Search results for "Biological system"
showing 10 items of 319 documents
Analyzing the feasibility of time correlated spectral entropy for the assessment of neuronal synchrony
2016
In this paper, we study neuronal network analysis based on microelectrode measurements. We search for potential relations between time correlated changes in spectral distributions and synchrony for neuronal network activity. Spectral distribution is quantified by spectral entropy as a measure of uniformity/complexity and this measure is calculated as a function of time for the recorded neuronal signals, i.e., time variant spectral entropy. Time variant correlations in the spectral distributions between different parts of a neuronal network, i.e., of concurrent measurements via different microelectrodes, are calculated to express the relation with a single scalar. We demonstrate these relati…
Variance component analysis to assess protein quantification in biomarker discovery. Application to MALDI-TOF mass spectrometry.
2017
International audience; Controlling the technological variability on an analytical chain is critical for biomarker discovery. The sources of technological variability should be modeled, which calls for specific experimental design, signal processing, and statistical analysis. Furthermore, with unbalanced data, the various components of variability cannot be estimated with the sequential or adjusted sums of squares of usual software programs. We propose a novel approach to variance component analysis with application to the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) technology and use this approach for protein quantification by a classical signal processing algori…
Collective Cell Migration in a Fibrous Environment: A Hybrid Multiscale Modelling Approach
2021
International audience; The specific structure of the extracellular matrix (ECM), and in particular the density and orientation of collagen fibres, plays an important role in the evolution of solid cancers. While many experimental studies discussed the role of ECM in individual and collective cell migration, there are still unanswered questions about the impact of nonlocal cell sensing of other cells on the overall shape of tumour aggregation and its migration type. There are also unanswered questions about the migration and spread of tumour that arises at the boundary between different tissues with different collagen fibre orientations. To address these questions, in this study we develop …
One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!
2016
Abstract Cell growth is a complex phenotype widely used in systems biology to gauge the impact of genetic and environmental perturbations. Due to the magnitude of genome-wide studies, resolution is often sacrificed in favor of throughput, creating a demand for scalable, time-resolved, quantitative methods of growth assessment. We present ODELAY (One-cell Doubling Evaluation by Living Arrays of Yeast), an automated and scalable growth analysis platform. High measurement density and single-cell resolution provide a powerful tool for large-scale multiparameter growth analysis based on the modeling of microcolony expansion on solid media. Pioneered in yeast but applicable to other colony formin…
Automated detection of protein unfolding events in atomic force microscopy force curves
2016
Atomic force microscopy is not only a high-resolution imaging device but also a mechanical machine, which can be used either to indent or stretch (soft) biomaterials. Due to the statistical nature of such materials (i.e., hydrogels or polymers) hundreds of force-distance curves are required to describe their mechanical properties. In this manuscript, we present an automated system for polymer unfolding detection based on continuous wavelet analysis. We have tested the automated program on elastin, which is an important protein that provides elasticity to tissues and organs. Our results show that elastin changes its mechanical behavior in the presence of electrolytes. In particular, we show …
ODELAY: A Large-scale Method for Multi-parameter Quantification of Yeast Growth
2017
Growth phenotypes of microorganisms are a strong indicator of their underlying genetic fitness and can be segregated into 3 growth regimes: lag-phase, log-phase, and stationary-phase. Each growth phase can reveal different aspects of fitness that are related to various environmental and genetic conditions. High-resolution and quantitative measurements of all 3 phases of growth are generally difficult to obtain. Here we present a detailed method to characterize all 3 growth phases on solid media using an assay called One-cell Doubling Evaluation of Living Arrays of Yeast (ODELAY). ODELAY quantifies growth phenotypes of individual cells growing into colonies on solid media using time-lapse mi…
Label-Free Proteomics of Quantity-Limited Samples Using Ion Mobility-Assisted Data-Independent Acquisition Mass Spectrometry
2021
Over the past two decades, unbiased data-independent acquisition (DIA) approaches have gained increasing popularity in the bottom-up proteomics field. Here, we describe an ion mobility separation enhanced DIA workflow for large-scale label-free quantitative proteomics studies where starting material is limited. We set a special focus on the single pot solid-phase-enhanced sample preparation (SP3) protocol, which is well suited for the processing of quantity-limited samples.
Modeling of Particle Number Fluctuations in Entire Cells
2012
In a recent study we developed a method to model protein diffusion in cells [1], where special attention was given to generating from image data of the measured cell a realistic digital model cell in which protein dynamics were simulated. The method was shown to be well suited for modeling non-equilibrium situations that arise, e.g., in photobleaching experiments, and to be capable of producing more detailed information about protein motion than traditional modeling.Another experimental way to assess protein dynamics is to study fluctuations in the local protein number, as it is done, e.g., in fluorescence correlation spectroscopy (FCS), or in similar measurements that apply single-plane il…
The Dynamics of Aroma Release during the Consumption of Candies with Different Structures
2014
This chapter aims at investigating the role of candy texture on the dynamics of aroma release using dynamic instrumental and sensory methods. The highest in vivo release, monitored using proton transfer reaction mass spectrometry (PTR-MS), was obtained for the 2% gelatin sample for all aroma compounds. The temporal dominance of sensations (TDS) method highlighted that the dominant sensation for the liquid product was the “strawberry” note. For other products, the temporal characteristics of perceptions were more complex. Data highlighted that aroma release resulted from interaction between product properties and oral behavior. Some relations with the dynamics of perception have been establi…
pH Feedback Lifecycles Programmed by Enzymatic Logic Gates Using Common Foods as Fuels
2021
Abstract Artificial temporal signaling systems, which mimic living out‐of‐equilibrium conditions, have made large progress. However, systems programmed by enzymatic reaction networks in multicomponent and unknown environments, and using biocompatible components remain a challenge. Herein, we demonstrate an approach to program temporal pH signals by enzymatic logic gates. They are realized by an enzymatic disaccharide‐to‐monosaccharide‐to‐sugar acid reaction cascade catalyzed by two metabolic chains: invertase‐glucose oxidase and β‐galactosidase‐glucose oxidase, respectively. Lifetimes of the transient pH signal can be programmed from less than 15 min to more than 1 day. We study enzymatic k…