A Python based automated tracking routine for myosin II filaments

The study of motor protein dynamics within cytoskeletal networks is of high interest to physicists and biologists to understand how the dynamics and properties of individual motors lead to cooperative effects and control of overall network behaviour. Here, we report a method to detect and track muscular myosin II filaments within an actin network tethered to supported lipid bilayers. Based on the characteristic shape of myosin II filaments, this automated tracking routine allowed us to follow the position and orientation of myosin II filaments over time, and to reliably classify their dynamics into segments of diffusive and processive motion based on the analysis of displacements and angular changes between time steps. This automated, high throughput method will allow scientists to efficiently analyse motor dynamics in different conditions, and will grant access to more detailed information than provided by common tracking methods, without any need for time consuming manual tracking or generation of kymographs

Myosin II filament dynamics in actin networks revealed with interferometric scattering microscopy

The plasma membrane and the underlying cytoskeletal cortex constitute active platforms for a variety of cellular processes. Recent work has shown that the remodeling acto-myosin network modifies local membrane organization, but the molecular details are only partly understood due to difficulties with experimentally accessing the relevant time and length scales. Here, we use interferometric scattering (iSCAT) microscopy to investigate a minimal acto-myosin network linked to a supported lipid bilayer membrane. Using the magnitude of the interferometric contrast, which is proportional to molecular mass, and fast acquisition rates, we detect, and image individual membrane attached actin filaments diffusing within the acto-myosin network and follow individual myosin II filament dynamics. We quantify myosin II filament dwell times and processivity as functions of ATP concentration, providing experimental evidence for the predicted ensemble behavior of myosin head domains. Our results show how decreasing ATP concentrations lead to both increasing dwell times of individual myosin II filaments and a global change from a remodeling to a contractile state of the acto-myosin network

Application of Empirical Orthogonal Function Models to Analyze Shoreline Change at Bangkalan Madura

Bangkalan’s shoreline, especially on the opposite side of Surabaya, has been evaluated to determine the morphological changes due to wave attack, near-shore current, long-shore sediment transport and coastal configuration. This research aims to determine the dominant patterns of variation of Bangkalan’s shoreline change, expressed by Eigen-function in empirical orthogonal function (EOF) models. That was started with data collection such as oceanographic data (wave and tidal), bathymetry and topographic map and sediment data. All data was used for forecasting two-monthly shoreline. Coordinate of two-monthly shoreline was used as input of EOF model. The first Eigen mode is a profile of shoreline equilibrium. The second Eigen mode shows pivot point that separates the different behaviors, which indicates a positive balance of shoreline from the direction of the dominant force. The models execution based on 1986’s shoreline show the shoreline change significantly at some cells e.g. around Suramadu bridge (cell 1-40), Batuporon (cell 70-100), Jungdima (cell 142-170) and at Kamal port (cell 230-250). The model of shoreline change using EOF was validated with the One-line model and data of 1995’s map’s shoreline. The E.O.F. value of model RMSE, 0.02, is less than the root mean square error (RMSE) value of One-line model, 0.04, which shows that the EOF model performance better than One-line models

Measuring emission coordinates in a pulsar-based relativistic positioning system

A relativistic deep space positioning system has been proposed using four or more pulsars with stable repetition rates. (Each pulsar emits pulses at a fixed repetition period in its rest frame.) The positioning system uses the fact that an event in spacetime can be fully described by emission coordinates: the proper emission time of each pulse measured at the event. The proper emission time of each pulse from four different pulsars---interpolated as necessary---provides the four spacetime coordinates of the reception event in the emission coordinate system. If more than four pulsars are available, the redundancy can improve the accuracy of the determination and/or resolve degeneracies resulting from special geometrical arrangements of the sources and the event. We introduce a robust numerical approach to measure the emission coordinates of an event in any arbitrary spacetime geometry. Our approach uses a continuous solution of the eikonal equation describing the backward null cone from the event. The pulsar proper time at the instant the null cone intersects the pulsar world line is one of the four required coordinates. The process is complete (modulo degeneracies) when four pulsar world lines have been crossed by the light cone. The numerical method is applied in two different examples: measuring emission coordinates of an event in Minkowski spacetime using pulses from four pulsars stationary in the spacetime; and measuring emission coordinates of an event in Schwarzschild spacetime using pulses from four pulsars freely falling toward a static black hole. These numerical simulations are merely exploratory, but with improved resolution and computational resources the method can be applied to more pertinent problems. For instance one could measure the emission coordinates, and therefore the trajectory, of the Earth.Comment: 9 pages, 2 figures, v3: replaced with version accepted by Phys. Rev.

Probing environment fluctuations by two-dimensional electronic spectroscopy of molecular systems at temperatures below 5 K

Citation: Rancova, O., Jankowiak, R., & Abramavicius, D. (2015). Probing environment fluctuations by two-dimensional electronic spectroscopy of molecular systems at temperatures below 5 K. Journal of Chemical Physics, 142(21), 18. doi:10.1063/1.4918584Two-dimensional (2D) electronic spectroscopy at cryogenic and room temperatures reveals excitation energy relaxation and transport, as well as vibrational dynamics, in molecular systems. These phenomena are related to the spectral densities of nuclear degrees of freedom, which are directly accessible by means of hole burning and fluorescence line narrowing approaches at low temperatures (few K). The 2D spectroscopy, in principle, should reveal more details about the fluctuating environment than the 1D approaches due to peak extension into extra dimension. By studying the spectral line shapes of a dimeric aggregate at low temperature, we demonstrate that 2D spectra have the potential to reveal the fluctuation spectral densities for different electronic states, the interstate correlation of static disorder and, finally, the time scales of spectral diffusion with high resolution. (C) 2015 AIP Publishing LLC

Functional characterization of reappearing B cells after anti-CD20 treatment of CNS autoimmune disease.

The anti-CD20 antibody ocrelizumab, approved for treatment of multiple sclerosis, leads to rapid elimination of B cells from the blood. The extent of B cell depletion and kinetics of their recovery in different immune compartments is largely unknown. Here, we studied how anti-CD20 treatment influences B cells in bone marrow, blood, lymph nodes, and spleen in models of experimental autoimmune encephalomyelitis (EAE). Anti-CD20 reduced mature B cells in all compartments examined, although a subpopulation of antigen-experienced B cells persisted in splenic follicles. Upon treatment cessation, CD20+ B cells simultaneously repopulated in bone marrow and spleen before their reappearance in blood. In EAE induced by native myelin oligodendrocyte glycoprotein (MOG), a model in which B cells are activated, B cell recovery was characterized by expansion of mature, differentiated cells containing a high frequency of myelin-reactive B cells with restricted B cell receptor gene diversity. Those B cells served as efficient antigen-presenting cells (APCs) for activation of myelin-specific T cells. In MOG peptide-induced EAE, a purely T cell-mediated model that does not require B cells, in contrast, reconstituting B cells exhibited a naive phenotype without efficient APC capacity. Our results demonstrate that distinct subpopulations of B cells differ in their sensitivity to anti-CD20 treatment and suggest that differentiated B cells persisting in secondary lymphoid organs contribute to the recovering B cell pool

Magnetic Resonance Investigation of the Human Brain after 6 Days of Acclimatization to 4554 m - Preliminary Results of the EFA study -

Objective: Hypoxia is the main trigger of acute mountain sickness (AMS). However it is not the cause of the actual symptoms of AMS. The biochemical mechanisms underlying the AMS development are not well understood what leads to a high uncertainty regarding the likeliness of AMS development in astronauts living in future moderate hypobaric hypoxic habitats on Mars or moon. The hypothesis of the EFA study (Edema Formation in the High Alps) was that hypoxia triggered inflammatory processes lead to a breakdown of the capillary barrier and edema formation in vulnerable tissues as the brain. Methods: 11 subjects (5 women) ascended within 48 h from 1154 m to the Capanna Regina Margherita in 4554 m. Brain magnetic resonance imaging (MRI) was performed at sea level before the altitude exposure and within the first 12 h after descent. MRI included amongst others an anatomical 3D volumetric T1-weighted MPRAGE (magnetization-prepared rapid acquisition of gradient echo) scan, a susceptibility weighted gradient echo sequence, T2 weighted spin echo sequences and a diffusion weighted sequence to gain an apparent diffusion coefficient mapping and a trace image to test for volume changes of the different brain compartments, for hypoxic triggered brain edema and for micro-bleedings. Baseline measurements were performed at the DLR MRI lab in Cologne (77 m) whereas post line measurements were performed at the MRI department of the German Air Force in Fürstenfeldbruck (517 m) by applying identical sequences at both centers. Results: Neither mean global intracranial volume (p=7.97) nor mean volumes of the particular brain compartments grey (p=0.279) and white matter (p=0.758) or cerebrospinal fluid (p=0.586) showed any significant differences after the altitude exposure with respect to baseline. However 6 days of altitude exposure lead to the exacerbation of pre-existing white matter lesions in one subject and the occurrence of a local hypoxic edema in the splenium of a second subjects in the sense of a reversible splenial lesion syndrome (RESLES) (1, 2). Conclusion: Contradictory to the current literature (3) we were not able to show a general volume gain of the intracranial compartments after high altitude adaptation. However our findings of white matter lesions (4) and RESLES in two subjects not presenting any symptoms of a high altitude cerebral edema (HACE) have, as far as we know, not been described before (5)