scholarly journals Scattering fingerprints of two-state dynamics

2022 ◽  
Author(s):  
Cai Dieball ◽  
Diego Krapf ◽  
Matthias Weiss ◽  
Aljaz Godec
Keyword(s):  
Spin Echo ◽  
Tracer Particle ◽  
Dynamic Structure ◽  
Living Cells ◽  
Model Systems ◽  
Small Scale ◽  
Complex Environments ◽  
Intermediate Scattering Function ◽  
Quasielastic Neutron ◽  
Spatio Temporal

Abstract Particle transport in complex environments such as the interior of living cells is often (transiently) non-Fickian or anomalous, that is, it deviates from the laws of Brownian motion. Such anomalies may be the result of small-scale spatio-temporal heterogeneities in, or viscoelastic properties of, the medium, molecular crowding, etc. Often the observed dynamics displays multi-state characteristics, i.e. distinct modes of transport dynamically interconverting between each other in a stochastic manner. Reliably distinguishing between single- and multi-state dynamics is challenging and requires a combination of distinct approaches. To complement the existing methods relying on the analysis of the particle’s mean squared displacement, position- or displacement-autocorrelation function, and propagators, we here focus on “scattering fingerprints” of multi-state dynamics. We develop a theoretical framework for two-state scattering signatures – the intermediate scattering function and dynamic structure factor – and apply it to the analysis of simple model systems as well as particle-tracking experiments in living cells. We consider inert tracer-particle motion as well as systems with an internal structure and dynamics. Our results may generally be relevant for the interpretation of state-of-the-art differential dynamic microscopy experiments on complex particulate systems, as well as inelastic or quasielastic neutron (incl. spin-echo) and X-ray scattering scattering probing structural and dynamical properties of macromolecules, when the underlying dynamics displays two-state transport.

Application of FRAP and digitized fluorescence microscopy to problems in cell membrane dynamics

1988 ◽  
Vol 46 ◽  
pp. 118-119
Author(s):  
K. Jacobson ◽  
A. Ishihara ◽  
B. Holifield ◽  
F. Zhang
Keyword(s):  
Fluorescence Microscopy ◽  
Cell Biology ◽  
Extended Period ◽  
Dynamic Structure ◽  
Living Cells ◽  
Membrane Dynamics ◽  
Molecular Cell Biology ◽  
Image Averaging ◽  
Single Living Cells ◽  
Single Living

Our laboratory is concerned with understanding the dynamic structure of the plasma membrane with particular reference to the movement of membrane constituents during cell locomotion. In addition to the standard tools of molecular cell biology, we employ both fluorescence recovery after photo- bleaching (FRAP) and digitized fluorescence microscopy (DFM) to investigate individual cells. FRAP allows the measurement of translational mobility of membrane and cytoplasmic molecules in small regions of single, living cells. DFM is really a new form of light microscopy in that the distribution of individual classes of ions, molecules, and macromolecules can be followed in single, living cells. By employing fluorescent antibodies to defined antigens or fluorescent analogs of cellular constituents as well as ultrasensitive, electronic image detectors and video image averaging to improve signal to noise, fluorescent images of living cells can be acquired over an extended period without significant fading and loss of cell viability.

Modulated polarization microscopy displays the dynamics of cytoskeletal structures in living, motile cells

1995 ◽  
Vol 53 ◽  
pp. 902-903
Author(s):  
J. R. Kuhn ◽  
M. Poenie
Keyword(s):  
Mitotic Spindle ◽  
Actin Filaments ◽  
Cell Shape ◽  
Dynamic Structure ◽  
Living Cells ◽  
Cytoskeletal Proteins ◽  
Polarization Microscopy ◽  
Video Enhancement ◽  
Ultrastructural Studies ◽  
Motile Cells

Cell shape and movement are controlled by elements of the cytoskeleton including actin filaments an microtubules. Unfortunately, it is difficult to visualize the cytoskeleton in living cells and hence follow it dynamics. Immunofluorescence and ultrastructural studies of fixed cells while providing clear images of the cytoskeleton, give only a static picture of this dynamic structure. Microinjection of fluorescently Is beled cytoskeletal proteins has proved useful as a way to follow some cytoskeletal events, but long terry studies are generally limited by the bleaching of fluorophores and presence of unassembled monomers.Polarization microscopy has the potential for visualizing the cytoskeleton. Although at present, it ha mainly been used for visualizing the mitotic spindle. Polarization microscopy is attractive in that it pro vides a way to selectively image structures such as cytoskeletal filaments that are birefringent. By combing ing standard polarization microscopy with video enhancement techniques it has been possible to image single filaments. In this case, however, filament intensity depends on the orientation of the polarizer and analyzer with respect to the specimen.

Microtubule Dynamics and Organelle Transport in Reticulomyxa

1990 ◽  
Vol 48 (3) ◽  
pp. 194-195
Author(s):  
Yih-Tai Chen ◽  
Ursula Euteneuer ◽  
Ken B. Johnson ◽  
Michael P. Koonce ◽  
Manfred Schliwa
Keyword(s):  
Plasma Membrane ◽  
Light Microscopy ◽  
Cytoplasmic Dynein ◽  
Living Cells ◽  
Microtubule Dynamics ◽  
Model Systems ◽  
Organelle Transport ◽  
Biochemical Characteristics ◽  
Dependent Transport

The application of video techniques to light microscopy and the development of motility assays in reactivated or reconstituted model systems rapidly advanced our understanding of the mechanism of organelle transport and microtubule dynamics in living cells. Two microtubule-based motors have been identified that are good candidates for motors that drive organelle transport: kinesin, a plus end-directed motor, and cytoplasmic dynein, which is minus end-directed. However, the evidence that they do in fact function as organelle motors is still indirect.We are studying microtubule-dependent transport and dynamics in the giant amoeba, Reticulomyxa. This cell extends filamentous strands backed by an extensive array of microtubules along which organelles move bidirectionally at up to 20 μm/sec (Fig. 1). Following removal of the plasma membrane with a mild detergent, organelle transport can be reactivated by the addition of ATP (1). The physiological, pharmacological and biochemical characteristics show the motor to be a cytoplasmic form of dynein (2).

scholarly journals Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Alexey Bondar ◽  
Olga Rybakova ◽  
Josef Melcr ◽  
Jan Dohnálek ◽  
Petro Khoroshyy ◽  
...  
Keyword(s):  
Biological Systems ◽  
Linear Dichroism ◽  
Quantitative Information ◽  
Living Cells ◽  
Software Tools ◽  
Model Systems ◽  
Membrane Properties ◽  
Polarization Microscopy ◽  
Molecular Processes ◽  
Wide Range

AbstractFluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well as obtaining quantitative information on orientation of fluorescent molecules associated with cellular features. Such information can provide insights into protein structure, aid in development of genetically encoded probes, and allow determinations of lipid membrane properties. However, quantitating and interpreting linear dichroism in biological systems has been laborious and unreliable. Here we present a set of open source ImageJ-based software tools that allow fast and easy linear dichroism visualization and quantitation, as well as extraction of quantitative information on molecular orientations, even in living systems. The tools were tested on model synthetic lipid vesicles and applied to a variety of biological systems, including observations of conformational changes during G-protein signaling in living cells, using fluorescent proteins. Our results show that our tools and model systems are applicable to a wide range of molecules and polarization-resolved microscopy techniques, and represent a significant step towards making polarization microscopy a mainstream tool of biological imaging.

scholarly journals Small-scale spatio-temporal characteristics of accumulation rates in western Dronning Maud Land, Antarctica

2008 ◽  
Vol 54 (185) ◽  
pp. 315-323 ◽  
Author(s):  
Helgard Anschütz ◽  
Daniel Steinhage ◽  
Olaf Eisen ◽  
Hans Oerter ◽  
Martin Horwath ◽  
...  
Keyword(s):  
Accumulation Rate ◽  
Temporal Variations ◽  
Spatial Variations ◽  
Small Scale ◽  
Accumulation Rates ◽  
Order Of Magnitude ◽  
Dronning Maud Land ◽  
Spatio Temporal ◽  
Ground Penetrating ◽  
Firn Core

AbstractSpatio-temporal variations of the recently determined accumulation rate are investigated using ground-penetrating radar (GPR) measurements and firn-core studies. The study area is located on Ritscherflya in western Dronning Maud Land, Antarctica, at an elevation range 1400–1560 m. Accumulation rates are derived from internal reflection horizons (IRHs), tracked with GPR, which are connected to a dated firn core. GPR-derived internal layer depths show small relief along a 22 km profile on an ice flowline. Average accumulation rates are about 190 kg m−2 a−1 (1980–2005) with spatial variability (1σ) of 5% along the GPR profile. The interannual variability obtained from four dated firn cores is one order of magnitude higher, showing 1σ standard deviations around 30%. Mean temporal variations of GPRderived accumulation rates are of the same magnitude or even higher than spatial variations. Temporal differences between 1980–90 and 1990–2005, obtained from two dated IRHs along the GPR profile, indicate temporally non-stationary processes, linked to spatial variations. Comparison with similarly obtained accumulation data from another coastal area in central Dronning Maud Land confirms this observation. Our results contribute to understanding spatio-temporal variations of the accumulation processes, necessary for the validation of satellite data (e.g. altimetry studies and gravity missions such as Gravity Recovery and Climate Experiment (GRACE)).

Kalmag: a high spatio temporal model of the Geomagnetic field

2021 ◽  
Author(s):  
Julien Baerenzung ◽  
Matthias Holschneider
Keyword(s):  
Geomagnetic Field ◽  
Learning Algorithm ◽  
Dynamical Evolution ◽  
Small Scale ◽  
Large Set ◽  
The Core ◽  
Resolution Model ◽  
Auto Regressive ◽  
Spatio Temporal ◽  
Marine Vessels

<p>We present a new high resolution model of the Geomagnetic field spanning the last 121 years. The model derives from a large set of data taken by low orbiting satellites, ground based observatories, marine vessels, airplane and during land surveys. It is obtained by combining a Kalman filter to a smoothing algorithm. Seven different magnetic sources are taken into account. Three of them are of internal origin. These are the core, the lithospheric  and the induced / residual ionospheric fields. The other four sources are of external origin. They are composed by a close, a remote and a fluctuating magnetospheric fields as well as a source associated with field aligned currents. The dynamical evolution of each source is prescribed by an auto regressive process of either first or second order, except for the lithospheric field which is assumed to be static. The parameters of the processes were estimated through a machine learning algorithm with a sample of data taken by the low orbiting satellites of the CHAMP and Swarm missions. In this presentation we will mostly focus on the rapid variations of the core field, and the small scale lithospheric field.  We will also discuss the nature of model uncertainties and the limitiations they imply.</p>

Effect of background clutter on neural discrimination in the bat auditory midbrain

2021 ◽  
Author(s):  
Kathryne M Allen ◽  
Angeles Salles ◽  
Sanwook Park ◽  
Mounya Elhilali ◽  
Cynthia F. Moss
Keyword(s):  
Acoustic Scattering ◽  
Object Discrimination ◽  
Complex Environments ◽  
Acoustic Features ◽  
Temporal Separation ◽  
Complex Sounds ◽  
Electrophysiological Recordings ◽  
Background Clutter ◽  
Spatio Temporal ◽  
Neural Underpinnings

The discrimination of complex sounds is a fundamental function of the auditory system. This operation must be robust in the presence of noise and acoustic clutter. Echolocating bats are auditory specialists that discriminate sonar objects in acoustically complex environments. Bats produce brief signals, interrupted by periods of silence, rendering echo snapshots of sonar objects. Sonar object discrimination requires that bats process spatially and temporally overlapping echoes to make split-second decisions. The mechanisms that enable this discrimination are not well understood, particularly in complex environments. We explored the neural underpinnings of sonar object discrimination in the presence of acoustic scattering caused by physical clutter. We performed electrophysiological recordings in the inferior colliculus of awake big brown bats, to broadcasts of pre-recorded echoes from physical objects. We acquired single unit responses to echoes and discovered a sub-population of IC neurons that encode acoustic features that can be used to discriminate between sonar objects. We further investigated the effects of environmental clutter on this population's encoding of acoustic features. We discovered that the effect of background clutter on sonar object discrimination is highly variable and depends on object properties and target-clutter spatio-temporal separation. In many conditions, clutter impaired discrimination of sonar objects. However, in some instances clutter enhanced acoustic features of echo returns, enabling higher levels of discrimination. This finding suggests that environmental clutter may augment acoustic cues used for sonar target discrimination and provides further evidence in a growing body of literature that noise is not universally detrimental to sensory encoding.

scholarly journals Spatio-temporal patterns and movement analysis of pigs from smallholder farms and implications for African swine fever spread, Limpopo province, South Africa

2015 ◽  
Vol 82 (1) ◽  
Author(s):  
Folorunso O. Fasina ◽  
Japhta M. Mokoele ◽  
B. Tom Spencer ◽  
Leo A.M.L. Van Leengoed ◽  
Yvette Bevis ◽  
...  
Keyword(s):  
South Africa ◽  
Smallholder Farmers ◽  
Animal Health ◽  
African Swine Fever ◽  
Limpopo Province ◽  
Small Scale ◽  
Network Analyses ◽  
Critical Control Points ◽  
Spatio Temporal ◽  
Disease Dispersal

Infectious and zoonotic disease outbreaks have been linked to increasing volumes of legal and illegal trade. Spatio-temporal and trade network analyses have been used to evaluate the risks associated with these challenges elsewhere, but few details are available for the pig sector in South Africa. Regarding pig diseases, Limpopo province is important as the greater part of the province falls within the African swine fever control area. Emerging small-scale pig farmers in Limpopo perceived pig production as an important means of improving their livelihood and an alternative investment. They engage in trading and marketing their products with a potential risk to animal health, because the preferred markets often facilitate potential longdistance spread and disease dispersal over broad geographic areas. In this study, we explored the interconnectedness of smallholder pig farmers in Limpopo, determined the weaknesses and critical control points, and projected interventions that policy makers can implement to reduce the risks to pig health. The geo-coordinates of surveyed farms were used to draw maps, links and networks. Predictive risks to pigs were determined through the analyses of trade networks, and the relationship to previous outbreaks of African swine fever was postulated. Auction points were identified as high-risk areas for the spread of animal diseases. Veterinary authorities should prioritise focused surveillance and diagnostic efforts in Limpopo. Early disease detection and prompt eradication should be targeted and messages promoting enhanced biosecurity to smallholder farmers are advocated. The system may also benefit from the restructuring of marketing and auction networks. Since geographic factors and networks can rapidly facilitate pig disease dispersal over large areas, a multi-disciplinary approach to understanding the complexities that exist around the animal disease epidemiology becomes mandatory.

scholarly journals CAL-1 as Cellular Model System to Study CCR7-Guided Human Dendritic Cell Migration

2021 ◽  
Vol 12 ◽  
Author(s):  
Edith Uetz-von Allmen ◽  
Guerric P. B. Samson ◽  
Vladimir Purvanov ◽  
Takahiro Maeda ◽  
Daniel F. Legler
Keyword(s):  
T Cell ◽  
Cell Line ◽  
Neoplastic Cell ◽  
Model System ◽  
Model Systems ◽  
Cellular Model ◽  
Gm Csf ◽  
Endogenous Expression ◽  
Dendritic Cell Migration ◽  
Spatio Temporal

Dendritic cells (DCs) are potent and versatile professional antigen-presenting cells and central for the induction of adaptive immunity. The ability to migrate and transport peripherally acquired antigens to draining lymph nodes for subsequent cognate T cell priming is a key feature of DCs. Consequently, DC-based immunotherapies are used to elicit tumor-antigen specific T cell responses in cancer patients. Understanding chemokine-guided DC migration is critical to explore DCs as cellular vaccines for immunotherapeutic approaches. Currently, research is hampered by the lack of appropriate human cellular model systems to effectively study spatio-temporal signaling and CCR7-driven migration of human DCs. Here, we report that the previously established human neoplastic cell line CAL-1 expresses the human DC surface antigens CD11c and HLA-DR together with co-stimulatory molecules. Importantly, if exposed for three days to GM-CSF, CAL-1 cells induce the endogenous expression of the chemokine receptor CCR7 upon encountering the clinically approved TLR7/8 agonist Resiquimod R848 and readily migrate along chemokine gradients. Further, we demonstrate that CAL-1 cells can be genetically modified to express fluorescent (GFP)-tagged reporter proteins to study and visualize signaling or can be gene-edited using CRISPR/Cas9. Hence, we herein present the human CAL-1 cell line as versatile and valuable cellular model system to effectively study human DC migration and signaling.

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