Absolute determination of photoluminescence quantum efficiency using an integrating sphere setup

An integrating sphere-based setup to obtain a quick and reliable determination of the internal quantum efficiency of strongly scattering luminescent materials is presented. In literature, two distinct but similar measurement procedures are frequently mentioned: a "two measurement" and a "three measurement" approach. Both methods are evaluated by applying the rigorous integrating sphere theory. It was found that both measurement procedures are valid. Additionally, the two methods are compared with respect to the uncertainty budget of the obtained values of the quantum efficiency. An inter-laboratory validation using the two distinct procedures was performed. The conclusions from the theoretical study were confirmed by the experimental data.

Thermocapillary fingering in surfactant-laden water droplets

The drying of sessile droplets represents an intriguing problem, being a simple experiment to perform but displaying complexities that are archetypical for many free surface and coating flows. Drying can leave behind distinct deposits of initially well dispersed colloidal matter. For example, in the case of the coffee ring effect, particles are left in a well-defined macroscopic pattern with particles accumulating at the edge, controlled by the internal flow in the droplet. Recent studies indicate that the addition of surfactants strongly influences this internal flow field, even reversing it and suppressing the coffee ring effect. In this work, we explore the behavior of droplets at high surfactant loadings and observe unexpected outward fingering instabilities. The experiments start out with droplets with a pinned contact line, and fast confocal microscopy is used to quantify a radially outward surfactant-driven Marangoni flow, in line with earlier observations. However, the Marangoni flows are observed to become unstable, and local vortex cells are now observed in a direction along the contact line. The occurrence of these vortices cannot be explained on the basis of the effects of surfactants alone. Thermal imaging shows that thermocapillary effects are superimposed on the surfactant-driven flows. These local vortex cells acts as little pumps and push the fluid outward in a fingering instability, rather than an expected inward retraction of the drying droplet. This leads to a deposition of colloids in a macroscopical flower-shaped pattern. A scaling analysis is used to rationalize the observed wavelengths and velocities, and practical implications are briefly discussed.

A hybrid tool for spectral ray tracing simulations of luminescent cascade systems

To perform adequate simulations of luminescent cascade systems, a hybrid method combining a commercial ray tracer and a programming tool is presented. True Monte Carlo algorithms for luminescent materials, treating each ray individually, are adapted to allow wavelength conversion of ray sets. Two solutions for the wavelength conversion of ray sets are discussed: a random approach, where absorption events are randomly selected to create emission events, and a combined approach, where information from multiple absorption events is combined to create emission events. Both methods are applied to simulate the performance of a virtual remote phosphor light-emitting diode module. When using the combined approach, the required computation time to achieve sufficient accuracy is a factor 2 lower, compared to the time required when applying the random approach.

Effect of microstructure on population growth parameters of Escherichia coli in gelatin-dextran systems

Current literature acknowledges the effect of food structure on bacterial dynamics. Most studies introduce this "structure" factor using a single gelling agent, resulting in a homogeneous environment, whereas in practice most food products are heterogeneous. Therefore, this study focuses on heterogeneous protein-polysaccharide mixtures, based on gelatin and dextran. These mixtures show phase separation, leading to a range of heterogeneous microstructures by adjusting relative concentrations of both gelling agents. Based on confocal microscope observations, the growth of Escherichia coli in gelatin-dextran systems was observed to occur in the dextran phase. To find a relation between microscopic and population behavior, growth experiments were performed in binary and singular gelatin-dextran systems and culture broth at 23.5°C, with or without adding 2.9% (wt/vol) NaCl. The Baranyi and Roberts growth model was fitted to the experimental data and parameter estimates were statistically compared. For salted binary mixtures, a decrease in the population maximum cell density was observed with increasing gelatin concentration. In this series, for one type of microstructure, i.e., a gelatin matrix phase with a disperse dextran phase, the maximum cell density decreased with decreasing percentage of dextran phase. However, this relation no longer held when other types of microstructure were observed. Compared to singular systems, adding a second gelling agent in the presence of NaCl had an effect on population lag phases and maximum cell densities. For unsalted media, the growth parameters of singular and binary mixtures were comparable. Introducing this information into mathematical models leads to more reliable growth predictions and enhanced food safety.

Live-cell SERS endoscopy using plasmonic nanowire waveguides

Live-cell surface-enhanced Raman spectroscopy (SERS) endoscopy is developed by using plasmonic nanowire waveguides as endoscopic probes. It is demonstrated that the probe insertion does not stress the cell. Opposed to conventional SERS endoscopy, with excitation at the hotspot within the cell, the remote excitation method yields low-background SERS spectra from specific cell compartments with minimal associated photodamage.

Reporter cell activity within hydrogel constructs quantified from oxygen-independent bioluminescence

By providing a three-dimensional (3D) support to cells, hydrogels offer a more relevant in vivo tissue-like environment as compared to two-dimensional cell cultures. Hydrogels can be applied as screening platforms to investigate in 3D the role of biochemical and biophysical cues on cell behaviour using bioluminescent reporter cells. Gradients in oxygen concentration that result from the interplay between molecular transport and cell metabolism can however cause substantial variability in the observed bioluminescent reporter cell activity. To assess the influence of these oxygen gradients on the emitted bioluminescence for various hydrogel geometries, a combined experimental and modelling approach was implemented. We show that the applied model is able to predict oxygen gradient independent bioluminescent intensities which correlate better to the experimentally determined viable cell numbers, as compared to the experimentally measured bioluminescent intensities. By analysis of the bioluminescence reaction dynamics we obtained a quantitative description of cellular oxygen metabolism within the hydrogel, which was validated by direct measurements of oxygen concentration within the hydrogel. Bioluminescence peak intensities can therefore be used as a quantitative measurement of reporter cell activity within a hydrogel, but an unambiguous interpretation of these intensities requires a compensation for the influence of cell-induced oxygen gradients on the luciferase activity.

A causal relation between bioluminescence and oxygen to quantify the cell niche

Bioluminescence imaging assays have become a widely integrated technique to quantify effectiveness of cell-based therapies by monitoring fate and survival of transplanted cells. To date these assays are still largely qualitative and often erroneous due to the complexity and dynamics of local micro-environments (niches) in which the cells reside. Here, we report, using a combined experimental and computational approach, on oxygen that besides being a critical niche component responsible for cellular energy metabolism and cell-fate commitment, also serves a primary role in regulating bioluminescent light kinetics. We demonstrate the potential of an oxygen dependent Michaelis-Menten relation in quantifying intrinsic bioluminescence intensities by resolving cell-associated oxygen gradients from bioluminescent light that is emitted from three-dimensional (3D) cell-seeded hydrogels. Furthermore, the experimental and computational data indicate a strong causal relation of oxygen concentration with emitted bioluminescence intensities. Altogether our approach demonstrates the importance of oxygen to evolve towards quantitative bioluminescence and holds great potential for future microscale measurement of oxygen tension in an easily accessible manner.

Shear-stress-induced conformational changes of von Willebrand factor in a water-glycerol mixture observed with single molecule microscopy

The von Willebrand factor (VWF) is a human plasma protein that plays a key role in the initiation of the formation of thrombi under high shear stress in both normal and pathological situations. It is believed that VWF undergoes a conformational transition from a compacted, globular to an extended form at high shear stress. In this paper, we develop and employ an approach to visualize the large-scale conformation of VWF in a (pressure-driven) Poiseuille flow of water-glycerol buffers with wide-field single molecule fluorescence microscopy as a function of shear stress. Comparison of the imaging results for VWF with the results of a control with λ-phage double-stranded DNA shows that the detection of individual VWF multimers in flow is feasible. A small fraction of VWF multimers are observed as visibly extended along one axis up to lengths of 2.0 μm at high applied shear stresses. The size of this fraction of molecules seems to exhibit an apparent dependency on shear stress. We further demonstrate that the obtained results are independent of the charge of the fluorophore used to label VWF. The obtained results support the hypothesis of the conformational extension of VWF in shear flow.

The use of the adding-doubling method for the optical optimization of planar luminescent down shifting layers for solar cells

To enhance the efficiency of solar cells, a luminescent down shifting layer can be applied in order to adapt the solar spectrum to the spectral internal quantum efficiency of the semiconductor. Optimization of such luminescent down shifting layers benefits from quick and direct evaluation methods. In this paper, the potential of the adding-doubling method is investigated to simulate the optical behavior of an encapsulated solar cell including a planar luminescent down shifting layer. The results of the adding-doubling method are compared with traditional Monte Carlo ray tracing simulations. The average relative deviation is found to be less than 1.5% for the absorptance in the active layer and the reflectance from the encapsulated cell, while the computation time can be decreased with a factor 52. Furthermore, the adding-doubling method is adopted to investigate the suitability of the SrB4O7:5%Sm2 + ,5%Eu2 + phosphor as a luminescent down shifting material in combination with a Copper Indium Gallium Selenide solar cell. A maximum increase of 9.0% in the short-circuit current can be expected if precautions are taken to reduce the scattering by matching the refractive index of host material to the phosphor particles. To be useful as luminescent down shifting material, the minimal value of the quantum yield of the phosphor is determined to be 0.64.

Membrane remodeling processes induced by phospholipase action

Important cellular events such as division require drastic changes in the shape of the membrane. These remodeling processes can be triggered by the binding of specific proteins or by changes in membrane composition and are linked to phospholipid metabolism for which dedicated enzymes, named phospholipases, are responsible. Here wide-field fluorescence microscopy is used to visualize shape changes induced by the action of phospholipase A1 on dye-labeled supported membranes of POPC (1-palmitoyl-2-oleoly-sn-glycero-3-phosphocholine). Time-lapse imaging demonstrates that layers either shrink and disappear or fold and collapse into vesicles. These vesicles can undergo further transformations such as budding, tubulation, and pearling within 5 min of formation. Using dye-labeled phospholipases, we can monitor the presence of the enzyme at specific positions on the membrane as the shape transformations occur. Furthermore, incorporating the products of hydrolysis into POPC membranes is shown to induce transformations similar to those observed for enzyme action. The results suggest that phospholipase-mediated hydrolysis plays an important role in membrane transformations by altering the membrane composition, and a model is proposed for membrane curvature based on the presence and shape of hydrolysis products.

HIV virions as nanoscopic test tubes for probing oligomerization of the integrase enzyme

Employing viruses as nanoscopic lipid-enveloped test tubes allows the miniaturization of protein-protein interaction (PPI) assays while preserving the physiological environment necessary for particular biological processes. Applied to the study of the human immunodeficiency virus type 1 (HIV-1), viral biology and pathology can also be investigated in novel ways, both in vitro as well as in infected cells. In this work we report on an experimental strategy that makes use of engineered HIV-1 viral particles, to allow for probing PPIs of the HIV-1 integrase (IN) inside viruses with single-molecule Förster resonance energy transfer (FRET) using fluorescent proteins (FP). We show that infectious fluorescently labeled viruses can be obtained and that the quantity of labels can be accurately measured and controlled inside individual viral particles. We demonstrate, with proper control experiments, the formation of IN oligomers in single viral particles and inside viral complexes in infected cells. Finally, we show a clear effect on IN oligomerization of small molecule inhibitors of interactions of IN with its natural human cofactor LEDGF/p75, corroborating that IN oligomer enhancing drugs are active already at the level of the virus and strongly suggesting the presence of a dynamic, enhanceable equilibrium between the IN dimer and tetramer in viral particles. Although applied to the HIV-1 IN enzyme, our methodology for utilizing HIV virions as nanoscopic test tubes for probing PPIs is generic, i.e., other PPIs targeted into the HIV-1, or PPIs targeted into other viruses, can potentially be studied with a similar strategy.

Estimation of the effective phase function of bulk diffusing materials with the inverse adding-doubling method

The accuracy of optical simulations including bulk diffusors is heavily dependent on the accuracy of the bulk scattering properties. If no knowledge on the physical scattering effects is available, an iterative procedure is usually used to obtain the scattering properties, such as the inverse Monte Carlo method or the inverse adding-doubling (AD) method. In these methods, a predefined phase function with one free parameter is usually used to limit the number of free parameters. In this work, three predefined phase functions (Henyey-Greenstein, two-term Henyey-Greenstein, and Gegenbauer kernel (GK) phase function) are implemented in the inverse AD method to determine the optical properties of two strongly diffusing materials: low-density polyethylene and TiO₂ particles. Using the presented approach, an estimation of the effective phase function was made. It was found that the use of the GK phase function resulted in the best agreement between calculated and experimental transmittance, reflectance, and scattered radiant intensity distribution for the LDPE sample. For the TiO₂ sample, a good agreement was obtained with both the two-term Henyey-Greenstein and the GK phase function.

Single particle tracking of ADAMTS13 (a disintegrin and metalloprotease with thrombospondin type-1 repeats) molecules on endothelial von Willebrand factor strings

von Willebrand factor (VWF) strings are removed from the endothelial surface by ADAMTS13 (a disintegrin and metalloprotease with thrombospondin type-1 repeats)-mediated proteolysis. To visualize how single ADAMTS13 molecules bind to these long strings, we built a customized single molecule fluorescence microscope and developed single particle tracking software. Extensive analysis of over 6,000 single inactive ADAMTS13(E225Q) enzymes demonstrated that 20% of these molecules could be detected in at least two consecutive 60-ms frames and followed two types of trajectories. ADAMTS13(E225Q) molecules either decelerated in the vicinity of VWF strings, whereas sometimes making brief contact with the VWF string before disappearing again, or readily bound to the VWF strings and this for 120 ms or longer. These interactions were observed at several sites along the strings. Control experiments using an IgG protein revealed that only the second type of trajectory reflected a specific interaction of ADAMTS13 with the VWF string. In conclusion, we developed a dedicated single molecule fluorescence microscope for detecting single ADAMTS13 molecules (nm scale) on their long, flow-stretched VWF substrates (μm scale) anchored on living cells. Comprehensive analysis of all detected enzymes showed a random interaction mechanism for ADAMTS13 with many available binding sites on the VWF strings.

Confocal imaging with a fluorescent bile acid analogue closely mimicking hepatic taurocholate disposition

This study aimed to characterize the in vitro hepatic transport mechanisms in primary rat and human hepatocytes of the fluorescent bile acid derivative N-(24-[7-(4-N,N-dimethylaminosulfonyl-2,1,3-benzoxadiazole)]amino-3α,7α,12α-trihydroxy-27-nor-5β-cholestan-26-oyl)-2'-aminoethanesulfonate (tauro-nor-THCA-24-DBD), previously synthesized to study the activity of the bile salt export pump (BSEP). The fluorescent bile acid derivative exhibited saturable uptake kinetics in suspended rat hepatocytes. Hepatic uptake was inhibited in the presence of substrates/inhibitors of the organic anion transporting polypeptide (Oatp) family and Na(+) -taurocholate cotransporting peptide (Ntcp). Concentration-dependent uptake of the fluorescent bile acid was also saturable in Chinese hamster ovary cells transfected with rNtcp, hNTCP, OATP1B1, or OATP1B3. The fluorescent bile acid derivative was actively excreted in the bile canaliculi of sandwich-cultured rat and human hepatocytes (SCRH and SCHH), with a biliary excretion index (BEI) of 26% and 32%, respectively. In SCRH, cyclosporin A significantly decreased the BEI to 5%. Quantification by real-time confocal imaging further confirmed canalicular transport of the fluorescent bile acid derivative (BEI = 75%). We conclude that tauro-nor-THCA-24-DBD is a useful probe to study interference of drugs with NTCP/Ntcp- and BSEP/Bsep-mediated transport in fluorescence-based in vitro assays.

Green-to-red photoconvertible Dronpa mutant for multimodal super-resolution fluorescence microscopy

Advanced imaging techniques crucially depend on the labels used. In this work, we present the structure-guided design of a fluorescent protein that displays both reversibly photochromic and green-to-red photoconversion behavior. We first designed ffDronpa, a mutant of the photochromic fluorescent protein Dronpa that matures up to three times faster while retaining its interesting photochromic features. Using a combined evolutionary and structure-driven rational design strategy, we developed a green-to-red photoconvertible ffDronpa mutant, called pcDronpa, and explored different optimization strategies that resulted in its improved version, pcDronpa2. This fluorescent probe combines a high brightness with low photobleaching and photoblinking. We herein show that, despite its tetrameric nature, pcDronpa2 allows for multimodal subdiffraction imaging by sequentially imaging a given sample using both super-resolution fluctuation imaging and localization microscopy.

Membrane distribution of the glycine receptor α3 studied by optical super-resolution microscopy

In this study, the effect of glycine receptor (GlyR) α3 alternative RNA splicing on the distribution of receptors in the membrane of human embryonic kidney 293 cells is investigated using optical super-resolution microscopy. Direct stochastic optical reconstruction microscopy is used to image both α3K and α3L splice variants individually and together using single- and dual-color imaging. Pair correlation analysis is used to extract quantitative measures from the resulting images. Autocorrelation analysis of the individually expressed variants reveals clustering of both variants, yet with differing properties. The cluster size is increased for α3L compared to α3K (mean radius 92 ± 4 and 56 ± 3 nm, respectively), yet an even bigger difference is found in the cluster density (9,870 ± 1,433 and 1,747 ± 200 μm(-2), respectively). Furthermore, cross-correlation analysis revealed that upon co-expression, clusters colocalize on the same spatial scales as for individually expressed receptors (mean co-cluster radius 94 ± 6 nm). These results demonstrate that RNA splicing determines GlyR α3 membrane distribution, which has consequences for neuronal GlyR physiology and function.

Biofilm formation of a bacterial consortium on linuron at micropollutant concentrations in continuous flow chambers and the impact of dissolved organic matter

Bacterial multispecies biofilms are catalysts for pollutant degradation in aqueous ecosystems. Their activity in systems where xenobiotics occur as micropollutants (μg L(-1) level) and natural dissolved organic matter provides carbon and energy instead remains uncharacterized. Biofilm formation of a bacterial consortium consisting of the linuron-degrading Variovorax sp. WDL1 and metabolite-degrading strains Comamonas sp. WDL7 and Hyphomicrobium sp. WDL6 at micropollutant linuron concentrations and the impact of auxiliary carbon sources on degradation and biofilm composition were investigated. Biofilms formed at concentrations of 1000, 100, and 10 μg L(-1) linuron. The highest biomass, organized in mixed-species mounds, was observed at 1000 μg L(-1) linuron, while at 100 and 10 μg L(-1) , thin layers of cells occurred. Linuron removal efficiencies decreased from c. 85% when fed with 100 and 1000 μg L(-1) linuron to 30% in case of 10 μg L(-1) linuron due to reduced specific activity. Biofilms grown on 10 μg L(-1) linuron were subsequently fed with easily and less degradable carbon sources in addition to 10 μg L(-1) linuron. Although co-feeding with more degradable C-sources increased biofilm biomass, linuron removal remained 30%. Calculations based on biofilm volume measurements pointed toward reduced specific activity, compensated by a higher biomass. Uncertainties about biofilm heterogeneity and cell volume can undo this explanation.

A surface-bound molecule that undergoes optically biased Brownian rotation

Developing molecular systems with functions analogous to those of macroscopic machine components, such as rotors, gyroscopes and valves, is a long-standing goal of nanotechnology. However, macroscopic analogies go only so far in predicting function in nanoscale environments, where friction dominates over inertia. In some instances, ratchet mechanisms have been used to bias the ever-present random, thermally driven (Brownian) motion and drive molecular diffusion in desired directions. Here, we visualize the motions of surface-bound molecular rotors using defocused fluorescence imaging, and observe the transition from hindered to free Brownian rotation by tuning medium viscosity. We show that the otherwise random rotations can be biased by the polarization of the excitation light field, even though the associated optical torque is insufficient to overcome thermal fluctuations. The biased rotation is attributed instead to a fluctuating-friction mechanism in which photoexcitation of the rotor strongly inhibits its diffusion rate.

Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).

Cellular localization and dynamics of the Mrr type IV restriction endonuclease of Escherichia coli

In this study, we examined the intracellular whereabouts of Mrr, a cryptic type IV restriction endonuclease of Escherichia coli K12, in response to different conditions. In absence of stimuli triggering its activity, Mrr was found to be strongly associated with the nucleoid as a number of discrete foci, suggesting the presence of Mrr hotspots on the chromosome. Previously established elicitors of Mrr activity, such as exposure to high (hydrostatic) pressure (HP) or expression of the HhaII methyltransferase, both caused nucleoid condensation and an unexpected coalescence of Mrr foci. However, although the resulting Mrr/nucleoid complex was stable when triggered with HhaII, it tended to be only short-lived when elicited with HP. Moreover, HP-mediated activation of Mrr typically led to cellular blebbing, suggesting a link between chromosome and cellular integrity. Interestingly, Mrr variants could be isolated that were specifically compromised in either HhaII- or HP-dependent activation, underscoring a mechanistic difference in the way both triggers activate Mrr. In general, our results reveal that Mrr can take part in complex spatial distributions on the nucleoid and can be engaged in distinct modes of activity.

Photoswitchable fluorescent proteins for superresolution fluorescence microscopy circumventing the diffraction limit of light

In the last two decades, fluorescent proteins became an indispensable tool to noninvasively label a protein in living cells. The discovery of photoswitchable fluorescent proteins expanded the applications of the fluorescent proteins to techniques such as molecular tracking and highlighting on a microscope. Recently, a new microscopic modality to achieve a superresolution circumventing the diffraction limit of light (photoactivated localization microscopy, PALM) has been developed based on the photoswitchable fluorescent proteins. Here we introduce a basic protocol of PALM through the visualization of actin bundles with superresolution.