NanoPASS: an easy-to-use user interface for nanoparticle dosimetry with the 3DSDD model.

Nanoparticles exhibit a specific diffusion and sedimentation behavior under cell culture conditions as used in nantoxicological in vitro testing. How a particular particle suspension behaves depends on the particular physicochemical characteristics of the particles and the cell culture system. Only a fraction of the nanoparticles applied to a cell culture will thus reach the cells within a given time frame. Therefore, dosimetric calculations are essential not only to determine the exact fraction of nanoparticles that has come into contact with the cells, but also to ensure experimental comparability and correct interpretation of results, respectively. Yet, the use of published dosimetry models is limited. Not the least because the correct application of these in silico tools usually requires bioinformatics knowledge, which often is perceived a hurdle. Moreover, not all models are freely available and accessible. In order to overcome this obstacle, we have now developed an easy-to-use interface for our recently published 3DSDD dosimetry model, called NanoPASS (NanoParticle Administration Sedimentation Simulator). The interface is freely available to all researchers. It will facilitate the use of in silico dosimetry in nanotoxicology and thus improve interpretation and comparability of in vitro results in the field.

In vitro nanoparticle dosimetry for adherent growing cell monolayers covering bottom and lateral walls.

BACKGROUND: Even though a continuously high number of in vitro studies on nanoparticles are being published, the issue of correct dose matter is often not sufficiently taken into account. Due to their size, the diffusion of nanoparticles is slower, as compared to soluble chemicals, and they sediment slowly. Therefore, the administered dose of particles in in vitro experiments is not necessarily the same (effective) dose that comes into contact with the cellular system. This can lead to misinterpretations of experimental toxic effects and disturbs the meaningfulness of in vitro studies. In silico calculations of the effective nanoparticle dose can help circumventing this problem. RESULTS: This study addresses more complex in vitro models like the human intestinal cell line Caco-2 or the human liver cell line HepaRG, which need to be differentiated over a few weeks to reach their full complexity. During the differentiation time the cells grow up the wall of the cell culture dishes and therefore a three-dimensional-based in silico model of the nanoparticle dose was developed to calculate the administered dose received by different cell populations at the bottom and the walls of the culture dish. Moreover, the model can perform calculations based on the hydrodynamic diameter which is measured by light scattering methods, or based on the diffusion coefficient measured by nanoparticle tracking analysis (NTA). This 3DSDD (3D-sedimentation-diffusion-dosimetry) model was experimentally verified against existing dosimetry models and was applied to differentiated Caco-2 cells incubated with silver nanoparticles. CONCLUSIONS: The 3DSDD accounts for the 3D distribution of cells in in vitro cell culture dishes and is therefore suitable for differentiated cells. To encourage the use of dosimetry calculating software, our model can be downloaded from the supporting information.

Binding kinetics and multi-bond: Finding correlations by synthesizing interactions between ligand-coated bionanoparticles and receptor surfaces.

The number of bonds formed between one single bionanoparticle and many surface receptors is an important subject to be studied but is seldom quantitatively investigated. A new evaluation of the correlation between binding kinetics and number of bonds is presented by varying ligand density and receptor density. An experimental system was developed using measurements with surface plasmon resonance spectroscopy. A corresponding multi-site adsorption model elucidated the correlation. The results show that with the increase of the receptor density, the adsorption rate first decreased when the number of bonds was below a maximum value and then increased when the number of bonds stayed at this maximum value. The investigation on ligand density variation suggests that the coating density on top of the bionanoparticle surface may have a particular value below which more ligand will accelerate the adsorption rate. The ratio of ligand amount bound by the receptors to the total ligand amount associated with a single bionanoparticle will remain constant even if one attaches more ligands to a bionanoparticle. We envision that the bionanoparticle desorption will not depend on density changes from either ligand or receptor when the number of bonds reaches a specific efficient value.

The interaction of protein-coated bionanoparticles and surface receptors reevaluated: how important is the number of bonds?

Specifically designed bionanoparticles with a function-oriented protein-coating layer interact with self-prepared receptor surfaces as the counterpart. Based on surface plasmon resonance biosensing experiments, a model framework is validated to estimate the number of bonds formed between these bionanoparticles and the receptor surface based on multivalent interactions. Our multi-site kinetic model is able to analyze the adsorption rate constants and the number of bonds from experimental data of natural and synthetic bionanoparticles. The influence of the mass transport on the adsorption kinetics is modeled including a diffusional boundary layer where a helpful analytical solution has been derived. Our model framework extends previous studies to include a higher number of bonds, ranging from 1 up to 1000. An almost linear relationship between the number of bonds and the adsorption amount of bionanoparticles makes the model framework suitable to predict, for example, ligand density and to further assess coating performance. The proposed model framework can serve as a design tool for multivalent interaction experiments under variable process conditions.

Quantifying resolution limiting factors in subtomogram averaged cryo-electron tomography using simulations.

Cryo-electron tomography (CET) is the only available technique capable of characterizing the structure of biological macromolecules in conditions close to the native state. With the advent of subtomogram averaging, as a post-processing step to CET, resolutions in the (sub-) nanometer range have become within reach. In addition to advances in instrumentation and experiments, the reconstruction scheme has improved by inclusion of more accurate contrast transfer function (CTF) correction methods, better defocus estimation, and better alignments of the tilt-series and subtomograms. To quantify the importance of each contribution, we have split the full process from data collection to reconstruction into different steps. For the purpose of evaluation we have acquired tilt-series of ribosomes in such a way that we could precisely determine the defocus of each macromolecule. Then, we simulated tilt-series using the InSilicoTEM package and applied tomogram reconstruction and subtomogram averaging. Through large scale simulations under different conditions and parameter settings we find that tilt-series alignment is the resolution limiting factor for our experimental data. Using simulations, we find that when this alignment inaccuracy is alleviated, tilted CTF correction improves the final resolution, or equivalently, the same resolution can be achieved using less particles. Furthermore, we predict from which resolution onwards better CTF correction and defocus estimation methods are required. We obtain a final average using 3198 ribosomes with a resolution of 2.2nm on the experimental data. Our simulations suggest that with the same number of particles a resolution of 1.2nm could be achieved by improving the tilt-series alignment.

Perforation of the sigmoid colon due to intradiscal spacer dislocation.

A case of late dislocation of a disc spacer L5/S1 with perforation of the sigmoid colon and transanal passage 4 years after implantation is reported. The objective is to describe an uncommon complication of anterior endoscopic spondylodesis L5/S1. To our knowledge, this is the first report on this rare complication. A 39-year-old patient suffering from a spondylolisthesis L5/S1 (Meyerding grade 2) with bilateral lysis L5 was operated with posterior instrumentation L5/S1 and anterior endoscopic insertion of two disc spacers. 4 years after surgery the patient noticed one of the spacers in the toilet. Radiographic examination of the colon with contrast dye revealed a perforation at the distal sigmoid colon. At the lumbosacral junction there was a bony defect at the site of the absent spacer and an anterior dislocation of the second spacer. A partial resection of the colon at the perforation site with end-to-end anastomosis was performed. The second spacer was removed, and the defect was packed with autologous cancellous bone and local antibiotics. The further course was uneventful. 2 weeks postoperatively the patient was discharged without signs of infection. The radiographic examination after 6 months showed healing of the bone graft with bony fusion L5/S1. In case of incomplete or absent bony fusion the dislocation of intradiscal spacers may arise even years after the primary surgery. In consequence periodical radiographic examinations of spinal instrumentations are recommended until complete bony fusion occurred. Unclear abdominal symptoms following anterior spine surgery require immediate examination.

Nanodroplet cluster formation in ionic liquid microemulsions.

A common ionic liquid (IL), 1-butyl-3-methylimidazolium tetrafluoroborate (bmimBF(4)), is used as polar solvent to induce the formation of a reverse bmimBF(4)-in-toluene IL microemulsion with the aid of the nonionic surfactant Triton X-100. The swelling process of the microemulsion droplets by increasing bmimBF(4) content is detected by dynamic light scattering (DLS), conductivity, UV/Vis spectroscopy, and freeze-fracture transmission electron microscopy (FF-TEM). The results show that the microemulsion droplets initially formed are enlarged by the addition of bmimBF(4). However, successive addition of bmimBF(4) lead to the appearance of large-sized microemulsion droplet clusters (200-400 nm). NMR spectroscopic analysis reveal that the special structures and properties of bmimBF(4) and Triton X-100 together with the polar nature of toluene contribute to the formation of such self-assemblies. These unique self-assembled structures of IL-based microemulsion droplet clusters may have some unusual and unique properties with a number of interesting possibilities for potential applications.

Decrease of droplet size of the reverse microemulsion 1-butyl-3-methylimidazolium tetrafluoroborate/Triton X-100/cyclohexane by addition of water.

In the present contribution, results concerning the role of small amounts of water in the 1-butyl-3-methylimidazolium tetrafluoroborate (bmimBF4)-in-cyclohexane ionic liquid (IL) reverse microemulsions are reported. Dynamic light scattering (DLS) revealed that the size of microemulsion droplets decreased remarkably with increasing water content although water is often used as a polar component to swell reverse microemulsions. It was thus deduced that the number of microemulsion droplets was increased which was confirmed by conductivity measurements. The states of dissolved water were investigated by Fourier transform IR (FTIR) spectroscopic analysis showing that water molecules mainly act as bound water. 1H NMR along with two-dimensional rotating frame nuclear Overhauser effect (NOE) experiments (ROESY) further revealed that water molecules were mainly located in the periphery of the polar core of the microemulsion droplets and behave like a chock being inserted in the palisade layer of the droplet. This increased the curvature of the surfactant film at the IL/cyclohexane interface and thus led to the decrease of the microemulsion droplet size. The order of surfactant molecules arranged in the interface film was increased and thus induced a loss of entropy. Isothermal titration calorimetry (ITC) indicated that an enthalpy increase compensates for the loss of entropy during the process of microstructural transition.

Laser Doppler field sensor for high resolution flow velocity imaging without camera.

In this paper we present a laser sensor for highly spatially resolved flow imaging without using a camera. The sensor is an extension of the principle of laser Doppler anemometry (LDA). Instead of a parallel fringe system, diverging and converging fringes are employed. This method facilitates the determination of the tracer particle position within the measurement volume and leads to an increased spatial and velocity resolution compared to conventional LDA. Using a total number of four fringe systems the flow is resolved in two spatial dimensions and the orthogonal velocity component. Since no camera is used, the resolution of the sensor is not influenced by pixel size effects. A spatial resolution of 4 microm in the x direction and 16 microm in the y direction and a relative velocity resolution of 1x10(-3) have been demonstrated up to now. As a first application we present the velocity measurement of an injection nozzle flow. The sensor is also highly suitable for applications in nano- and microfluidics, e.g., for the measurement of flow rates.

Electrically Tunable Dye Emission via Microcavity Integrated PDMS Gel Actuator.

Electrically tunable microcavities are essential elements for tunable laser sources indispensable for modern telecommunication and spectroscopy. However, most device concepts suffer from extensive lithography or etching for membrane processing. Here, we present an electrically and continuously tunable, multi-half-wavelength microcavity with a quality factor > 1000 as an easy-to-fabricate platform with potential use for vertical-cavity surface-emitting lasers. The microcavity has a Fabry-Pérot structure consisting of ultrasoft PDMS gel with a thickness of 14-15 µm and capped by a distributed Bragg reflector on the bottom end and a silver layer serving as top mirror and electrode. Additionally, we have embedded a pyrromethene dye into the PDMS matrix to prove efficient gain medium integration. By means of an integrated dielectric elastomer actuator, the microcavity thickness is varied 1.3 µm (9%) with a driving voltage of 70 V. The subsequent silver mirror deflection achieves a reversible 40 nm tuning of the cavity resonance wavelength. The tuning range is limited by the lateral bending of the electrodes for increasing voltages. This characteristic bending is confirmed by simulations with finite elements method. The dynamic behavior of the microcavity is characterized by capacitance measurements and modeled by viscoelastic theory. Our research provides in-depth examinations of electrically tunable, PDMS gel-based microcavities with the future goal of building simple, miniaturized, and cost-efficient laser sources with high tuning range.

Coarsening of axial segregation patterns of slurries in a horizontally rotating drum.

Segregation structures of granular mixtures in rotating drums represent classical examples of pattern formation in granular material. We investigate the coarsening of axial segregation patterns of slurries in a long horizontally rotating cylinder. The dynamics and the three-dimensional geometry of the segregation structures are analyzed with optical methods and nuclear magnetic resonance imaging. Previous studies have mainly considered global statistical features of the pattern dynamics. In order to get insight into driving mechanisms for the coarsening process, we focus on the details of the dissolution of individual bands. We treat the coarsening as a consequence of interactions of adjacent bands in the pattern, which are determined by their geometrical relations. In addition to initially homogeneous mixtures, which evolve to spontaneously formed patterns, we study the evolution of specially prepared simple initial states. The role of the three-dimensional geometry of the axial core in the dissolution process of segregation bands is demonstrated. Relations between geometry and dynamic processes are established, which may help to find the correct microscopic models for the coarsening mechanism.

Surface dynamics of voltage-gated ion channels.

Neurons encode information in fast changes of the membrane potential, and thus electrical membrane properties are critically important for the integration and processing of synaptic inputs by a neuron. These electrical properties are largely determined by ion channels embedded in the membrane. The distribution of most ion channels in the membrane is not spatially uniform: they undergo activity-driven changes in the range of minutes to days. Even in the range of milliseconds, the composition and topology of ion channels are not static but engage in highly dynamic processes including stochastic or activity-dependent transient association of the pore-forming and auxiliary subunits, lateral diffusion, as well as clustering of different channels. In this review we briefly discuss the potential impact of mobile sodium, calcium and potassium ion channels and the functional significance of this for individual neurons and neuronal networks.

Integrated Microfluidic Membrane Transistor Utilizing Chemical Information for On-Chip Flow Control.

Microfluidics is a great enabling technology for biology, biotechnology, chemistry and general life sciences. Despite many promising predictions of its progress, microfluidics has not reached its full potential yet. To unleash this potential, we propose the use of intrinsically active hydrogels, which work as sensors and actuators at the same time, in microfluidic channel networks. These materials transfer a chemical input signal such as a substance concentration into a mechanical output. This way chemical information is processed and analyzed on the spot without the need for an external control unit. Inspired by the development electronics, our approach focuses on the development of single transistor-like components, which have the potential to be used in an integrated circuit technology. Here, we present membrane isolated chemical volume phase transition transistor (MIS-CVPT). The device is characterized in terms of the flow rate from source to drain, depending on the chemical concentration in the control channel, the source-drain pressure drop and the operating temperature.

Dynamic association of calcium channel subunits at the cellular membrane.

High voltage gated calcium channels (VGCCs) are composed of at least three subunits, one pore forming [Formula: see text]-subunit, an intracellular [Formula: see text]-variant, and a mostly extracellular [Formula: see text]-variant. Interactions between these subunits determine the kinetic properties of VGCCs. It is unclear whether these interactions are stable over time or rather transient. Here, we used single-molecule tracking to investigate the surface diffusion of [Formula: see text]- and [Formula: see text]-subunits at the cell surface. We found that [Formula: see text]-subunits show higher surface mobility than [Formula: see text]-subunits, and that they are only transiently confined together, suggesting a weak association between [Formula: see text]- and [Formula: see text]-subunits. Moreover, we observed that different [Formula: see text]-subunits engage in different degrees of association with the [Formula: see text]-subunit, revealing the tighter interaction of [Formula: see text] with [Formula: see text]. These data indicate a distinct regulation of the [Formula: see text] interaction in VGCC subtypes. We modeled their membrane dynamics in a Monte Carlo simulation using experimentally determined diffusion constants. Our modeling predicts that the ratio of associated [Formula: see text]- and [Formula: see text]-subunits mainly depends on their expression density and confinement in the membrane. Based on the different motilities of particular [Formula: see text]-subunit combinations, we propose that their dynamic assembly and disassembly represent an important mechanism to regulate the signaling properties of VGCC.

Mobility of calcium channels in the presynaptic membrane.

Unravelling principles underlying neurotransmitter release are key to understand neural signaling. Here, we describe how surface mobility of voltage-dependent calcium channels (VDCCs) modulates release probabilities (P(r)) of synaptic vesicles (SVs). Coupling distances of <10 to >100 nm have been reported for SVs and VDCCs in different synapses. Tracking individual VDCCs revealed that within hippocampal synapses, ∼60% of VDCCs are mobile while confined to presynaptic membrane compartments. Intracellular Ca(2+) chelation decreased VDCC mobility. Increasing VDCC surface populations by co-expression of the α2δ1 subunit did not alter channel mobility but led to enlarged active zones (AZs) rather than higher channel densities. VDCCs thus scale presynaptic scaffolds to maintain local mobility. We propose that dynamic coupling based on mobile VDCCs supports calcium domain cooperativity and tunes neurotransmitter release by equalizing Pr for docked SVs within AZs.

Spinal cord compression: an unusual presentation of hepatocellular carcinoma.

Hepatocellular carcinoma is the 5(th) most common cancer in men and the 2(nd) common cause of death from cancer worldwide. The tumour commonly metastasizes to the lungs, regional lymph nodes and bone. Spinal cord compression secondary to metastatic disease as a first presentation is uncommon. We describe a patient who presented with paraplegia as a first presentation of hepatocellular carcinoma. 46 year old Namibian man presented with progressive leg weakness that was associated with a dull back ache and inability to pass urine and stool. He had no history of trauma nor did he have chronic cough, night sweats or fevers. He has been treated several times for alcohol dependence. On examination he was wasted, power 0/5 in both lower limbs and a sensory level at T12. He also had a non-tender hepatomegaly with Alpha-fetoprotein of 2000. The Chest X-ray and Chest CT showed nodular opacities indicating metastatic disease and the X-ray and CT of the thoracic spine showed osteolytic lesion with destruction of the pedicle of L1. Liver and spinal biopsy confirmed the hepatocellular carcinoma. The extra hepatic manifestations of HCC are diverse and Spinal cord metastasis is of pertinent clinical importance and should thus be greatly considered.

Nonvasoconstrictive hemoglobin particles as oxygen carriers.

Artificial oxygen carriers, favorably hemoglobin-based oxygen carriers (HBOCs), are being investigated intensively during the last 30 years with the aim to develop a universal blood substitute. However, serious side effects mainly caused by vasoconstriction triggered by nitric oxide (NO) scavenging due to penetration of nanosized HBOCs through the endothelial gaps of the capillary walls and/or oxygen oversupply in the precapillary arterioles due to their low oxygen affinity led to failure of clinical trials and FDA disapproval. To avoid these effects, HBOCs with a size between 100 and 1000 nm and high oxygen affinity are needed. Here we present for the first time unique hemoglobin particles (HbPs) of around 700 nm with high oxygen affinity and low immunogenicity using a novel, highly effective, and simple technique. The fabrication procedure provides particles with a narrow size distribution and nearly uniform morphology. The content of hemoglobin (Hb) in the particles corresponded to 80% of the Hb content in native erythrocytes. Furthermore, we demonstrate a successful perfusion of isolated mouse glomeruli with concentrated HbP suspensions in vitro. A normal, nonvasoconstrictive behavior of the afferent arterioles is observed, suggesting no oxygen oversupply and limited NO scavenging by these particles, making them a highly promising blood substitute.

Fluidic microchemomechanical integrated circuits processing chemical information.

Lab-on-a-chip (LOC) technology has blossomed into a major new technology fundamentally influencing the sciences of life and nature. From a systemic point of view however, microfluidics is still in its infancy. Here, we present the concept of a microfluidic central processing unit (CPU) which shows remarkable similarities to early electronic Von Neumann microprocessors. It combines both control and execution units and, moreover, the complete power supply on a single chip and introduces the decision-making ability regarding chemical information into fluidic integrated circuits (ICs). As a consequence of this system concept, the ICs process chemical information completely in a self-controlled manner and energetically self-sustaining. The ICs are fabricated by layer-by-layer deposition of several overlapping layers based on different intrinsically active polymers. As examples we present two microchips carrying out long-term monitoring of critical parameters by around-the-clock sampling.