Allan Variance Analysis as Useful Tool to Determine Noise in Various Single-Molecule Setups

One limitation on the performance of optical traps is the noise inherently present in every setup. Therefore, it is the desire of most experimentalists to minimize and possibly eliminate noise from their optical trapping experiments. A step in this direction is to quantify the actual noise in the system and to evaluate how much each particular component contributes to the overall noise. For this purpose we present Allan variance analysis as a straightforward method. In particular, it allows for judging the impact of drift which gives rise to low-frequency noise, which is extremely difficult to pinpoint by other methods. We show how to determine the optimal sampling time for calibration, the optimal number of data points for a desired experiment, and we provide measurements of how much accuracy is gained by acquiring additional data points. Allan variances of both micrometer-sized spheres and asymmetric nanometer-sized rods are considered.Comment: 14 pages, 6 figures, presented at SPIE Optics+Photonics 2009 in San Diego, CA, US

In vivo anomalous diffusion and weak ergodicity breaking of lipid granules

Combining extensive single particle tracking microscopy data of endogenous lipid granules in living fission yeast cells with analytical results we show evidence for anomalous diffusion and weak ergodicity breaking. Namely we demonstrate that at short times the granules perform subdiffusion according to the laws of continuous time random walk theory. The associated violation of ergodicity leads to a characteristic turnover between two scaling regimes of the time averaged mean squared displacement. At longer times the granule motion is consistent with fractional Brownian motion.Comment: 4 pages, 4 figures, REVTeX. Supplementary Material. Physical Review Letters, at pres

Quantitative analysis of single particle trajectories: mean maximal excursion method

An increasing number of experimental studies employ single particle tracking to probe the physical environment in complex systems. We here propose and discuss new methods to analyze the time series of the particle traces, in particular, for subdiffusion phenomena. We discuss the statistical properties of mean maximal excursions, i.e., the maximal distance covered by a test particle up to time t. Compared to traditional methods focusing on the mean squared displacement we show that the mean maximal excursion analysis performs better in the determination of the anomalous diffusion exponent. We also demonstrate that combination of regular moments with moments of the mean maximal excursion method provides additional criteria to determine the exact physical nature of the underlying stochastic subdiffusion processes. We put the methods to test using experimental data as well as simulated time series from different models for normal and anomalous dynamics, such as diffusion on fractals, continuous time random walks, and fractional Brownian motion.Comment: 10 pages, 7 figures, 2 tables. NB: Supplementary material may be found in the downloadable source file

Biomimetic Carbon-Fiber Systems Engineering: A Modular Design Strategy to Generate Biofunctional Composites from Graphene and Carbon Nanofibers

electrical conductivity. It is additionally advantageous if such materials resembled the structural and biochemical features of the natural extracellular environment. Here we show a novel modular design strategy to engineer biomimetic carbon-fiber based scaffolds. Highly porous ceramic zinc oxide (ZnO) microstructures serve as 3D sacrificial templates and are infiltrated with carbon nanotube (CNT) or graphene dispersions. Once the CNTs and graphene uniformly coat the ZnO template, the ZnO is either removed by hydrolysis or converted into carbon by chemical vapor deposition (CVD). The resulting 3D carbon scaffolds are both hierarchically ordered and free-standing. The properties of the micro-fibrous scaffolds were tailored with a high porosity (up to 93 %), high Young’s modulus (~0.027 to ~22 MPa), and an electrical conductivity of (~0.1 to ~330 S/m), as well as different surface compositions. Cell viability and fibroblast proliferation rate and protein adsorption rate assays have shown that the generated scaffolds are biocompatible and have a high protein adsorption capacity (up to 77.32 ±6.95 mg/cm3), so that they not only are able to resemble the ECM structurally, but also biochemically. The scaffolds also allow for the successful growth and adhesion of fibroblast cells showing that we provide a novel, highly scalable modular design strategy to generate biocompatible carbon-fiber systems that mimic the extracellular matrix with the additional feature of conductivity.RA gratefully acknowledges partial project funding by the Deutsche Forschungsgemeinschaft under contract FOR1616. This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. GrapheneCore2 785219. CS is supported by the European Research Council (ERC StG 336104 CELLINSPIRED, ERC PoC 768740 CHANNELMAT), by the German Research Foundation (RTG 2154, SFB 1261 project B7). MT acknowledges support from the German Academic Exchange Service (DAAD) through a research grant for doctoral candidates (91526555-57048249). We acknowledge funding from EPSRC grants EP/P02534X/1, ERC grant 319277 (Hetero2D) the Royal Academy of Engineering Enterprise Scheme, the Trinity College, Cambridge, and the Isaac Newton Trust

Morphological correlates of pyramidal cell axonal myelination in mouse and human neocortex

The axons of neocortical pyramidal neurons are frequently myelinated. Heterogeneity in the topography of axonal myelination in the cerebral cortex has been attributed to a combination of electrophysiological activity, axonal morphology, and neuronal-glial interactions. Previously, we showed that axonal segment length and caliber are critical local determinants of fast-spiking interneuron myelination. However, the factors that determine the myelination of individual axonal segments along neocortical pyramidal neurons remain largely unexplored. Here, we used structured illumination microscopy to examine the extent to which axonal morphology is predictive of the topography of myelination along neocortical pyramidal neurons. We identified critical thresholds for axonal caliber and interbranch distance that are necessary, but not sufficient, for myelination of pyramidal cell axons in mouse primary somatosensory cortex (S1). Specifically, we found that pyramidal neuron axonal segments with a caliber &lt; 0.24 μm or interbranch distance &lt; 18.10 μm are rarely myelinated. Moreover, we further confirmed that these findings in mice are similar for human neocortical pyramidal cell myelination (caliber &lt; 0.25 μm, interbranch distance &lt; 19.00 μm), suggesting that this mechanism is evolutionarily conserved. Taken together, our findings suggest that axonal morphology is a critical correlate of the topography and cell-type specificity of neocortical myelination.</p

Biological measurement beyond the quantum limit

Quantum noise places a fundamental limit on the per photon sensitivity attainable in optical measurements. This limit is of particular importance in biological measurements, where the optical power must be constrained to avoid damage to the specimen. By using non-classically correlated light, we demonstrated that the quantum limit can be surpassed in biological measurements. Quantum enhanced microrheology was performed within yeast cells by tracking naturally occurring lipid granules with sensitivity 2.4 dB beyond the quantum noise limit. The viscoelastic properties of the cytoplasm could thereby be determined with a 64% improved measurement rate. This demonstration paves the way to apply quantum resources broadly in a biological context

Single particle tracking in systems showing anomalous diffusion: the role of weak ergodicity breaking

Anomalous diffusion has been widely observed by single particle tracking microscopy in complex systems such as biological cells. The resulting time series are usually evaluated in terms of time averages. Often anomalous diffusion is connected with non-ergodic behaviour. In such cases the time averages remain random variables and hence irreproducible. Here we present a detailed analysis of the time averaged mean squared displacement for systems governed by anomalous diffusion, considering both unconfined and restricted (corralled) motion. We discuss the behaviour of the time averaged mean squared displacement for two prominent stochastic processes, namely, continuous time random walks and fractional Brownian motion. We also study the distribution of the time averaged mean squared displacement around its ensemble mean, and show that this distribution preserves typical process characteristic even for short time series. Recently, velocity correlation functions were suggested to distinguish between these processes. We here present analytucal expressions for the velocity correlation functions. Knowledge of the results presented here are expected to be relevant for the correct interpretation of single particle trajectory data in complex systems.Comment: 15 pages, 15 figures; References adde

Handheld imaging photonic crystal biosensor for multiplexed, label-free protein detection.

We present a handheld biosensor system for the label-free and specific multiplexed detection of several biomarkers employing a spectrometer-free imaging measurement system. A photonic crystal surface functionalized with multiple specific ligands forms the optical transducer. The photonic crystal slab is fabricated on a glass substrate by replicating a periodic grating master stamp with a period of 370 nm into a photoresist via nanoimprint lithography and deposition of a 70-nm titanium dioxide layer. Capture molecules are coupled covalently and drop-wise to the photonic crystal surface. With a simple camera and imaging optics the surface-normal transmission is detected. In the transmission spectrum guided-mode resonances are observed that shift due to protein binding. This shift is observed as an intensity change in the green color channel of the camera. Non-functionalized image sections are used for continuous elimination of background drift. In a first experiment we demonstrate the specific and time-resolved detection of 90.0 nm CD40 ligand antibody, 90.0 nM EGF antibody, and 500 nM streptavidin in parallel on one sensor chip. In a second experiment, aptamers with two different spacer lengths are used as receptor. The binding kinetics with association and dissociation of 250 nM thrombin and regeneration of the sensor surface with acidic tris-HCl-buffer (pH 5.0) is presented for two measurement cycles

3D Hydrogels Containing Interconnected Microchannels of Subcellular Size for Capturing Human Pathogenic Acanthamoeba Castellanii

3D Hydrogels Containing Interconnected Microchannels of Subcellular Size for Capturing Human Pathogenic Acanthamoeba Castellani