373 research outputs found
Fused Fiber Photometry
No full textThe code allows reproduction of the analysis of data presented in the manuscript "A flexible and versatile system for multi-color fiber photometry and optogenetic manipulation", Cell Method Reports, 2023, by Formozov, Dieter, and Wiegert.
It is suitable for a general analysis of fiber photometry together with other behaviorally relevant parameters. </p
Pomeroy, L.R. & Wiegert, R.G. (Editors). — The ecology of a salt marsh. Berlin, Heidelberg and New York, Springer Verlag, Ecological Studies, volume 38, 1981
No full textBourlière François. Pomeroy, L.R. & Wiegert, R.G. (Editors). — The ecology of a salt marsh. Berlin, Heidelberg and New York, Springer Verlag, Ecological Studies, volume 38, 1981. In: Revue d'Écologie (La Terre et La Vie), tome 36, n°3, 1982. p. 477
Continuous-time System Identification: A Bilinear Optimization Approach
No full textIn the noiseless case, the identification of a grey-box model can be posed as a feasibility problem, i.e. determining if existent - and if so - finding a parameter vector such that the parametric model equals the actual model (or its associated input-output data). Being that in this thesis we are interested in continuous-time grey-box identification, we shall be dealing with models that allow for forming a direct relationship with physical meaningful quantities. Such models include the state space representation and the matrix differential equation. In general, identifying such grey-box models turns out to be a non-convex problem. In this thesis, we initially review a framework which allows us to solve feasibility problems which have bilinear constraints. It turns out that most of the aforementioned non-convexities can be captured into a single bilinear matrix equation. However, the resulting feasibility problem, including the bilinear matrix equations, makes the overall search for the actual parameter vector NP-hard. In order to come up with numerical tractable algorithms, we use a heuristic known as Sequential Convex Relaxation to relax the bilinear equality constraints. This iterative scheme is flexible enough to allow for additional (in)equality constraints, possibly resembling any other physical constraints. We explore two different approaches to identify both the state space model and the matrix differential equation; one, by directly identifying the model from the given frequency response function; two, by first identifying a black-box model before performing a small scale optimization problem, transforming the black-box model such that it fits the grey-box parameterization. In addition, we present a novel method which uses the Power Spectral Density to estimate a 2nd order model. All methods are numerically validated.Mechanical Engineering | Systems and Contro
Definition of the σW regulon of Bacillus subtilis in the absence of stress
No full textBacteria employ extracytoplasmic function (ECF) sigma factors for their responses to environmental stresses. Despite intensive research, the molecular dissection of ECF sigma factor regulons has remained a major challenge due to overlaps in the ECF sigma factor-regulated genes and the stimuli that activate the different ECF sigma factors. Here we have employed tiling arrays to single out the ECF σW regulon of the Gram-positive bacterium Bacillus subtilis from the overlapping ECF σX, σY, and σM regulons. For this purpose, we profiled the transcriptome of a B. subtilis sigW mutant under non-stress conditions to select candidate genes that are strictly σW-regulated. Under these conditions, σW exhibits a basal level of activity. Subsequently, we verified the σW-dependency of candidate genes by comparing their transcript profiles to transcriptome data obtained with the parental B. subtilis strain 168 grown under 104 different conditions, including relevant stress conditions, such as salt shock. In addition, we investigated the transcriptomes of rasP or prsW mutant strains that lack the proteases involved in the degradation of the σW anti-sigma factor RsiW and subsequent activation of the σW-regulon. Taken together, our studies identify 89 genes as being strictly σW-regulated, including several genes for non-coding RNAs. The effects of rasP or prsW mutations on the expression of σW-dependent genes were relatively mild, which implies that σW-dependent transcription under non-stress conditions is not strictly related to RasP and PrsW. Lastly, we show that the pleiotropic phenotype of rasP mutant cells, which have defects in competence development, protein secretion and membrane protein production, is not mirrored in the transcript profile of these cells. This implies that RasP is not only important for transcriptional regulation via σW, but that this membrane protease also exerts other important post-transcriptional regulatory functions
A proposed alternative dynamical history for 2P/Encke which explains the taurid meteoroid complex
No full textInternational audienceAbstract The Taurid Meteoroid Complex (TMC) is a broad stream of meteoroids that produces several annual meteor showers on Earth. If the linkage between these showers and 2P/Encke is at the centre of most TMC models, the small size and low activity of the comet suggest that 2P/Encke is not the unique parent body of the Taurids. Here we simulate the formation of the TMC from 2P/Encke and several NEAs. In total, we explored more than a hundred stream formation scenarios using clones of 2P/Encke. Each modelled stream was integrated and compared with present-day Taurid observations. As previously reported, we find that even slight variations of 2P/Encke’s orbit modifies considerably the characteristics of the simulated showers. Most of the comet’s clones, including the nominal one, appear to reproduce the radiant structure of the Taurid meteors but do not match the observed time and duration of the showers. However, the radiants and timing of most Taurid showers are well reproduced by a particular clone of the comet. Our analysis thus suggest that with this specific dynamical history, 2P/Encke is the sole parent of the four major TMC showers which have ages from 7-21 ka. Our modelling also predicts that the 2022 Taurid Resonant Swarm return will be comparable in strength to the 1998, 2005 and 2015 returns. While purely dynamical models of Encke’s orbit -limited by chaos- may fail to reveal the comet’s origin, its meteor showers may provide the trail of breadcrumbs needed to backtrack our way out of the labyrinth
An observational synthesis of the Taurid meteor complex
No full textInternational audienceWe provide an overview of the observational properties of the four major Taurid showers, namely the Northern and Southern Taurids (#017 NTA and #002 STA), the β Taurids (#173 BTA), and the ζ Perseids (#172 ZPE). Analysing more than two decades of meteor observations from visual, optical, and radar measurements, we present the Taurids average activity, annual variations in strength, radiant drift, and orbital variations as a function of solar longitude and particle size. The Taurid showers are detected over several weeks in the spring and autumn, but their annual activity level is generally low (less than 15 visual meteors per hour). We find the STA to be pre-dominant in autumn, while its twin, the ZPE, dominates over the BTA in spring. Due to their long duration, the position of each shower's radiant and orbital elements are variable with time. Optical measurements have previously recorded enhanced STA activity and increased fireball rates caused by the return of a swarm of meteoroids trapped in the 7:2 mean motion resonance with Jupiter. However, we find no presence of the swarm in radar data, suggesting that small meteoroids are removed from the resonance faster than fireball-producing meteoroids. We also find the STA to be enriched in smaller particles early in their activity period. The differences we identify in our analysis between the showers at different particle sizes provide strong observational constraints to future dynamical modelling of the Taurid Meteoroid Complex
Cellular and nuclear morphology…and calcium signaling: revealing the interplay between structure and function
No full textPoster presentation: Calcium plays a pivotal role in relaying electrical signals of the cell to subcellular compartments, such as the nucleus. Since this one ion type is used by the cell for many processes a neuron needs to establish finely tuned calcium pathways in order to be able to differentiate multiple tasks, [1-3].
While it is known that neurons can actively change their shape upon neuronal activity, [4-7], we here present novel findings of activity-regulated nuclear morphology, [8,9]. With the help of an experimental and computational modeling approach, we show that hippocampal neurons can change the previously spherical shape of their nuclei to complex and infolded morphologies. This morphology regulation is demonstrated to be regulated by NMDA-receptor gated calcium, while synaptic and extra-synaptic NMDA-receptors elicit opposing effects on nuclear morphology, [8].
The structural alterations of the cell nucleus have significant effects on nuclear calcium dynamics. Compartmentalization of the nucleus, due to membrane infoldings, changes calcium frequencies, amplitudes and spatial distributions, [8,10]. Since these parameters have been shown to control downstream events towards gene transcription, [11,12], the results elucidate the cellular control of nuclear function with the help of morphology modulation. With respect to processes downstream of calcium, we show that histone H3 phosphorylation is closely linked to nuclear morphology. Investigating the nuclear morphologies of hippocampal neurons, two major classes were identified [9,10]. One class contains non-infolded nuclei that have the function of calcium signal integrators, while the other class contains highly infolded nuclei, which function as frequency detectors of nuclear calcium, [10].
Extending this interdisciplinary approach of investigating structure/function relationships in neurons, the effects of cellular morphology – as well as the morphology of the endoplasmic reticulum and other organelles – on neuronal calcium signals is currently being investigated. This endeavor makes use of highly detailed, three-dimensional models of neuronal calcium dynamics, including the three-dimensional morphology of the cell and its organelles
Preliminary Results on the Gravitational Slingshot Effect and the Population of Hyperbolic Meteoroids at Earth
No full textInterstellar meteoroids, solid particles arriving from outside our Solar System, are not easily distinguished from local meteoroids. A velocity above the escape velocity of the Sun is often used as an indicator of a possible interstellar origin. We demonstrate that the gravitational slingshot effect, resulting from the passage of local meteoroid near a planet, can produce hyperbolic meteoroids at the Earth s orbit with excess velocities comparable to those expected of interstellar meteoroids
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