scholarly journals Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Natalie M Clark ◽  
Elizabeth Hinde ◽  
Cara M Winter ◽  
Adam P Fisher ◽  
Giuseppe Crosti ◽  
...  
Keyword(s):  
Steady State ◽  
Cell Fate ◽  
Protein Interactions ◽  
Temporal Dynamics ◽  
Quantitative Information ◽  
Correlation Spectroscopy ◽  
Oligomeric State ◽  
Downstream Target ◽  
Regulatory Processes ◽  
Spatio Temporal

To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction with its downstream target SCARECROW (SCR) control root patterning and cell fate specification. However, quantitative information about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction is currently unavailable. Here, we quantify parameters including SHR mobility, oligomeric state, and association with SCR using a combination of Fluorescent Correlation Spectroscopy (FCS) techniques. We then incorporate these parameters into a mathematical model of SHR and SCR, which shows that SHR reaches a steady state in minutes, while SCR and the SHR-SCR complex reach a steady-state between 18 and 24 hr. Our model reveals the timing of SHR and SCR dynamics and allows us to understand how protein movement and protein-protein stoichiometry contribute to development.

scholarly journals Fluctuations as a source of information in fluorescence microscopy

2008 ◽  
Vol 6 (suppl_1) ◽  
Author(s):  
Zdeněk Petrášek ◽  
Petra Schwille
Keyword(s):  
Single Molecule ◽  
Single Point ◽  
Quantitative Information ◽  
Correlation Spectroscopy ◽  
Image Correlation ◽  
Photon Detection ◽  
Fluorescence Correlation ◽  
Additional Information ◽  
Image Correlation Spectroscopy ◽  
Spatio Temporal

Fluctuations in fluorescence spectroscopy and microscopy have traditionally been regarded as noise—they lower the resolution and contrast and do not permit high acquisition rates. However, fluctuations can also be used to gain additional information about a system. This fact has been exploited in single-point microscopic techniques, such as fluorescence correlation spectroscopy and analysis of single molecule trajectories, and also in the imaging field, e.g. in spatio-temporal image correlation spectroscopy. Here, we discuss how fluctuations are used to obtain more quantitative information from the data than that given by average values, while minimizing the effects of noise due to stochastic photon detection.

scholarly journals Dynamic changes in Sox2 spatio-temporal expression promote the second cell fate decision through Fgf4/Fgfr2 signaling in preimplantation mouse embryos

2018 ◽  
Vol 475 (6) ◽  
pp. 1075-1089 ◽  
Author(s):  
Tapan Kumar Mistri ◽  
Wibowo Arindrarto ◽  
Wei Ping Ng ◽  
Choayang Wang ◽  
Leng Hiong Lim ◽  
...  
Keyword(s):  
Cell Fate ◽  
Target Genes ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Correlation Spectroscopy ◽  
Binding Interaction ◽  
Regulatory Motifs ◽  
Sox2 Expression ◽  
Spatio Temporal ◽  
Fate Decision

Oct4 and Sox2 regulate the expression of target genes such as Nanog, Fgf4, and Utf1, by binding to their respective regulatory motifs. Their functional cooperation is reflected in their ability to heterodimerize on adjacent cis regulatory motifs, the composite Sox/Oct motif. Given that Oct4 and Sox2 regulate many developmental genes, a quantitative analysis of their synergistic action on different Sox/Oct motifs would yield valuable insights into the mechanisms of early embryonic development. In the present study, we measured binding affinities of Oct4 and Sox2 to different Sox/Oct motifs using fluorescence correlation spectroscopy. We found that the synergistic binding interaction is driven mainly by the level of Sox2 in the case of the Fgf4 Sox/Oct motif. Taking into account Sox2 expression levels fluctuate more than Oct4, our finding provides an explanation on how Sox2 controls the segregation of the epiblast and primitive endoderm populations within the inner cell mass of the developing rodent blastocyst.

Spatio-temporal dynamics near the steady state of a planktonic system

2018 ◽  
Vol 75 (12) ◽  
pp. 4490-4504 ◽  
Author(s):  
Tonghua Zhang ◽  
Xia Liu ◽  
Xinzhu Meng ◽  
Tongqian Zhang
Keyword(s):  
Steady State ◽  
Temporal Dynamics ◽  
Spatio Temporal

Local meteorological conditions, dynamics of seroconversion to Toxoplasma gondii in cats (Felis catus) and oocyst burden in a rural environment

2009 ◽  
Vol 138 (8) ◽  
pp. 1105-1113 ◽  
Author(s):  
E. AFONSO ◽  
P. THULLIEZ ◽  
E. GILOT-FROMONT
Keyword(s):  
Toxoplasma Gondii ◽  
Temporal Dynamics ◽  
Temporal Distribution ◽  
Quantitative Information ◽  
Spatial And Temporal Variability ◽  
Local Conditions ◽  
Modified Agglutination Test ◽  
Incidence Risk ◽  
Spatio Temporal ◽  
Study Sites

SUMMARYThe aim of this study was to analyse the spatio-temporal dynamics of Toxoplasma gondii infection in long-term monitoring of domestic cats (8–15 years) in three populations living in rural France. Overall seroprevalence was 52·7% (modified agglutination test ⩾1:40). Incidence was 0·26–0·39 seroconversions/cat per year, and the estimated rate of soil contamination by T. gondii oocysts ranged between 31 and 3600 oocysts/m2 per year, depending on the population. Incidence risk in cats was related to mean precipitation, explaining both the spatial and temporal variability in risk: local conditions explained differences between the three study sites and incidence risk increased during rainy years. This study brings rare quantitative information on the level of contamination of the environment by T. gondii oocysts, and suggests that the spatio-temporal distribution of incidence risk in cats may reflect both the influence of rain on prey populations and infectivity of T. gondii oocysts.

scholarly journals The dynamics of reading complex words: evidence from steady-state visual evoked potentials

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Elisabeth Beyersmann ◽  
Veronica Montani ◽  
Johannes C. Ziegler ◽  
Jonathan Grainger ◽  
Ivilin Peev Stoianov
Keyword(s):  
Steady State ◽  
Evoked Potentials ◽  
Visual Evoked Potentials ◽  
Temporal Dynamics ◽  
Naming Task ◽  
Activation Pattern ◽  
Different Types ◽  
Spatio Temporal ◽  
Complex Words ◽  
Visual Evoked

AbstractThe present study used steady-state visual evoked potentials (SSVEPs) to examine the spatio-temporal dynamics of reading morphologically complex words and test the neurophysiological activation pattern elicited by stems and suffixes. Three different types of target words were presented to proficient readers in a delayed naming task: truly suffixed words (e.g., farmer), pseudo-suffixed words (e.g., corner), and non-suffixed words (e.g., cashew). Embedded stems and affixes were flickered at two different frequencies (18.75 Hz and 12.50 Hz, respectively). The stem data revealed an earlier SSVEP peak in the truly suffixed and pseudo-suffixed conditions compared to the non-suffixed condition, thus providing evidence for the form-based activation of embedded stems during reading. The suffix data also showed a dissociation in the SSVEP response between suffixes and non-suffixes with an additional activation boost for truly suffixed words. The observed differences are discussed in the context of current models of complex word recognition.

scholarly journals Nonlinear dynamics of core-annular film flows in the presence of surfactant

2009 ◽  
Vol 626 ◽  
pp. 415-448 ◽  
Author(s):  
S. A. KAS-DANOUCHE ◽  
D. T. PAPAGEORGIOU ◽  
M. SIEGEL
Keyword(s):  
Steady State ◽  
Evolution Equations ◽  
Temporal Dynamics ◽  
Travelling Waves ◽  
Coupled System ◽  
Travelling Wave ◽  
Nonlinear Evolution Equations ◽  
Two Phase ◽  
Spatio Temporal ◽  
Time Periodic

The nonlinear stability of two-phase core-annular flow in a cylindrical pipe is studied. A constant pressure gradient drives the flow of two immiscible liquids of different viscosities and equal densities, and surface tension acts at the interface separating the phases. Insoluble surfactants are included, and we assess their effect on the flow stability and ensuing spatio-temporal dynamics. We achieve this by developing an asymptotic analysis in the limit of a thin annular layer – which is usually the relevant regime in applications – to derive a coupled system of nonlinear evolution equations that govern the dynamics of the interface and the local surfactant concentration on it. In the absence of surfactants the system reduces to the Kuramoto–Sivashinsky (KS) equation, and its modifications due to viscosity stratification (present when the phases have unequal viscosities) are derived elsewhere. We report on extensive numerical experiments to evaluate the effect of surfactants on KS dynamics (including chaotic states, for example), in both the absence and the presence of viscosity stratification. We find that chaos is suppressed in the absence of viscosity differences and that the new flow consists of successive windows (in parameter space) of steady-state travelling waves separated by time-periodic attractors. The intricate structure of the travelling pulses is also explained physically. When viscosity stratification is present we observe a transition from time-periodic dynamics, for instance, to steady-state travelling wave pulses of increasing amplitudes and speeds. Numerical evidence is presented that indicates that the transition occurs through a reverse Feigenbaum cascade in phase space.

scholarly journals Dynamic changes in Sox2 spatio-temporal expression direct the second cell fate decision throughFgf4/Fgfr2signaling in preimplantation mouse embryos

2016 ◽  
Author(s):  
Tapan Kumar Mistri ◽  
Wibowo Arindrarto ◽  
Wei Ping Ng ◽  
Choayang Wang ◽  
Leng Hiong Lim ◽  
...  
Keyword(s):  
Cell Fate ◽  
Target Genes ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Regulatory Elements ◽  
Correlation Spectroscopy ◽  
Binding Interaction ◽  
Preimplantation Mouse ◽  
Spatio Temporal ◽  
Fate Decision

ABSTRACTOct4 and Sox2 regulate the expression of target genes such asNanog, Fgf4andUtf1, by binding to their respective regulatory motifs. Their functional cooperation is reflected in their ability to heterodimerise on adjacentcisregulatory elements, the composite Sox/Oct motif. Given that Oct4 and Sox2 regulate many developmental genes, a quantitative analysis of their synergistic action on different Sox/Oct motifs would yield valuable insights into the mechanisms of early embryonic development. In this study, we measured binding affinities of Oct4 and Sox2 to different Sox/Oct motifs using fluorescence correlation spectroscopy (FCS). We found that the synergistic binding interaction is driven mainly by the level of Sox2 in the case of theFgf4Sox/Oct motif. Taking into accountSox2expression levels fluctuate more thanOct4, our finding provides an explanation on how Sox2 controls the segregation of the epiblast (EPI) and primitive endoderm (PE) populations within the inner cell mass (ICM) of the developing rodent blastocyst.

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