Sources of variability in cytosolic calcium transients triggered by stimulation of homogeneous uro-epithelial cell monolayers

Epithelial tissue structure is the emergent outcome of the interactions between large numbers of individual cells. Experimental cell biology offers an important tool to unravel these complex interactions, but current methods of analysis tend to be limited to mean field approaches or representation by selected subsets of cells. This may result in bias towards cells that respond in a particular way and/or neglect local, context-specific cell responses. Here, an automated algorithm was applied to examine in detail the individual calcium transients evoked in genetically homogeneous, but asynchronous populations of cultured non-immortalized normal human urothelial cells when subjected to either the global application of an external agonist or a localized scratch wound. The recorded calcium transients were classified automatically according to a set of defined metrics and distinct sub-populations of cells that responded in qualitatively different ways were observed. The nature of this variability in the homogeneous cell population was apportioned to two sources: intrinsic variation in individual cell responses and extrinsic variability due to context-specific factors of the environment, such as spatial heterogeneity. Statistically significant variation in the features of the calcium transients evoked by scratch wounding according to proximity to the wound edge was identified. The manifestation of distinct sub-populations of cells is considered central to the coordination of population-level response resulting in wound closure.

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A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes

10.1101/112201 ◽

2017 ◽

Author(s):

Jens Hansen ◽

David Meretzky ◽

Simeneh Woldesenbet ◽

Gustavo Stolovitzky ◽

Ravi Iyengar

Keyword(s):

Cell Biology ◽

Cell Function ◽

Biological Knowledge ◽

Dependent Manner ◽

Whole Cell ◽

Cell Functions ◽

Cell Responses ◽

Growing Cell ◽

Cell Ontology ◽

Context Specific

AbstractWhole cell responses arise from coordinated interactions between diverse human gene products functioning within various pathways underlying sub-cellular processes (SCP). Lower level SCPs interact to form higher level SCPs, often in a context specific manner to give rise to whole cell function. We sought to determine if capturing such relationships enables us to describe the emergence of whole cell functions from interacting SCPs. We developed the “Molecular Biology of the Cell” ontology based on standard cell biology and biochemistry textbooks and review articles. Currently, our ontology contains 5,385 genes, 753 SCPs and 19,180 expertly curated gene-SCP associations. Our algorithm to populate the SCPs with genes enables extension of the ontology on demand and the adaption of the ontology to the continuously growing cell biological knowledge. Since whole cell responses most often arise from the coordinated activity of multiple SCPs, we developed a dynamic enrichment algorithm that flexibly predicts SCP-SCP relationships beyond the current taxonomy. This algorithm enables us to identify interactions between SCPs as a basis for higher order function in a context dependent manner, allowing us to provide a detailed description of how SCPs together can give rise to whole cell functions. We conclude that this ontology can, from omics data sets, enable the development of detailed multidimensional SCP networks for predictive modeling of emergent whole cell functions.

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Spatial moment description of birth-death-movement processes incorporating the effects of crowding and obstacles

10.1101/267708 ◽

2018 ◽

Author(s):

Anudeep Surendran ◽

Michael J. Plank ◽

Matthew J. Simpson

Keyword(s):

Spatial Structure ◽

Cell Biology ◽

Mean Field ◽

Population Level ◽

Individual Level ◽

Spatial Moment ◽

Motile Cells ◽

Stationary Obstacles ◽

Birth Death

AbstractBirth-death-movement processes, modulated by interactions between individuals, are fundamental to many cell biology processes. A key feature of the movement of cells within in vivo environments are the interactions between motile cells and stationary obstacles. Here we propose a multi-species model of individual-level motility, proliferation and death. This model is a spatial birth-death-movement stochastic process, a class of individual-based model (IBM) that is amenable to mathematical analysis. We present the IBM in a general multi-species framework, and then focus on the case of a population of motile, proliferative agents in an environment populated by stationary, non-proliferative obstacles. To analyse the IBM, we derive a system of spatial moment equations governing the evolution of the density of agents and the density of pairs of agents. This approach avoids making the usual mean-field assumption so that our models can be used to study the formation of spatial structure, such as clustering and aggregation, and to understand how spatial structure influences population-level outcomes. Overall the spatial moment model provides a reasonably accurate prediction of the system dynamics, including important effects such as how varying the properties of the obstacles leads to different spatial patterns in the population of agents.

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Faculty Opinions recommendation of Reorientation of seedlings in the earth's gravitational field induces cytosolic calcium transients.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1007177.89555 ◽

2002 ◽

Author(s):

Patrick Masson

Keyword(s):

Gravitational Field ◽

Cytosolic Calcium ◽

Calcium Transients ◽

Earth’S Gravitational Field

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PDE limits of stochastic SIS epidemics on networks

Journal of Complex Networks ◽

10.1093/comnet/cnaa043 ◽

2020 ◽

Vol 8 (4) ◽

Author(s):

F Di Lauro ◽

J-C Croix ◽

L Berthouze ◽

I Z Kiss

Keyword(s):

Network Inference ◽

Mean Field ◽

Population Level ◽

Death Process ◽

Disease Dynamics ◽

Epidemic Outbreak ◽

Numerical Tests ◽

Mean Field Models ◽

Stochastic Epidemic ◽

Fokker Planck Equations

Abstract Stochastic epidemic models on networks are inherently high-dimensional and the resulting exact models are intractable numerically even for modest network sizes. Mean-field models provide an alternative but can only capture average quantities, thus offering little or no information about variability in the outcome of the exact process. In this article, we conjecture and numerically demonstrate that it is possible to construct partial differential equation (PDE)-limits of the exact stochastic susceptible-infected-susceptible epidemics on Regular, Erdős–Rényi, Barabási–Albert networks and lattices. To do this, we first approximate the exact stochastic process at population level by a Birth-and-Death process (BD) (with a state space of $O(N)$ rather than $O(2^N)$) whose coefficients are determined numerically from Gillespie simulations of the exact epidemic on explicit networks. We numerically demonstrate that the coefficients of the resulting BD process are density-dependent, a crucial condition for the existence of a PDE limit. Extensive numerical tests for Regular, Erdős–Rényi, Barabási–Albert networks and lattices show excellent agreement between the outcome of simulations and the numerical solution of the Fokker–Planck equations. Apart from a significant reduction in dimensionality, the PDE also provides the means to derive the epidemic outbreak threshold linking network and disease dynamics parameters, albeit in an implicit way. Perhaps more importantly, it enables the formulation and numerical evaluation of likelihoods for epidemic and network inference as illustrated in a fully worked out example.

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Mouse embryonic stem cell-derived cardiomyocytes cease to beat following exposure to monochromatic light: association with increased ROS and loss of calcium transients

AJP Cell Physiology ◽

10.1152/ajpcell.00188.2019 ◽

2019 ◽

Vol 317 (4) ◽

pp. C725-C736

Author(s):

Gurbind Singh ◽

Divya Sridharan ◽

Mahmood Khan ◽

Polani B. Seshagiri

Keyword(s):

Cell Biology ◽

Fluorescent Protein ◽

Es Cells ◽

Monochromatic Light ◽

Embryonic Stem ◽

Mouse Embryonic Stem Cell ◽

Medical Diagnostics ◽

Calcium Transients ◽

Egfp Expression ◽

Mitochondrial Activity

We earlier established the mouse embryonic stem (ES) cell “GS-2” line expressing enhanced green fluorescent protein (EGFP) and have been routinely using it to understand the molecular regulation of differentiation into cardiomyocytes. During such studies, we made a serendipitous discovery that functional cardiomyocytes derived from ES cells stopped beating when exposed to blue light. We observed a gradual cessation of contractility within a few minutes, regardless of wavelength (nm) ranges tested: blue (~420–495), green (~510–575), and red (~600–700), with green light manifesting the strongest impact. Following shifting of cultures back into the incubator (darkness), cardiac clusters regained beatings within a few hours. The observed light-induced contractility-inhibition effect was intrinsic to cardiomyocytes and not due to interference from other cell types. Also, this was not influenced by any physicochemical parameters or intracellular EGFP expression. Interestingly, the light-induced cardiomyocyte contractility inhibition was accompanied by increased intracellular reactive oxygen species (ROS), which could be abolished in the presence of N-acetylcysteine (ROS quencher). Besides, the increased intracardiomyocyte ROS levels were incidental to the inhibition of calcium transients and suppression of mitochondrial activity, both being essential for sarcomere function. To the best of our knowledge, ours is the first report to demonstrate the monochromatic light-mediated inhibition of contractions of cardiomyocytes with no apparent loss of cell viability and contractility. Our findings have implications in cardiac cell biology context in terms of 1) mechanistic insights into light impact on cardiomyocyte contraction, 2) potential use in laser beam-guided (cardiac) microsurgery, photo-optics-dependent medical diagnostics, 3) transient cessation of hearts during coronary artery bypass grafting, and 4) functional preservation of hearts for transplantation.

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(Tissue) P systems with cell polarity

Mathematical Structures in Computer Science ◽

10.1017/s0960129509990156 ◽

2009 ◽

Vol 19 (6) ◽

pp. 1141-1160 ◽

Cited By ~ 2

Author(s):

DANIELA BESOZZI ◽

NADIA BUSI ◽

PAOLO CAZZANIGA ◽

CLAUDIO FERRETTI ◽

ALBERTO LEPORATI ◽

...

Keyword(s):

Cell Polarity ◽

Formal System ◽

Cell Junctions ◽

P Systems ◽

Intestinal Lumen ◽

Epithelial Tissue ◽

Specific Cell ◽

Formal Property ◽

Intestinal Epithelial ◽

Cell Cell

We consider the structure of the intestinal epithelial tissue and of cell–cell junctions as the biological model inspiring a new class of P systems. First we define the concept of cell polarity, a formal property derived from epithelial cells, which present morphologically and functionally distinct regions of the plasma membrane. Then we show two preliminary results for this new model of computation: on the theoretical side, we show that P systems with cell polarity are computationally (Turing) complete; on the modelling side, we show that the transepithelial movement of glucose from the intestinal lumen into the blood can be described by such a formal system. Finally, we define tissue P systems with cell polarity, where each cell has fixed connections to the neighbouring cells and to the environment, according to both the cell polarity and specific cell–cell junctions.

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COVID-19 guidance in humanitarian settings: The need for dynamic guidelines adapted to changing humanitarian crisis contexts

10.21203/rs.3.rs-625232/v1 ◽

2021 ◽

Author(s):

Alex Odlum ◽

Rosemary James ◽

Audrey Mahieu ◽

Karl Blanchet ◽

Chiara Altare ◽

...

Keyword(s):

Field Experiences ◽

Local Context ◽

Inclusion Criteria ◽

Structured Interviews ◽

Humanitarian Crisis ◽

Humanitarian Settings ◽

Complex Process ◽

Global Guidance ◽

Guidance Documents ◽

Context Specific

Abstract Background: For humanitarian organisations to respond effectively to complex crises, they require access to up-to-date evidence-based guidance. In addition, the COVID-19 crisis has highlighted the importance of adapting and updating global guidance to context-specific and evolving needs in fragile and humanitarian settings. Our study aimed to understand the use of evidence in humanitarian responses during COVID-19.Methods: We collected and analysed COVID-19 guidance documents, and conducted semi-structured interviews remotely with a variety of humanitarian organisations responding and adapting to the COVID-19 pandemic. We used the COVID-19 Humanitarian platform, a website established by three universities in March 2020, to solicit, collate and document these experiences and knowledge.Results: We collected 180 guidance documents, and after excluding those that did not meet our inclusion criteria, analysed 131. We conducted 80 interviews with humanitarian organisations in the field, generating 61 published field experiences. Although COVID-19 guidance was quickly developed and disseminated in the initial phases of the crisis (from January to May 2020), updates or ongoing revision of the guidance has been limited. Interviews conducted between April and September 2020 showed that humanitarian organisations have responded to COVID-19 in innovative and context-specific ways, but have often had to adapt existing guidance to inform their operations in complex humanitarian settings.Conclusion: Experiences from the field indicate that adopting guidance to respond and adapt to COVID-19 is a complex process requiring innovation and collaboration based on the local context and resource availability. Global guidance aimed at humanitarian actors could be improved through responsive incorporation of contextualised field experiences in a timely manner using real-time feedback loops through online platforms like the COVID-19 Humanitarian platform.

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Induction of Genotype Cross-Reactive, Hepatitis C Virus-Specific, Cell-Mediated Immunity in DNA-Vaccinated Mice

Journal of Virology ◽

10.1128/jvi.02133-17 ◽

2018 ◽

Vol 92 (8) ◽

pp. e02133-17 ◽

Cited By ~ 15

Author(s):

Danushka K. Wijesundara ◽

Jason Gummow ◽

Yanrui Li ◽

Wenbo Yu ◽

Benjamin J. Quah ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Dna Vaccine ◽

Target Cells ◽

Cell Mediated Immunity ◽

Specific Cell ◽

Universal Vaccine ◽

Cell Responses ◽

Single Genotype

ABSTRACTA universal hepatitis C virus (HCV) vaccine should elicit multiantigenic, multigenotypic responses, which are more likely to protect against challenge with the range of genotypes and subtypes circulating in the community. A vaccine cocktail and vaccines encoding consensus HCV sequences are attractive approaches to achieve this goal. Consequently, in a series of mouse vaccination studies, we compared the immunogenicity of a DNA vaccine encoding a consensus HCV nonstructural 5B (NS5B) protein to that of a cocktail of DNA plasmids encoding the genotype 1b (Gt1b) and Gt3a NS5B proteins. To complement this study, we assessed responses to a multiantigenic cocktail regimen by comparing a DNA vaccine cocktail encoding Gt1b and Gt3a NS3, NS4, and NS5B proteins to a single-genotype NS3/4/5B DNA vaccine. To thoroughly evaluatein vivocytotoxic T lymphocyte (CTL) and T helper (Th) cell responses against Gt1b and Gt3a HCV peptide-pulsed target cells, we exploited a novel fluorescent-target array (FTA). FTA and enzyme-linked immunosorbent spot (ELISpot) analyses collectively indicated that the cocktail regimens elicited higher responses to Gt1b and Gt3a NS5B proteins than those with the consensus vaccine, while the multiantigenic DNA cocktail significantly increased the responses to NS3 and NS5B compared to those elicited by the single-genotype vaccines. Thus, a DNA cocktail vaccination regimen is more effective than a consensus vaccine or a monovalent vaccine at increasing the breadth of multigenotypic T cell responses, which has implications for the development of vaccines for communities where multiple HCV genotypes circulate.IMPORTANCEDespite the development of highly effective direct-acting antivirals (DAA), infections with hepatitis C virus (HCV) continue, particularly in countries where the supply of DAA is limited. Furthermore, patients who eliminate the virus as a result of DAA therapy can still be reinfected. Thus, a vaccine for HCV is urgently required, but the heterogeneity of HCV strains makes the development of a universal vaccine difficult. To address this, we developed a novel cytolytic DNA vaccine which elicits robust cell-mediated immunity (CMI) to the nonstructural (NS) proteins in vaccinated animals. We compared the immune responses against genotypes 1 and 3 that were elicited by a consensus DNA vaccine or a DNA vaccine cocktail and showed that the cocktail induced higher levels of CMI to the NS proteins of both genotypes. This study suggests that a universal HCV vaccine can most readily be achieved by use of a DNA vaccine cocktail.

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