scholarly journals TipQAD: an automated tool for quantifying apical fluorescence dynamics in tip-growing cells

2020 ◽  
Author(s):  
Asongu L. Tambo ◽  
Bir Bhanu ◽  
Nan Luo ◽  
Duoyan Rong ◽  
Fei Wang ◽  
...  

ABSTRACTCell polarity is a fundamental property essential for the function and development of all cellular organisms. Tip growth is an extreme form of polar growth requiring spatiotemporally dynamic but highly coordinated cellular activities. Quantification of these dynamic activities is important for the systematic study of the mechanisms controlling cell polarity, but an automated and unbiased method for analyzing and quantification of tip-growing cells has been missing. In this paper, we developed a computational model and an associated tool called TipQAD for quantifying the spatiotemporal dynamics of fluorescence protein (FP) labeled molecules or structures in tip-growing cells. This tool robustly and accurately measured the spatial distribution and temporal dynamics of FP-labeled proteins in the cytoplasm or the plasma membrane at the tip region of several types of tip-growing cells. We also demonstrated its ability to analyze data from FRAP experiments. In conclusion, this tool showed great potential for automated measurements of the spatiotemporal dynamics of fluorescent-labeled cellular molecules and structures.

2016 ◽  
Vol 199 (1) ◽  
Author(s):  
Katsuya Fuchino ◽  
Klas Flärdh ◽  
Paul Dyson ◽  
Nora Ausmees

ABSTRACT Most bacteria are likely to face osmotic challenges, but there is yet much to learn about how such environmental changes affect the architecture of bacterial cells. Here, we report a cell-biological study in model organisms of the genus Streptomyces, which are actinobacteria that grow in a highly polarized fashion to form branching hyphae. The characteristic apical growth of Streptomyces hyphae is orchestrated by protein assemblies, called polarisomes, which contain coiled-coil proteins DivIVA and Scy, and recruit cell wall synthesis complexes and the stress-bearing cytoskeleton of FilP to the tip regions of the hyphae. We monitored cell growth and cell-architectural changes by time-lapse microscopy in osmotic upshift experiments. Hyperosmotic shock caused arrest of growth, loss of turgor, and hypercondensation of chromosomes. The recovery period was protracted, presumably due to the dehydrated state of the cytoplasm, before hyphae could restore their turgor and start to grow again. In most hyphae, this regrowth did not take place at the original hyphal tips. Instead, cell polarity was reprogrammed, and polarisomes were redistributed to new sites, leading to the emergence of multiple lateral branches from which growth occurred. Factors known to regulate the branching pattern of Streptomyces hyphae, such as the serine/threonine kinase AfsK and Scy, were not involved in reprogramming of cell polarity, indicating that different mechanisms may act under different environmental conditions to control hyphal branching. Our observations of hyphal morphology during the stress response indicate that turgor and sufficient hydration of cytoplasm are required for Streptomyces tip growth. IMPORTANCE Polar growth is an intricate manner of growth for accomplishing a complicated morphology, employed by a wide range of organisms across the kingdoms of life. The tip extension of Streptomyces hyphae is one of the most pronounced examples of polar growth among bacteria. The expansion of the cell wall by tip extension is thought to be facilitated by the turgor pressure, but it was unknown how external osmotic change influences Streptomyces tip growth. We report here that severe hyperosmotic stress causes cessation of growth, followed by reprogramming of cell polarity and rearrangement of growth zones to promote lateral hyphal branching. This phenomenon may represent a strategy of hyphal organisms to avoid osmotic stress encountered by the growing hyphal tip.


Author(s):  
Ekaterina Maksimova ◽  
Ekaterina Maksimova ◽  
Vladimir Zhigulsky ◽  
Vladimir Zhigulsky ◽  
Vladimir Shuisky ◽  
...  

The macrophyte thicket ecosystems of higher aquatic vegetation in the Neva Bay (NB) and Eastern Gulf of Finland (EGoF) perform many important roles, including acting as the habitats, nesting sites and migration sites for aquatic and semi-aquatic birds, creating the specific conditions necessary for the spawning and growth of many species of fish, and taking part in the self-purification of the aquatic ecosystems. Many anthropogenic disturbances, hydraulic works in particular, have a significant negative impact on these macrophyte thicket ecosystems. In recent years, the active growth of a new type of macrophyte thicket has been observed in the NB. This is due to the aftereffects of the construction of the Saint Petersburg Flood Prevention Facility Complex (FPFC). It is quite likely that the total macrophyte thicket area in these waters is currently increasing. In the future, it will be necessary to assess the environmental impacts of the hydraulic works on the macrophyte thicket of the NB and EGoF, taking into account the background processes of the spatiotemporal dynamics of the reed beds in the waters in question. To do this, it will be necessary to carry out a comprehensive study of these ecosystems and identify patterns in their spatial and temporal dynamics. The program of the study has been developed and is currently being implemented by Eco-Express-Service, a St. Petersburg eco-design company.


2017 ◽  
Vol 74 (11) ◽  
pp. 1845-1861 ◽  
Author(s):  
Matthew V. Lauretta ◽  
Daniel R. Goethel

The development of a reliable tagging program requires simulation testing the experimental design. However, the potential for model misspecification, particularly in the underlying spatiotemporal dynamics, is often ignored. A continuous time, spatially explicit, age-structured, capture–recapture operating model was developed to better emulate real-world population dynamics typically overlooked in spatially aggregated or discrete time tagging models. Various spatiotemporal model parametrizations, including case studies with Atlantic bluefin tuna (Thunnus thynnus) and yellowfin tuna (Thunnus albacares), were explored to evaluate the bias associated with Brownie tag return estimation models. Simulations demonstrated that accounting for connectivity was essential for obtaining unbiased parameter estimates and that migration rates could be reliably estimated without the correlation associated with other parameters (e.g., between tag reporting and mortality). Mortality parameter estimates were particularly sensitive to the temporal dynamics of the tagging and fishing seasons, but accounting for the seasonality in tag releases and fishery recaptures allowed for relatively unbiased estimation. Our results indicate that parameter bias and uncertainty can be severely underestimated when discrete time or spatially aggregated operating models are used to determine optimal experimental design of tagging studies.


2009 ◽  
Vol 99 (8) ◽  
pp. 974-984 ◽  
Author(s):  
Jonas Franke ◽  
Steffen Gebhardt ◽  
Gunter Menz ◽  
Hans-Peter Helfrich

Plant diseases are dynamic systems that progress or regress in spatial and temporal dimensions. Site-specific or temporally optimized disease control requires profound knowledge about the development of each stressor. The spatiotemporal dynamics of leaf rust (Puccinia recondite f. sp. tritici) and powdery mildew (Blumeria graminis f. sp. tritici) in wheat was analyzed in order to evaluate typical species-dependent characteristics of disease spread. During two growing seasons, severity data and other relevant plant growth parameters were collected in wheat fields. Spatial characteristics of both diseases were assessed by cluster analyses using spatial analysis by distance indices, whereas the temporal epidemic trends were assessed using statistical parameters. Multivariate statistics were used to identify parameters suitable for characterizing disease trends into four classes of temporal dynamics. The results of the spatial analysis showed that both diseases generally occurred in patches but a differentiation between the diseases by their spatial patterns and spread was not possible. In contrast, temporal characteristics allowed for a differentiation of the diseases, due to the fact that a typical trend was found for leaf rust which differed from the trend of powdery mildew. Therefore, these trends suggested a high potential for temporally optimized disease control. Precise powdery mildew control would be more complicated due to the observed high variability in spatial and temporal dynamics. The general results suggest that, in spite of the high variability in spatiotemporal dynamics, disease control that is optimized in space and time is generally possible but requires consideration of disease- and case-dependent characteristics.


2021 ◽  
Author(s):  
Gargi Majumdar ◽  
Fahd Yazin ◽  
Arpan Banerjee ◽  
Dipanjan Roy

What fundamental property of our environment would be most valuable and optimal in characterizing the emotional dynamics we experience in our daily life? Empirical work has shown that an accurate estimation of uncertainty is necessary for our optimal perception, learning, and decision-making. However, the role of this uncertainty in governing our affective dynamics remains unexplored. Using Bayesian encoding, decoding and computational modelling, we show that emotional experiences naturally arise due to ongoing uncertainty estimations in a hierarchical neural architecture. This hierarchical organization involves a number of prefrontal sub-regions, with the lateral orbitofrontal cortex having the highest representational complexity of uncertainty. Crucially, this representational complexity, was sensitive to temporal fluctuations in uncertainty and was predictive of participants predisposition to anxiety. Furthermore, the temporal dynamics of uncertainty revealed a distinct functional double dissociation within the OFC. Specifically, the medial OFC showed higher connectivity with the DMN, while the lateral OFC with that of the FPN in response to the evolving affect. Finally, we uncovered a temporally predictive code updating individual beliefs swiftly in the face of fluctuating uncertainty in the lateral OFC. A biologically relevant and computationally crucial parameter in theories of brain function, we extend uncertainty to be a defining component of complex emotions.


Author(s):  
Ekaterina Maksimova ◽  
Ekaterina Maksimova ◽  
Vladimir Zhigulsky ◽  
Vladimir Zhigulsky ◽  
Vladimir Shuisky ◽  
...  

The macrophyte thicket ecosystems of higher aquatic vegetation in the Neva Bay (NB) and Eastern Gulf of Finland (EGoF) perform many important roles, including acting as the habitats, nesting sites and migration sites for aquatic and semi-aquatic birds, creating the specific conditions necessary for the spawning and growth of many species of fish, and taking part in the self-purification of the aquatic ecosystems. Many anthropogenic disturbances, hydraulic works in particular, have a significant negative impact on these macrophyte thicket ecosystems. In recent years, the active growth of a new type of macrophyte thicket has been observed in the NB. This is due to the aftereffects of the construction of the Saint Petersburg Flood Prevention Facility Complex (FPFC). It is quite likely that the total macrophyte thicket area in these waters is currently increasing. In the future, it will be necessary to assess the environmental impacts of the hydraulic works on the macrophyte thicket of the NB and EGoF, taking into account the background processes of the spatiotemporal dynamics of the reed beds in the waters in question. To do this, it will be necessary to carry out a comprehensive study of these ecosystems and identify patterns in their spatial and temporal dynamics. The program of the study has been developed and is currently being implemented by Eco-Express-Service, a St. Petersburg eco-design company.


2000 ◽  
Vol 113 (3) ◽  
pp. 365-375 ◽  
Author(s):  
D. Pruyne ◽  
A. Bretscher

The ability to polarize is a fundamental property of cells. The yeast Saccharomyces cerevisiae has proven to be a fertile ground for dissecting the molecular mechanisms that regulate cell polarity during growth. Here we discuss the signaling pathways that regulate polarity. In the second installment of this two-part commentary, which appears in the next issue of Journal of Cell Science, we discuss how the actin cytoskeleton responds to these signals and guides the polarity of essentially all events in the yeast cell cycle. During the cell cycle, yeast cells assume alternative states of polarized growth, which range from tightly focused apical growth to non-focused isotropic growth. RhoGTPases, and in particular Cdc42p, are essential to guiding this polarity. The distribution of Cdc42p at the cell cortex establishes cell polarity. Cyclin-dependent protein kinase, Ras, and heterotrimeric G proteins all modulate yeast cell polarity in part by altering the distribution of Cdc42p. In turn, Cdc42p generates feedback signals to these molecules in order to establish stable polarity states and coordinate cytoskeletal organization with the cell cycle. Given that many of these signaling pathways are present in both fungi and animals, they are probably ancient and conserved mechanisms for regulating polarity.


2015 ◽  
Vol 264 ◽  
pp. 145
Author(s):  
Peter Rashkov ◽  
Bernhard A. Schmitt ◽  
Daniela Keilberg ◽  
Lotte Søgaard-Andersen ◽  
Stephan Dahlke

2019 ◽  
Author(s):  
Razan N. Alnahhas ◽  
James J. Winkle ◽  
Andrew J. Hirning ◽  
Bhargav Karamched ◽  
William Ott ◽  
...  

AbstractSynthetic microbial consortia consist of two or more engineered strains that grow together and share the same resources. When intercellular signaling pathways are included in the engineered strains, close proximity of the microbes can generate complex dynamic behaviors that are difficult to obtain using a single strain. However, when a consortium is not cultured in a well-mixed environment the constituent strains passively compete for space as they grow and divide, complicating cell-cell signaling. Here, we explore the temporal dynamics of the spatial distribution of consortia co-cultured in microfluidic devices. To do this, we grew two different strains ofEscherichia coliin microfluidic devices with cell-trapping regions (traps) of several different designs. We found that the size and shape of the traps are critical determinants of spatiotemporal dynamics. In small traps, cells can easily signal one another but the relative proportion of each strain within the trap can fluctuate wildly. In large traps, the relative ratio of strains is stabilized, but intercellular signaling can be hindered by distances between cells. This presents a trade-off between the trap size and the effectiveness of intercellular signaling, which can be mitigated by controlling the initial seeding of cells in the large trap. These results show how synthetic microbial consortia behave in microfluidic traps and provide a method to help remedy the spatial heterogeneity inherent to different trap geometries.


Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Alexander R Lyon ◽  
Jaeho Park ◽  
Lifan Liang ◽  
Roger J Hajjar ◽  
Fadi G Akar

The peripheral type benzodiazepine receptor (mBZR) is a key mediator of mitochondrial dysfunction during oxidative stress. In isolated cardiomyocytes agonists of the mBZR cause ΔΨ m depolarization, KATP channel activation, and subsequent loss of cellular excitability. However, the spatiotemporal dynamics of ΔΨ m in the intact heart and their relationship to arrhythmias are unknown. Here, we investigate the mechanistic link between mBZR and ΔΨ m directly using adenoviral mediated gene transfer of the mBZR encoding gene (PKBS) in rat myocardium. Methods : Optical imaging was performed at a subcellular resolution in ex vivo perfused hearts from AdPKBS (n=5), AdGFP (n=2), and normal (n=4) rats. Normalized ΔΨ m was measured using a novel quantitative technique of TMRM imaging during global ischemia (7.5 min) followed by reperfusion. Mean and SD of baseline corrected & normalized ΔΨ m across 6400 sites were compared between groups. Results : In sharp contrast to normal and GFP groups, 4 of 5 PKBS hearts exhibited a paradoxical increase in ΔΨ m during ischemia (Fig A ) as ΔΨ m was significantly (p<0.05) greater in PKBS (+0.18±0.07) compared to GFP (−0.62±0.21) and normal hearts (−0.17±0.16) following 7.5min of ischemia. A transient overshoot in ΔΨ m observed in all groups during early (<30sec) reperfusion was greatest in PKBS hearts (Fig A ). Finally, ΔΨ m heterogeneity indexed by SD was markedly greater in PKBS compared to GFP and normal hearts during ischemia (p<0.01) and reperfusion (p<0.01) (Fig B ). Conclusion : PKBS alters spatiotemporal dynamics of ΔΨ m and increases ΔΨ m heterogeneity across the intact heart. Modulating PKBS expression may be a novel therapeutic strategy for arrhythmias. Figure 1. Influence of PKBS gene transfer on myocardial ΔΨm during ischemia and reperfusion. Mean myocardial ΔΨm ( A ) and spatial Δψm heteroogeneity ( B ) during ischemia and reperfusion.


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