APM_GUI: analyzing particle movement on the cell membrane and determining confinement

<p>Abstract</p> <p>Background</p> <p>Single-particle tracking is a powerful tool for tracking individual particles with high precision. It provides useful information that allows the study of diffusion properties as well as the dynamics of movement. Changes in particle movement behavior, such as transitions between Brownian motion and temporary confinement, can reveal interesting biophysical interactions. Although useful applications exist to determine the paths of individual particles, only a few software implementations are available to analyze these data, and these implementations are generally not user-friendly and do not have a graphical interface,.</p> <p>Results</p> <p>Here, we present APM_GUI (Analyzing Particle Movement), which is a MatLab-implemented application with a Graphical User Interface. This user-friendly application detects confined movement considering non-random confinement when a particle remains in a region longer than a Brownian diffusant would remain. In addition, APM_GUI exports the results, which allows users to analyze this information using software that they are familiar with.</p> <p>Conclusions</p> <p>APM_GUI provides an open-source tool that quantifies diffusion coefficients and determines whether trajectories have non-random confinements. It also offers a simple and user-friendly tool that can be used by individuals without programming skills.</p

A spatially restricted increase in receptor mobility is involved in directional sensing during Dictyostelium discoideum chemotaxis

Biological and Soft Matter PhysicsAnimal science

Super-Resolution Imaging Strategies for Cell Biologists Using a Spinning Disk Microscope

In this study we use a spinning disk confocal microscope (SD) to generate super-resolution images of multiple cellular features from any plane in the cell. We obtain super-resolution images by using stochastic intensity fluctuations of biological probes, combining Photoactivation Light-Microscopy (PALM)/Stochastic Optical Reconstruction Microscopy (STORM) methodologies. We compared different image analysis algorithms for processing super-resolution data to identify the most suitable for analysis of particular cell structures. SOFI was chosen for X and Y and was able to achieve a resolution of ca. 80 nm; however higher resolution was possible >30 nm, dependant on the super-resolution image analysis algorithm used. Our method uses low laser power and fluorescent probes which are available either commercially or through the scientific community, and therefore it is gentle enough for biological imaging. Through comparative studies with structured illumination microscopy (SIM) and widefield epifluorescence imaging we identified that our methodology was advantageous for imaging cellular structures which are not immediately at the cell-substrate interface, which include the nuclear architecture and mitochondria. We have shown that it was possible to obtain two coloured images, which highlights the potential this technique has for high-content screening, imaging of multiple epitopes and live cell imaging

Barcoding T Cell Calcium Response Diversity with Methods for Automated and Accurate Analysis of Cell Signals (MAAACS)

International audienceWe introduce a series of experimental procedures enabling sensitive calcium monitoring in T cell populations by confocal video-microscopy. Tracking and post-acquisition analysis was performed using Methods for Automated and Accurate Analysis of Cell Signals (MAAACS), a fully customized program that associates a high throughput tracking algorithm, an intuitive reconnection routine and a statistical platform to provide, at a glance, the calcium barcode of a population of individual T-cells. Combined with a sensitive calcium probe, this method allowed us to unravel the heterogeneity in shape and intensity of the calcium response in T cell populations and especially in naive T cells, which display intracellular calcium oscillations upon stimulation by antigen presenting cells

Biogeography and contemporary climatic differentiation among Moroccan Salamandra algira

The opening of the Gibraltar land bridge occurred at the end of the Messinian Salinity Crisis approximately 5.3 Mya, and was one of the main causes of vicariance between European and north-west African amphibians, resulting in the origin of several new species. However, little is currently known about the causes for post-Messinian amphibian differentiation in the Maghreb, although it is acknowledged that the Pleistocene glaciations probably had considerable influence on several species. The current study uses both species distribution modelling (MAXENT) and information from a total of 694 bp of mitochondrial data (351 from cytochrome b and 342 from 12S rRNA) from 36 representatives of all three recognized subspecies of Moroccan Salamandra to infer the phylogeny and biogeography of Salamandra algira tingitana, which is characterized by both viviparous and ovoviviparous populations. According to the results, the split between S. a. tingitana and S. a. algira from the Rif and Middle Atlas mountains took place approximately 1.6 Mya, and could have been caused by a shift towards a colder and drier climate that occurred during the upper Pliocene, which may have resulted in the isolation of Salamandra at increasingly higher altitudes, or in other climatically favourable areas. Several lineages within S. a. tingitana originated during the Pleistocene climatic oscillations, one of which gave rise to the viviparous populations north of the Oued Martil. It is suggested that the origin of viviparity in S. a. tingitana occurred during the last 600 000 years. In order to further understand the origin of the unique viviparous population of S. algira from North Africa, predictive distribution models of the viviparous and ovoviviparous populations of S. a. tingitana were created using MAXENT to assess environmental differences. Niche divergence was subsequently determined using Schoener's D and Warren et al.'s I niche similarity metrics. Predictive modelling and niche divergence analyses revealed significant environmental differences between the two reproductive types, which could have influenced the transition from ovoviviparity to viviparity. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society.The mtDNA work was funded by grant CGL2009-11663/BOS from the Ministerio de Educación y Ciencia, Spain. S.C. is a member of the Grup de Recerca Emergent of the Generalitat de Catalunya: 2009SGR1462.Peer Reviewe

Roles of LTβR, RANK and CD40 signaling in mTEC expansion and maturation.

<p>2-dGUO-treated WT embryonic thymic lobes were cultured for 4 days in medium containing agonistic anti-LTβR antibodies, CD40L and/or RANKL. Control cultures were un-supplemented (medium) or not treated with 2-dGUO. (A) Representative FACS profiles are shown for Ly51 expression by CD45⁻EpCAM⁺ TECs (top) and I-Ab and CD80 expression by CD45⁻EpCAM⁺Ly51^−/lo mTECs (bottom) for the indicated cultures: percentages of cells are indicated. (B) Graphs show mTEC numbers (left) and frequencies of mature I-Ab^hiCD80^hi mTECs (right) for the indicated conditions: data from 3 experiments; lines represent medians.</p