scholarly journals Lipid tracking at kilohertz sampling rates on live cell membranes through Interferometric Scattering microscopy

2021 ◽  
Author(s):  
Francesco Reina ◽  
Christian Eggeling ◽  
Christoffer Lagerholm
Keyword(s):  
Sampling Rate ◽  
Physical Parameters ◽  
Diffusion Mode ◽  
Analysis Pipeline ◽  
Experimental Conditions ◽  
Lateral Dynamics ◽  
Diffusivity Measurements ◽  
Picket Fence ◽  
Diffusion Rates ◽  
Localization Uncertainty

The lateral dynamics of lipids on the cellular membranes are one of the most challenging topics to study in membrane biophysics, needing simultaneously high spatial and temporal resolution. In this study, we have employed Interferometric scattering Microscopy (ISCAT) to explore the dynamics of a biotinylated lipid analogue labelled with streptavidin-coated gold nanoparticles (20 and 40nm in diameter) at 2kHz sampling rate. We developed a statistics-driven analysis pipeline to analyse both ensemble average and single trajectory Mean Squared Displacements from each dataset, and to discern the most likely diffusion mode. We found that the use of larger tags slows down the target motion without affecting the diffusion mode. Moreover, we determined from our statistical analysis that the prevalent diffusion mode of the tracked gold-labelled lipids is compartmentalized diffusion. This model describes the motion of particles diffusing on a corralled surface, with a certain probability of changing compartment. This is compatible with the picket-fence model of membrane structure, already observed by similar studies. Through our analysis, we could determine significant physical parameters, such as average compartment size, dynamic localization uncertainty, and the intra- and inter-compartmental diffusion rates. We then simulated diffusion in an environment compatible with the experimentally-derived parameters and model. The closeness of the results from the analysis of experimental and simulated trajectories validates our analysis and the proposed description of the cell membrane. Finally, we introduce the confinement strength metric to compare diffusivity measurements across techniques and experimental conditions, which we used to successfully compare the present results with other related studies.

scholarly journals A gradient field defeats the inherent repulsion between magnetic nanorods

2014 ◽  
Vol 1 (2) ◽  
pp. 140271 ◽  
Author(s):  
Yu Gu ◽  
Ruslan Burtovyy ◽  
John Custer ◽  
Igor Luzinov ◽  
Konstantin G. Kornev
Keyword(s):  
Phase Portrait ◽  
High Speed ◽  
Uniform Magnetic Field ◽  
Gradient Field ◽  
Physical Parameters ◽  
Uniform Field ◽  
Experimental Conditions ◽  
Magnetic Nanorods ◽  
Field Gradients ◽  
And Control

When controlling the assembly of magnetic nanorods and chains of magnetic nanoparticles, it is extremely challenging to bring them together side by side while keeping a desired spacing between their axes. We show that this challenge can be successfully resolved by using a non-uniform magnetic field that defeats an inherent repulsion between nanorods. Nickel nanorods were suspended in a viscous film and a non-uniform field was used to control their placement. The in-plane movement of nanorods was tracked with a high-speed camera and a detailed image analysis was conducted to quantitatively characterize the behaviour of the nanorods. The analysis focused on the behaviour of a pair of neighbour nanorods, and a corresponding dynamic model was formulated and investigated. The complex two-dimensional dynamics of a nanorod pair was analysed analytically and numerically, and a phase portrait was constructed. Using this phase portrait, we classified the nanorod behaviour and revealed the experimental conditions in which nanorods could be placed side by side. Dependence of the distance between a pair of neighbour nanorods on physical parameters was analysed. With the aid of the proposed theory, one can build different lattices and control their spacing by applying different field gradients.

Precise hyperacuity estimation of spike timing from calcium imaging

2019 ◽  
Author(s):  
Huu Hoang ◽  
Masa-aki Sato ◽  
Shigeru Shinomoto ◽  
Shinichiro Tsutsumi ◽  
Miki Hashizume ◽  
...  
Keyword(s):  
Sampling Rate ◽  
Time Estimation ◽  
Spike Timing ◽  
Support Vector ◽  
High Temporal Resolution ◽  
Spike Time ◽  
Experimental Conditions ◽  
Two Photon ◽  
Photon Imaging ◽  
Two Photon Imaging

SummaryTwo-photon imaging is a major recording technique in neuroscience, but it suffers from several limitations, including a low sampling rate, the nonlinearity of calcium responses, the slow dynamics of calcium dyes and a low signal-to-noise ratio, all of which impose a severe limitation on the application of two-photon imaging in elucidating neuronal dynamics with high temporal resolution. Here, we developed a hyperacuity algorithm (HA_time) based on an approach combining a generative model and machine learning to improve spike detection and the precision of spike time inference. First, Bayesian inference estimates the calcium spike model by assuming the constancy of the spike shape and size. A support vector machine employs this information and detects spikes with higher temporal precision than the sampling rate. Compared with conventional thresholding, HA_time improved the precision of spike time estimation up to 20-fold for simulated calcium data. Furthermore, the benchmark analysis of experimental data from different brain regions and simulation of a broader range of experimental conditions showed that our algorithm was among the best in a class of hyperacuity algorithms. We encourage experimenters to use the proposed algorithm to precisely estimate hyperacuity spike times from two-photon imaging.

scholarly journals A versatile multivariate image analysis pipeline reveals features of Xenopus extract spindles

2016 ◽  
Vol 213 (1) ◽  
pp. 127-136 ◽  
Author(s):  
Andrew W. Grenfell ◽  
Magdalena Strzelecka ◽  
Marina E. Crowder ◽  
Kara J. Helmke ◽  
Anne-Lore Schlaitz ◽  
...  
Keyword(s):  
Quantitative Information ◽  
Analysis Pipeline ◽  
Experimental Conditions ◽  
Experimental Systems ◽  
General Utility ◽  
Segmentation Approach ◽  
Assembly Factor ◽  
Minimal Modification ◽  
Insight Into ◽  
Multivariate Image

Imaging datasets are rich in quantitative information. However, few cell biologists possess the tools necessary to analyze them. Here, we present a large dataset of Xenopus extract spindle images together with an analysis pipeline designed to assess spindle morphology across a range of experimental conditions. Our analysis of different spindle types illustrates how kinetochore microtubules amplify spindle microtubule density. Extract mixing experiments reveal that some spindle features titrate, while others undergo switch-like transitions, and multivariate analysis shows the pleiotropic morphological effects of modulating the levels of TPX2, a key spindle assembly factor. We also apply our pipeline to analyze nuclear morphology in human cell culture, showing the general utility of the segmentation approach. Our analyses provide new insight into the diversity of spindle types and suggest areas for future study. The approaches outlined can be applied by other researchers studying spindle morphology and adapted with minimal modification to other experimental systems.

Receiver function analyses and joint inversion with gravity data: new constraints on the Ivrea geophysical body along a high-resolution profile

2020 ◽  
Author(s):  
Matteo Scarponi ◽  
György Hetényi ◽  
Jaroslava Plomerová ◽  
Stefano Solarino ◽  
Ludovic Baron
Keyword(s):  
Receiver Function ◽  
Joint Inversion ◽  
Gravity Data ◽  
Sampling Rate ◽  
Seismic Refraction ◽  
Western Alps ◽  
Transverse Component ◽  
Reference Points ◽  
Physical Parameters ◽  
S Wave

<p>We collected new seismological and gravity data in the Val Sesia and Lago Maggiore regions in NW Italy to constrain the geometry and properties of the Ivrea Geophysical Body. This piece of lower Adriatic lithosphere is known to be at anomalously shallow depth along the inner arc of the Western Alps, yet existing seismological constraints (vintage seismic refraction data, local earthquake tomography) are spatially sparse. With the aim to reach higher spatial resolution in imaging the structure of the IGB, we analyze the seismological data with various receiver function approaches to map the main velocity discontinuities, followed by joint inversion with gravity data to fill the bulk properties of bodies with densities.</p><p>The new data acquisition consisted of two type of campaigns. For seismology, we deployed 10 broadband seismic stations (MOBNET pool, IG CAS Prague) along a linear West-East profile at 5 km spacing along Val Sesia and across the Lago Maggiore. This network continuously recorded seismic data for 27 months at 100 Hz sampling rate. For gravimetry, we compiled existing datasets and then completed the spatial gaps by relative gravity surveys, tied to absolute reference points, to achieve 1 gravity point every 1-2 km along the profile.</p><p>The receiver function (RF) analyses aim at detecting velocity increases with depth: primarily the Moho and the shallow IGB interfaces and their crustal reverberations (multiples), together with their potential dip by analyzing the transverse component RFs. Furthermore, we aim at investigating the sharpness of the velocity gradient across the discontinuities by analyzing the frequency dependence of the corresponding RF peaks. We aim at reproducing the observations by simple synthetic models.</p><p>The 2D joint inversion combines S wave velocity V<sub>S</sub> and bulk density as physical parameters to match both the seismological and gravimetry data. The relationship between the two parameters is initially chosen from the literature, but depending on the first results the relation itself may be inverted for, considering the various high-grade metamorphic rocks observed at the surface in the area, whose properties may not align with classical V<sub>S</sub>–density equations. In conclusion, we propose new constraints on the IGB, demonstrating the advantage of using multi-disciplinary geophysical observations and improved data coverage across the study area.</p>

Cross-comparison of diagnostic and 0D modeling of a micro-hollow cathode discharge in the stationary regime in an Ar/N2 gas mixture

2021 ◽  
Author(s):  
Alice Remigy ◽  
Salima Kasri ◽  
Thibault Darny ◽  
Hiba Kabbara ◽  
Ludovic William ◽  
...  
Keyword(s):  
Hollow Cathode ◽  
Ultra Violet ◽  
Hollow Cathode Discharge ◽  
Tunable Diode Laser ◽  
Physical Parameters ◽  
Gas Mixture ◽  
High Electron ◽  
Experimental Conditions ◽  
Wide Range ◽  
Averaged Model

Abstract A micro-hollow cathode discharge (MHCD) operated in Ar/N2 gas mixture, working in the normal regime, was studied both experimentally and with a 0D (volume-averaged) model in this work. This source provides high electron densities (up to 1015 cm-3) at low injected power (1W). To understand the mechanisms leading to the production of N atoms, the densities of electrons, N atoms and argon metastable atoms (Ar*) were monitored over a wide range of experimental conditions. Electrons, N atoms and Ar* densities were probed by means of Optical Emission Spectroscopy (OES), Vacuum Ultra Violet Fourier Transform Spectroscopy (VUV FTS) and Tunable Diode Laser Absorption Spectroscopy (TDLAS), respectively. Measurements showed that using a smaller hole diameter enables to work with less injected power, while increasing the power density inside the hole and, subsequently, increasing the densities of excited species. Varying the percentage of N2 in the gas mixture highlighted that, up to 80%, the density of N atoms increases although the dissociation rate drops. Looking at the processes involved in the production of N atoms with the help of the 0D model, we found that at very low N2 fraction, N atoms are mostly produced through dissociative electron-ion recombination. However, adding more N2 decreases drastically the electron density. The density of N atoms does not drop thanks to the contribution of Ar* atoms, which are the main species dissociating N2 between 5 and 55% of N2 in the gas mixture. A reasonable agreement is found between the experiments and the model results. This study shows that, with this MHCD, it is possible to significantly modify the production of N atoms when modifying the physical parameters, making it particularly relevant for applications requiring a N atoms source, such as nitride deposition.

Reshaping biological membranes in endocytosis: crossing the configurational space of membrane-protein interactions

2014 ◽  
Vol 395 (3) ◽  
pp. 275-283 ◽  
Author(s):  
Mijo Simunovic ◽  
Patricia Bassereau
Keyword(s):  
Membrane Protein ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Full Range ◽  
Biological Membranes ◽  
Membrane Properties ◽  
Physical Parameters ◽  
Membrane Remodeling ◽  
Experimental Conditions ◽  
The Way

Abstract Lipid membranes are highly dynamic. Over several decades, physicists and biologists have uncovered a number of ways they can change the shape of membranes or alter their phase behavior. In cells, the intricate action of membrane proteins drives these processes. Considering the highly complex ways proteins interact with biological membranes, molecular mechanisms of membrane remodeling still remain unclear. When studying membrane remodeling phenomena, researchers often observe different results, leading them to disparate conclusions on the physiological course of such processes. Here we discuss how combining research methodologies and various experimental conditions contributes to the understanding of the entire phase space of membrane-protein interactions. Using the example of clathrin-mediated endocytosis we try to distinguish the question ‘how can proteins remodel the membrane?’ from ‘how do proteins remodel the membrane in the cell?’ In particular, we consider how altering physical parameters may affect the way membrane is remodeled. Uncovering the full range of physical conditions under which membrane phenomena take place is key in understanding the way cells take advantage of membrane properties in carrying out their vital tasks.

scholarly journals Multiwalled Carbon Nanotube Synthesis Using Arc Discharge with Hydrocarbon as Feedstock

2013 ◽  
Vol 2013 ◽  
pp. 1-13 ◽  
Author(s):  
K. T. Chaudhary ◽  
Z. H. Rizvi ◽  
K. A. Bhatti ◽  
J. Ali ◽  
P. P. Yupapin
Keyword(s):  
Electron Microscopy ◽  
Carbon Nanotube ◽  
Arc Discharge ◽  
Ambient Pressure ◽  
Multiwalled Carbon Nanotube ◽  
Physical Parameters ◽  
Discharge Process ◽  
Multiwalled Carbon ◽  
Experimental Conditions ◽  
Arc Current

Synthesis of multiwalled carbon nanotube (MWCNT) by arc discharge process is investigated with methane (CH4) as background and feedstock gas. The arc discharge is carried out between two graphite electrodes for ambient pressures 100, 300, and 500 torr and arc currents 50, 70, and 90 A. Plasma kinetics such as the density and temperature for arc discharge carbon plasma is determined to find out the contribution of physical parameters as arc current and ambient pressure on the plasma dynamics and growth of MWCNT. With increase in applied arc current and ambient pressure, an increase in plasma temperature and density is observed. The synthesized samples of MWCNT at different experimental conditions are characterized by transmission electron microscopy, scanning electron microscopy, Raman spectroscopy, Fourier transform infrared spectroscopy, and X-ray diffraction. A decrease in the diameter and improvement in structure quality and growth of MWCNT are observed with increase in CH4ambient pressure and arc current. For CH4ambient pressure 500 torr and arc current 90 A, the well-aligned and straight MWCNT along with graphene stakes are detected.

Instrumentation and Fundamental Studies on Glow Discharge—Microwave-Induced Plasma (GD-MIP) Tandem Source for Optical Emission Spectrometry

1996 ◽  
Vol 50 (8) ◽  
pp. 977-984 ◽  
Author(s):  
Yixiang Duan ◽  
Yimu Li ◽  
Zhaohui Du ◽  
Qinhan Jin ◽  
Jose A. Olivares
Keyword(s):  
Glow Discharge ◽  
Microwave Plasma ◽  
Sampling Rate ◽  
Experimental Results ◽  
Emission Spectrometry ◽  
Line Pair ◽  
Excitation Temperature ◽  
Experimental Conditions ◽  
Microwave Induced Plasma ◽  
Pair Method

Instrumentation and fundamental studies on glow discharge–microwave-induced plasma (GD-MIP) tandem source are described in this paper. Mutual effects among parameters, vacuum pressure, discharge current, voltage, and microwave power are examined with different cathode materials. Sputtering rates with and without microwave boost are measured under various experimental conditions. The experimental results demonstrate that the introduction of a microwave plasma will significantly decrease the sampling rate. A possible mechanism for the more uniform erosion obtained with microwave plasma boosting is suggested and discussed. Excitation temperatures are measured with the line-pair method and Boltzmann plot. A considerable increase in the excitation temperature (from about 3500 to 4200 K by using the line-pair method) is found with the addition of microwave plasma boosting. A comparison of the behavior of glow discharge alone and the GD-MIP tandem source is made. Significant enhancements in signal intensities are observed. The experimental results suggest that the excitation temperature plays an important role in signal enhancement.

scholarly journals Separation of hemodynamic signals from GCaMP fluorescence measured with widefield imaging

2019 ◽  
Author(s):  
M.T. Valley ◽  
M.G. Moore ◽  
J Zhuang ◽  
N Mesa ◽  
D Castelli ◽  
...  
Keyword(s):  
Calcium Imaging ◽  
Sampling Rate ◽  
Large Field ◽  
Physical Parameters ◽  
Imaging Data ◽  
Calcium Signals ◽  
Detailed Model ◽  
High Sampling Rate ◽  
Transgenic Lines ◽  
Multi Wavelength

ABSTRACTWidefield calcium imaging is often used to measure brain dynamics in behaving mice. With a large field of view and a high sampling rate, widefield imaging can monitor activity from several distant cortical areas simultaneously, revealing cortical interactions. Interpretation of widefield images is complicated, however, by the absorption of light by hemoglobin, which can substantially affect the measured fluorescence. One approach to separating hemodynamics and calcium signals is to use multi-wavelength backscatter recordings to measure light absorption by hemoglobin. Following this approach, we develop a spatially-detailed regression-based method to estimate hemodynamics. The spatially-detailed model is based on a linear form of the Beer-Lambert relationship, but is fit at every pixel in the image and does not rely on the estimation of physical parameters. In awake mice of three transgenic lines, the Spatial Model offers improved separation of hemodynamics and changes in GCaMP fluorescence. The improvement is pronounced near blood vessels and, in contrast with other models based on regression or the Beer-Lambert law, can remove vascular artifacts along the sagittal midline. Compared to other separation approaches, the spatially-detailed model permits more accurate fluorescence-based determination of neuronal activity across the cortex.NEW & NOTEWORTHYThis manuscript addresses a well-known and strong source of contamination in widefield calcium imaging data: hemodynamics. To guide researchers towards the best method to separate calcium signals from hemodynamics, we compare the performance of several commonly used methods in three commonly-used Cre-driver lines, and we present a novel regression model that out-performs the other techniques we consider.

A simulation program for quantitative procedure in EPMA

1996 ◽  
Vol 54 ◽  
pp. 480-481
Author(s):  
Claude Merlet
Keyword(s):  
Electron Probe ◽  
Quantitative Methods ◽  
Depth Distribution ◽  
Physical Parameters ◽  
Light Elements ◽  
Distribution Models ◽  
Experimental Conditions ◽  
X Ray ◽  
Gaussian Profile ◽  
Quantitative Procedure

In the last ten years the development of new X-ray depth distribution models in electron probe microanalysis (EPMA), has allowed to obtain accurate quantitative programs for stratified and massive samples. With these new quantitative methods, for the energy lines greater than 1keV and for massive samples, the results of the quantification are independent of the accelerating voltage (for an excited line). Nevertheless, for light elements, and for soft X-ray emission in complexe compounds, the choice of these optimum experimental conditions is not trivial. Moreover, the physical parameters and boundary conditions of the measurements are not well known.In an attempt to choose the optimum accelerating voltage, and to solve some difficulties in the quantification of low energy lines, a software (freeware) has been developed on PC and under the WINDOWS operating system. The calculation procedure is based upon the double partial gaussian profile ϕ(ρz) (recently developed for massive compounds). This description, flexible, precise and mathematically simple allows to compute rapidly the X-ray intensities. The program, which has been designed mainly for WDS electron probe, uses graphic simulations, and includes two sections:

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