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Find video protocols related to scientific articles indexed in Pubmed.
A new tool to quantify receptor recruitment to cell contact sites during host-pathogen interaction.
PLoS Comput. Biol.
PUBLISHED: 05-01-2014
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To understand the process of innate immune fungal recognition, we developed computational tools for the rigorous quantification and comparison of receptor recruitment and distribution at cell-cell contact sites. We used these tools to quantify pattern recognition receptor spatiotemporal distributions in contacts between primary human dendritic cells and the fungal pathogens C. albicans, C. parapsilosis and the environmental yeast S. cerevisiae, imaged using 3D multichannel laser scanning confocal microscopy. The detailed quantitative analysis of contact sites shows that, despite considerable biochemical similarity in the composition and structure of these species' cell walls, the receptor spatiotemporal distribution in host-microbe contact sites varies significantly between these yeasts. Our findings suggest a model where innate immune cells discriminate fungal microorganisms based on differential mobilization and coordination of receptor networks. Our analysis methods are also broadly applicable to a range of cell-cell interactions central to many biological problems.
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Using hierarchical clustering and dendrograms to quantify the clustering of membrane proteins.
Bull. Math. Biol.
PUBLISHED: 06-03-2011
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Cell biologists have developed methods to label membrane proteins with gold nanoparticles and then extract spatial point patterns of the gold particles from transmission electron microscopy images using image processing software. Previously, the resulting patterns were analyzed using the Hopkins statistic, which distinguishes nonclustered from modestly and highly clustered distributions, but is not designed to quantify the number or sizes of the clusters. Clusters were defined by the partitional clustering approach which required the choice of a distance. Two points from a pattern were put in the same cluster if they were closer than this distance. In this study, we present a new methodology based on hierarchical clustering to quantify clustering. An intrinsic distance is computed, which is the distance that produces the maximum number of clusters in the biological data, eliminating the need to choose a distance. To quantify the extent of clustering, we compare the clustering distance between the experimental data being analyzed with that from simulated random data. Results are then expressed as a dimensionless number, the clustering ratio that facilitates the comparison of clustering between experiments. Replacing the chosen cluster distance by the intrinsic clustering distance emphasizes densely packed clusters that are likely more important to downstream signaling events.We test our new clustering analysis approach against electron microscopy images from an experiment in which mast cells were exposed for 1 or 2 minutes to increasing concentrations of antigen that crosslink IgE bound to its high affinity receptor, Fc?RI, then fixed and the Fc?RI ? subunit labeled with 5 nm gold particles. The clustering ratio analysis confirms the increase in clustering with increasing antigen dose predicted from visual analysis and from the Hopkins statistic. Access to a robust and sensitive tool to both observe and quantify clustering is a key step toward understanding the detailed fine scale structure of the membrane, and ultimately to determining the role of spatial organization in the regulation of transmembrane signaling.
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Generalization of symmetric alpha-stable Lévy distributions for q>1.
J Math Phys
PUBLISHED: 01-04-2010
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The alpha-stable distributions introduced by Lévy play an important role in probabilistic theoretical studies and their various applications, e.g., in statistical physics, life sciences, and economics. In the present paper we study sequences of long-range dependent random variables whose distributions have asymptotic power-law decay, and which are called (q,alpha)-stable distributions. These sequences are generalizations of independent and identically distributed alpha-stable distributions and have not been previously studied. Long-range dependent (q,alpha)-stable distributions might arise in the description of anomalous processes in nonextensive statistical mechanics, cell biology, finance. The parameter q controls dependence. If q=1 then they are classical independent and identically distributed with alpha-stable Lévy distributions. In the present paper we establish basic properties of (q,alpha)-stable distributions and generalize the result of Umarov et al. [Milan J. Math. 76, 307 (2008)], where the particular case alpha=2,q[1,3) was considered, to the whole range of stability and nonextensivity parameters alpha(0,2] and q[1,3), respectively. We also discuss possible further extensions of the results that we obtain and formulate some conjectures.
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Time series analysis of particle tracking data for molecular motion on the cell membrane.
Bull. Math. Biol.
PUBLISHED: 05-26-2009
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Biophysicists use single particle tracking (SPT) methods to probe the dynamic behavior of individual proteins and lipids in cell membranes. The mean squared displacement (MSD) has proven to be a powerful tool for analyzing the data and drawing conclusions about membrane organization, including features like lipid rafts, protein islands, and confinement zones defined by cytoskeletal barriers. Here, we implement time series analysis as a new analytic tool to analyze further the motion of membrane proteins. The experimental data track the motion of 40 nm gold particles bound to Class I major histocompatibility complex (MHCI) molecules on the membranes of mouse hepatoma cells. Our first novel result is that the tracks are significantly autocorrelated. Because of this, we developed linear autoregressive models to elucidate the autocorrelations. Estimates of the signal to noise ratio for the models show that the autocorrelated part of the motion is significant. Next, we fit the probability distributions of jump sizes with four different models. The first model is a general Weibull distribution that shows that the motion is characterized by an excess of short jumps as compared to a normal random walk. We also fit the data with a chi distribution which provides a natural estimate of the dimension d of the space in which a random walk is occurring. For the biological data, the estimates satisfy 1 < d < 2, implying that particle motion is not confined to a line, but also does not occur freely in the plane. The dimension gives a quantitative estimate of the amount of nanometer scale obstruction met by a diffusing molecule. We introduce a new distribution and use the generalized extreme value distribution to show that the biological data also have an excess of long jumps as compared to normal diffusion. These fits provide novel estimates of the microscopic diffusion constant. Previous MSD analyses of SPT data have provided evidence for nanometer-scale confinement zones that restrict lateral diffusion, supporting the notion that plasma membrane organization is highly structured. Our demonstration that membrane protein motion is autocorrelated and is characterized by an excess of both short and long jumps reinforces the concept that the membrane environment is heterogeneous and dynamic. Autocorrelation analysis and modeling of the jump distributions are powerful new techniques for the analysis of SPT data and the development of more refined models of membrane organization. The time series analysis also provides several methods of estimating the diffusion constant in addition to the constant provided by the mean squared displacement. The mean squared displacement for most of the biological data shows a power law behavior rather the linear behavior of Brownian motion. In this case, we introduce the notion of an instantaneous diffusion constant. All of the diffusion constants show a strong consistency for most of the biological data.
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Insights into cell membrane microdomain organization from live cell single particle tracking of the IgE high affinity receptor Fc?RI of mast cells.
Bull. Math. Biol.
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Current models propose that the plasma membrane of animal cells is composed of heterogeneous and dynamic microdomains known variously as cytoskeletal corrals, lipid rafts and protein islands. Much of the experimental evidence for these membrane compartments is indirect. Recently, live cell single particle tracking studies using quantum dot-labeled IgE bound to its high affinity receptor Fc?RI, provided direct evidence for the confinement of receptors within micrometer-scale cytoskeletal corrals. In this study, we show that an innovative time-series analysis of single particle tracking data for the high affinity IgE receptor, Fc?RI, on mast cells provides substantial quantitative information about the submicrometer organization of the membrane. The analysis focuses on the probability distribution function of the lengths of the jumps in the positions of the quantum dots labeling individual IgE Fc?RI complexes between frames in movies of their motion. Our results demonstrate the presence, within the micrometer-scale cytoskeletal corrals, of smaller subdomains that provide an additional level of receptor confinement. There is no characteristic size for these subdomains; their size varies smoothly from a few tens of nanometers to a over a hundred nanometers. In QD-IGE labeled unstimulated cells, jumps of less than 70 nm predominate over longer jumps. Addition of multivalent antigen to crosslink the QD-IgE-Fc?RI complexes causes a rapid slowing of receptor motion followed by a long tail of mostly jumps less than 70 nm. The reduced receptor mobility likely reflects both the membrane heterogeneity revealed by the confined motion of the monomeric receptor complexes and the antigen-induced cross linking of these complexes into dimers and higher oligomers. In both cases, the probability distribution of the jump lengths is well fit, from 10 nm to over 100 nm, by a novel power law. The fit for short jumps suggests that the motion of the quantum dots can be modeled as diffusion in a fractal space of dimension less than two.
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The shuttling scaffold model for prevention of yeast pheromone pathway misactivation.
Bull. Math. Biol.
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The molecular scaffold in the yeast pheromone pathway, Ste5, shuttles continuously between the nucleus and the cytoplasm. Ste5 undergoes oligomerization reaction in the nucleus. Upon pheromone stimulation, the Ste5 dimer is rapidly exported out of the nucleus and recruited to the plasma membrane for pathway activation. This clever device on part of the yeast cell is thought to prevent pathway misactivation at high enough levels of Ste5 in the absence of pheromone. We have built a spatiotemporal model of signaling in this pathway to describe its regulation. Our present work underscores the importance of spatial modeling of cell signaling networks to understand their control and functioning.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.