles in an aqueous environment via super-resolution microscopy. By localization of freely diffusing fluorophores inside the particle network we can resolve the three dimensional structure of one species of colloidal particles (thermoresponsive microgels) without altering their chemical composition through copolymerization with fluorescent monomers. Our approach utilizes the interaction of the fluorescent dye rhodamine 6G with the polymer network to achieve an indirect labeling. We calculate the 3D structure from the 2D images and compare the structure to previously published models for the microgel morphology, e.g. the fuzzy sphere model. To describe the differences in the data an extension of this model is suggested. Our method enables the tailor-made fabrication of colloidal particles which are used in various applications, such as paints or cosmetics, and are promising candidates for drug delivery, smart surface coatings, and nanocatalysis. With the precise knowledge of the particle morphology an understanding of the underlying structure-property relationships for various colloidal systems is possible.

Source at https://doi.org/10.1515/nanoph-2017-0055. Super-resolution fluorescence microscopy, also known as nanoscopy, has provided us with a glimpse of future impacts on cell biology. Far-field optical nanoscopy allows, for the first time, the study of sub-cellular nanoscale biological structures in living cells, which in the past was limited to electron microscopy (EM) (in fixed/dehydrated) cells or tissues. Nanoscopy has particular utility in the study of “fenestrations” – phospholipid transmembrane nanopores of 50–150 nm in diameter through liver sinusoidal endothelial cells (LSECs) that facilitate the passage of plasma, but (usually) not blood cells, to and from the surrounding hepatocytes. Previously, these fenestrations were only discernible with EM, but now they can be visualized in fixed and living cells using structured illumination microscopy (SIM) and in fixed cells using single molecule localization microscopy (SMLM) techniques such as direct stochastic optical reconstruction microscopy. Importantly, both methods use wet samples, avoiding dehydration artifacts. The use of nanoscopy can be extended to the in vitro study of fenestration dynamics, to address questions such as the following: are they actually dynamic structures, and how do they respond to endogenous and exogenous agents? A logical further extension of these methodologies to liver research (including the liver endothelium) will be their application to liver tissue sections from animal models with different pathological manifestations and ultimately to patient biopsies. This review will cover the current state of the art of the use of nanoscopy in the study of liver endothelium and the liver in general. Potential future applications in cell biology and the clinical implications will be discussed.

Surface-enhanced Raman scattering spectroscopy (SERS) was employed to investigate the formation of self-assembled monolayers (SAMs) of biphenylthiol, 4'-nitro-1,1'-biphenyl-4-thiol, and p-terphenylthiol on Au surfaces and their structural transformations into carbon nanomembranes (CNMs) induced by electron irradiation. The high sensitivity of SERS allows us to identify two types of Raman scattering in electron-irradiated SAMs: (1) Raman-active sites exhibit similar bands as those of pristine SAMs in the fingerprint spectral region, but with indications of an amorphization process and (2) Raman-inactive sites show almost no Raman-scattering signals, except a very weak and broad D band, indicating a lack of structural order but for the presence of graphitic domains. Statistical analysis showed that the ratio of the number of Raman-active sites to the total number of measurement sites decreases exponentially with increasing the electron irradiation dose. The maximum degree of cross-linking ranged from 97 to 99% for the three SAMs. Proof-of-concept experiments were conducted to demonstrate potential applications of Raman-inactive CNMs as a supporting membrane for Raman analysis.

Lipid storage provides energy for cell survival, growth, and reproduction and is closely related to the organismal response to stress imposed by toxic chemicals. However, the effects of toxicants on energy storage as it impacts certain life-history traits have rarely been investigated. Here, we used the nematode Caenorhabditis elegans as a test species for a chronic exposure to copper (Cu) at EC20 (0.50 mg Cu/l). Effects on the fatty acid distribution in C. elegans body were determined using coherent anti-Stokes Raman spectroscopy (CARS) to link population fitness responses with individual ecophysiological responses. Cu inhibited nematode reproductive capacity and offspring growth in addition to shortening the lifespan of exposed individuals. In adult nematodes, Cu exposure led to significant reduction of lipid storage compared to the Cu-free control: Under Cu, lipids filled only 0.5% of the nematode body volume vs. 7.5% in control nematodes, lipid droplets were on average 74% smaller and the number of tiny lipids (0–10 µm2) was increased. These results suggest that (1) Cu has an important effect on the life-history traits of nematodes; (2) the quantification of lipid storage can provide important information on the response of organisms to toxic stress; and (3) CARS microscopy is a promising tool for non-invasive quantitative and qualitative analyses of lipids as a measure of nematode fitness.

Cell membranes are composed of two-dimensional bilayers of amphipathic lipids, which allow a lateral movement of the respective membrane components. These components are arranged in an inhomogeneous manner as transient micro- and nanodomains, which are believed to be crucially involved in the regulation of signal transduction pathways in mammalian cells. Because of their small size (diameter 10-200 nm), membrane nanodomains cannot be directly imaged using conventional light microscopy. Here, we present direct visualization of cell membrane nanodomains by helium ion microscopy (HIM). We show that HIM is capable to image biological specimens without any conductive coating, and that HIM images clearly allow the identification of nanodomains in the ultrastructure of membranes with 1.5 nm resolution. The shape of these nanodomains is preserved by fixation of the surrounding unsaturated fatty acids while saturated fatty acids inside the nanodomains are selectively removed. Atomic force microscopy, fluorescence microscopy, 3D structured illumination microscopy and direct stochastic optical reconstruction microscopy provide additional evidence that the structures in the HIM images of cell membranes originate from membrane nanodomains. The nanodomains observed by HIM have an average diameter of 20 nm and are densely arranged with a minimal nearest neighbor distance of ~15 nm.

We introduce a novel and universal method for fast optical high, as well as super-resolution imaging. Our method is based on reconstructing super-resolved images from conventional image sequences containing rapid random signal fluctuations. Such sequences could be obtained from either wide-field single-molecule blinking experiments or rapid image sequences with fluorophores undergoing random intensity fluctuations. By calculating the local entropy (H) and cross-entropy (xH) values pixel-by-pixel, weighted with higher order statistics (HOS), a new image with pixel intensities representing the true information content in the time series is obtained. We show that analyzing image sequences by this formalism enables the reconstruction of super-resolved images, where the optical resolution that can be achieved depends only on the number of input frames and the higher order moments used for the calculation. We find that the acquisition of

Optical microscopy modalities that achieve spatial resolution beyond the resolution limit have opened up new opportunities in the biomedical sciences to reveal the structure and kinetics of biological processes on the nanoscale. These methods are, however, mostly restricted to fluorescence as Contrast mechanism, which limits the ultimate spatial resolution and observation time that can be achieved by photobleaching of the fluorescent probes. Here, we demonstrate that Raman scattering provides a valuable contrast mechanism for optical nanoscopy in the form of super-resolution to structured illumination microscopy. We find that nanotags, i.e., gold and silver nanoparticles that are capable of surface-enhanced Raman scattering (SERS), can be imaged with a spatial resolution beyond the diffraction limit in four dimensions alongside and with similar excitation power as fluorescent probes. The highly polarized nature of super-resolution structured illumination microscopy renders these nanotags elliptical in the reconstructed super-resolved images, which enables us to determine their orientation within the sample. The robustness of nanotags against photobleaching allows us to image these particles for unlimited periods of time. We demonstrate this by imaging isolated nanotags in a dense layer of fluorophores, as well as on the surface of and after internalization by osteosarcoma cells, always in the presence of fluorescent probes. Our results show that SERS nanotags have the potential to become highly multiplexed and chemically sensitive optical probes for optical nanoscopy that can replace fluorophores in applications where fluorescence photobleaching is prohibitive for following the evolution of biological processes for extended times.

Certain fluorophores, in particular those that can undergo photoinduced radical pair reactions are known to exhibit a magnetic field dependent fluorescence summarized in the term magnetic field effect (MFE). We tried to reproduce experiments that reported magnetic field enhanced fluorescence for commonly used organic dyes with a high quantum yield suitable for single molecule localization microscopy. We find that the enhanced fluorescence is due to fluorescence reflected by the magnet's surface rather than MFE.

Photosynthetic microalgae hold great promise as non-food feedstocks for the sustainable production of a range of bio-products and genetic engineering is an increasingly important strategy to improve the natural cellular features. For the vast majority of microalgal strains, however, genetic engineering is not yet possible and the establishment of efficient genetic tools for a broad range of microalgal species is an important task to reach biotechnological success. Stable DNA transformation is one of the crucial steps for most genetic engineering approaches. In this context, we report the first successful and stable nuclear genetic transformation of the biotechnologically promising oleaginous microalga M. neglectum. Transformation was achieved by electroporation and the efficiency could progressively be improved by implementation of an additional cell pretreatment step, aiming at weakening the rigid natural cell wall. Furthermore, a first reporter transgene was established for M. neglectum. As a result of this work, genetic engineering strategies now become accessible which are required to successfully establish M. neglectum as a novel host for biotechnological applications.

We demonstrate an approach to rapidly characterize living suspension cells in 4 dimensions while they are immobilized and manipulated within optical traps. A single, high numerical aperture objective lens is used to separate the imaging plane from the trapping plane. This facilitates full control over the position and orientation of multiple trapped cells using a spatial light modulator, including directed motion and object rotation, while also allowing rapid 4D imaging. This system is particularly useful in the handling and investigation of the behavior of non-adherent immune cells. We demonstrate these capabilities by imaging and manipulating living, fluorescently stained Jurkat T cells.

Imaging non-adherent cells by super-resolution far-field fluorescence microscopy is currently not possible because of their rapid movement while in suspension. Holographic optical tweezers (HOTs) enable the ability to freely control the number and position of optical traps, thus facilitating the unrestricted manipulation of cells in a volume around the focal plane. Here we show that immobilizing non-adherent cells by optical tweezers is sufficient to achieve optical resolution well below the diffraction limit using localization microscopy. Individual cells can be oriented arbitrarily but preferably either horizontally or vertically relative to the microscope's image plane, enabling access to sample sections that are impossible to achieve with conventional sample preparation and immobilization. This opens up new opportunities to super-resolve the nanoscale organization of chromosomal DNA in individual bacterial cells., Nanoscopy of non-adherent cells is currently not possible, due to their movement in solution. Here the authors immobilize and manipulate fixed E. coli by multiple optical traps; their holographic optical tweezers enable dSTORM imaging of orthogonal planes via 3D realignment of the sample.

One of the most challenging tasks in microscopy is the quantitative identification and characterization of molecular interactions. In living cells this task is typically performed by fluorescent labeling of the interaction partners with spectrally distinct fluorophores and imaging in different color channels. Current methods for determining colocalization of molecules result in outcomes that can vary greatly depending on signal-to-noise ratios, threshold and background levels, or differences in intensity between channels. Here, we present a novel and quantitative method for determining the degree of colocalization in live-cell fluorescence microscopy images for two and more data channels. Moreover, our method enables the construction of images that directly classify areas of high colocalization. (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim).

We demonstrate a novel and easy-to-use method to dramatically reduce noise and background contributions in advanced fluorescence microscopy experiments. The underlying idea is that the entropy value increases for systems with a large number of accessible energy states. Intensity fluctuations originating from photophysical or photochemical effects lead to an increased information content. Calculating the pixel-wise entropy value results in an enhancement of the signal-to-noise ratio by a factor of 90-100. Comparing ECI (entropy-based contrast-enhanced imaging) to superresolution methods such as STORM and SOFI, we find that this technique also bears substantial potential for enhancing fluctuation-based superresolution microscopies. (C) 2013 Elsevier B. V. All rights reserved.

We used coherent anti-Stokes scattering (CAS) to characterize individual gold nanorods (GNRs) and GNR aggregates. By creating samples with different densities of GNRs on silicon wafer substrates, we were able to determine surface coverage by scanning electron microscopy (SEM) and then correlate the coverage to the CAS intensities of the samples. The observed CAS signal intensity was quadratically dependent on the number of particles. We also examined the CAS signal as a function of the excitation polarization and found that the strongest signals in regularly oriented GNRs were observed when the beam polarization was aligned with the longitudinal axis of the GNRs. Irregularly oriented GNRs exhibited a different scattering pattern to that observed for regularly oriented GNRs. The polarization-dependent scattering from oriented GNRs showed cos(6)(θ) behavior. By imaging nanoscale-sized GNR patterns using CAS and evaluating the results with SEM, we show that CAS can be used for efficient, label-free imaging of nanoscale metallic particles.

BACKGROUND: Human embryonic stem cells (hESCs) can be efficiently and reproducibly directed into cardiomyocytes (CMs) using stage-specific induction protocols. However, their functional properties and suitability for clinical and other applications have not been evaluated. METHODS AND RESULTS: Here we showed that CMs derived from multiple pluripotent human stem cell lines (hESC: H1, HES2) and types (induced pluripotent stem cell) using different in vitro differentiation protocols (embryoid body formation, endodermal induction, directed differentiation) commonly displayed immature, proarrhythmic action potential properties such as high degree of automaticity, depolarized resting membrane potential, Phase 4- depolarization, and delayed after-depolarization. Among the panoply of sarcolemmal ionic currents investigated (I(Na)(+)/I(CaL)(+)/I(Kr)(+)/I(NCX)(+)/I(f)(+)/I(to)(+)/I(K1)(-)/I(Ks)(-)), we pinpointed the lack of the Kir2.1-encoded inwardly rectifying K(+) current (I(K1)) as the single mechanistic contributor to the observed immature electrophysiological properties in hESC-CMs. Forced expression of Kir2.1 in hESC-CMs led to robust expression of Ba(2+)-sensitive I(K1) and, more importantly, completely ablated all the proarrhythmic action potential traits, rendering the electrophysiological phenotype indistinguishable from the adult counterparts. These results provided the first link of a complex developmentally arrested phenotype to a major effector gene, and importantly, further led us to develop a bio-mimetic culturing strategy for enhancing maturation. CONCLUSIONS: By providing the environmental cues that are missing in conventional culturing method, this approach did not require any genetic or pharmacological interventions. Our findings can facilitate clinical applications, drug discovery, and cardiotoxicity screening by improving the yield, safety, and efficacy of derived CMs., link_to_OA_fulltext

Oleaginous photosynthetic microalgae hold great promise as non-food feedstocks for the sustainable production of bio-commodities. The algal lipid quality can be analysed by Raman micro-spectroscopy, and the lipid content can be imaged in vivo in a label-free and non-destructive manner by coherent anti-Stokes Raman scattering (CARS) microscopy. In this study, both techniques were applied to the oleaginous microalga Monoraphidium neglectum, a biotechnologically promising microalga resistant to commonly applied lipid staining techniques. The lipid-specific CARS signal was successfully separated from the interfering two-photon excited fluorescence of chlorophyll and for the first time, lipid droplet formation during nitrogen starvation could directly be analysed. We found that the neutral lipid content deduced from CARS image analysis strongly correlated with the neutral lipid content measured gravimetrically and furthermore, that the relative degree of unsaturation of fatty acids stored in lipid droplets remained similar. Interestingly, the lipid profile during cellular adaption to nitrogen starvation showed a two-phase characteristic with initially fatty acid recycling and subsequent de novo lipid synthesis. This works demonstrates the potential of quantitative CARS microscopy as a label-free lipid analysis technique for any microalgal species, which is highly relevant for future biotechnological applications and to elucidate the process of microalgal lipid accumulation.

Super-resolved structured illumination microscopy (SR-SIM) is an important tool for fluorescence microscopy. SR-SIM microscopes perform multiple image acquisitions with varying illumination patterns, and reconstruct them to a super-resolved image. In its most frequent, linear implementation, SR-SIM doubles the spatial resolution. The reconstruction is performed numerically on the acquired wide-field image data, and thus relies on a software implementation of specific SR-SIM image reconstruction algorithms. We present fairSIM, an easy-to-use plugin that provides SR-SIM reconstructions for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own implementations of super-resolution structured illumination microscopy, fairSIM takes away the hurdle of generating yet another implementation of the reconstruction algorithm. For users of commercial microscopes, it offers an additional, in-depth analysis option for their data independent of specific operating systems. As a modular, open-source solution, fairSIM can easily be adapted, automated and extended as the field of SR-SIM progresses., Reconstruction of super resolution structured illumination microscopy (SR-SIM) datasets typically relies upon commercial software. Here Müller et al. present an open-source ImageJ plugin to facilitate reconstruction of SR-SIM data from a broad range of microscopy platforms.

We demonstrate a passively synchronized two-color pulsed fiber laser with dual repetition rates, 20 MHz for 1.0 μ and 80 MHz for 782 nm. The wavelength tunability of both synchronized pulse sources is also investigated.

Yersinia pestis enters host cells and evades host defenses, in part, through interactions between Yersinia pestis proteins and host membranes. One such interaction is through the type III secretion system, which uses a highly conserved and ordered complex for Yersinia pestis outer membrane effector protein translocation called the injectisome. The portion of the injectisome that interacts directly with host cell membranes is referred to as the translocon. The translocon is believed to form a pore allowing effector molecules to enter host cells. To facilitate mechanistic studies of the translocon, we have developed a cell-free approach for expressing translocon pore proteins as a complex supported in a bilayer membrane mimetic nano-scaffold known as a nanolipoprotein particle (NLP) Initial results show cell-free expression of Yersinia pestis outer membrane proteins YopB and YopD was enhanced in the presence of liposomes. However, these complexes tended to aggregate and precipitate. With the addition of co-expressed (NLP) forming components, the YopB and/or YopD complex was rendered soluble, increasing the yield of protein for biophysical studies. Biophysical methods such as Atomic Force Microscopy and Fluorescence Correlation Spectroscopy were used to confirm that the soluble YopB/D complex was associated with NLPs. An interaction between the YopB/D complex and NLP was validated by immunoprecipitation. The YopB/D translocon complex embedded in a NLP provides a platform for protein interaction studies between pathogen and host proteins. These studies will help elucidate the poorly understood mechanism which enables this pathogen to inject effector proteins into host cells, thus evading host defenses.

The heterologous expression of terpene synthases in microbial hosts has opened numerous possibilities for bioproduction of desirable metabolites. Photosynthetic microbial hosts present a sustainable alternative to traditional fermentative systems, using freely available (sun)light and carbon dioxide as inputs for bio-production. Here, we report the expression of a patchoulol synthase from Pogostemon cablin Benth in the model green microalga Chlamydomonas reinhardtii. The sesquiterpenoid patchoulol was produced from the alga and was used as a marker of sesquiterpenoid production capacity. A novel strategy for gene loading was employed and patchoulol was produced up to 922±242µgg-1 CDW in six days. We additionally investigated the effect of carbon source on sesquiterpenoid productivity from C. reinhardtii in scale-up batch cultivations. It was determined that up to 1.03mgL-1 sesquiterpenoid products could be produced in completely photoautotrophic conditions and that the alga exhibited altered sesquiterpenoid production metabolism related to carbon source.

In this paper, we describe the synthesis and characterization of 2,5-dimercaptobenzoic acid as a novel pH-sensitive disulfide reporter molecule for surface-enhanced Raman scattering (SERS) capable of inducing the controlled aggregation of gold (Au) colloids in solution without the addition of salts. While weak acids have been shown to yield some pH sensitivity as reporter molecules for SERS measurements, the reproducibility and signal strength of nanoparticle probes based on such molecules can vary greatly. This limited reproducibility depends greatly on the salt-induced aggregation of the colloidal nanoprobes, which is required in order to obtain SERS signals strong enough to probe individual clusters. This complicates their use in live cell sensing applications. We show that our approach results in primarily bridged nanoparticles comprising a pH-sensitive nanoprobe that can quantify accurately pH values well below 5.5. The robustness and sensitivity of this system makes it a powerful tool for measuring pH values on the nanoscale under in vitro conditions.