TraCurate: Efficiently curating cell tracks

TraCurate is an open-source software tool to curate and manually annotate cell tracking data from time-lapse microscopy. Although many studies of cellular behavior require high-quality, long-term observations across generations of cells, automated cell tracking is often imperfect and typically yields fragmented results that still contain many errors. TraCurate provides the functionality for the curation and correction of cell tracking data with minimal user interaction and expenditure of time and supports the extraction of complete cell tracks and cellular genealogies from experimental data. Source code and binary packages for Linux, macOS and Windows are available at https://tracurate.gitlab.io/, as well as all other complementary tools described herein

Pan-embryo cell dynamics of germlayer formation in zebrafish

Cell movements are coordinated across spatio-temporal scales to achieve precise positioning of organs during vertebrate gastrulation. In zebrafish, mechanisms governing such morphogenetic movements have so far only been studied within a local region or a single germlayer. Here, we present pan-embryo analyses of fate specification and dynamics of all three germlayers simultaneously within a gastrulating embryo, showing that cell movement characteristics are predominantly determined by its position within the embryo, independent of its germlayer identity. The spatially confined fate specification establishes a distinct distribution of cells in each germlayer during early gastrulation. The differences in the initial distribution are subsequently amplified by a unique global movement, which organizes the organ precursors along the embryonic body axis, giving rise to the blueprint of organ formation

The Coma cluster magnetic field from Faraday rotation measures

The aim of the present work is to constrain the Coma cluster magnetic field strength, its radial profile and power spectrum by comparing Faraday Rotation Measure (RM) images with numerical simulations of the magnetic field. We have analyzed polarization data for seven radio sources in the Coma cluster field observed with the Very Large Array at 3.6, 6 and 20 cm, and derived Faraday Rotation Measures with kiloparsec scale resolution. Random three dimensional magnetic field models have been simulated for various values of the central intensity B_0 and radial power-law slope eta, where eta indicates how the field scales with respect to the gas density profile. We derive the central magnetic field strength, and radial profile values that best reproduce the RM observations. We find that the magnetic field power spectrum is well represented by a Kolmogorov power spectrum with minimum scale ~ 2 kpc and maximum scale ~ 34 kpc. The central magnetic field strength and radial slope are constrained to be in the range (B_0=3.9 microG; eta=0.4) and (B_0=5.4 microG; eta=0.7) within 1sigma. The best agreement between observations and simulations is achieved for B_0=4.7 microG; eta=0.5. Values of B_0>7 microG and 1.0 are incompatible with RM data at 99 % confidence level.Comment: 23 pages, 21 figures. Higher resolution available at http://www.ira.inaf.it/~bonafede/paper.pdf. A&A accepte

Radio Halos From Simulations And Hadronic Models II: The Scaling Relations of Radio Halos

We use results from a constrained, cosmological MHD simulation of the Local Universe to predict radio halos and their evolution for a volume limited set of galaxy clusters and compare to current observations. The simulated magnetic field inside the clusters is a result of turbulent amplification within them, with the magnetic seed originating from star-burst driven, galactic outflows. We evaluate three models, where we choose different normalizations for the Cosmic Ray proton population within clusters. Similar to our previous analysis of the Coma cluster (Donnert et al. 2010), the radial profile and the morphological properties of observed radio halos can not be reproduced, even with a radially increasing energy fraction within the cosmic ray proton population. Scaling relations between X-ray luminosity and radio power can be reproduced by all models, however all models fail in the prediction of clusters with no radio emission. Also the evolutionary tracks of our largest clusters in all models fail to reproduce the observed bi-modality in radio luminosity. This provides additional evidence that the framework of hadronic, secondary models is disfavored to reproduce the large scale diffuse radio emission of galaxy clusters. We also provide predictions for the unavoidable emission of $\gamma$-rays from the hadronic models for the full cluster set. None of such secondary models is yet excluded by the observed limits in $\gamma$-ray emission, emphasizing that large scale diffuse radio emission is a powerful tool to constrain the amount of cosmic ray protons in galaxy clusters

Clusters of galaxies : observational properties of the diffuse radio emission

Clusters of galaxies, as the largest virialized systems in the Universe, are ideal laboratories to study the formation and evolution of cosmic structures...(abridged)... Most of the detailed knowledge of galaxy clusters has been obtained in recent years from the study of ICM through X-ray Astronomy. At the same time, radio observations have proved that the ICM is mixed with non-thermal components, i.e. highly relativistic particles and large-scale magnetic fields, detected through their synchrotron emission. The knowledge of the properties of these non-thermal ICM components has increased significantly, owing to sensitive radio images and to the development of theoretical models. Diffuse synchrotron radio emission in the central and peripheral cluster regions has been found in many clusters. Moreover large-scale magnetic fields appear to be present in all galaxy clusters, as derived from Rotation Measure (RM) studies. Non-thermal components are linked to the cluster X-ray properties, and to the cluster evolutionary stage, and are crucial for a comprehensive physical description of the intracluster medium. They play an important role in the cluster formation and evolution. We review here the observational properties of diffuse non-thermal sources detected in galaxy clusters: halos, relics and mini-halos. We discuss their classification and properties. We report published results up to date and obtain and discuss statistical properties. We present the properties of large-scale magnetic fields in clusters and in even larger structures: filaments connecting galaxy clusters. We summarize the current models of the origin of these cluster components, and outline the improvements that are expected in this area from future developments thanks to the new generation of radio telescopes.Comment: Accepted for the publication in The Astronomy and Astrophysics Review. 58 pages, 26 figure

Radio Halos From Simulations And Hadronic Models I: The Coma cluster

We use the results from a constrained, cosmological MHD simulation of the Local Universe to predict the radio halo and the gamma-ray flux from the Coma cluster and compare it to current observations. The simulated magnetic field within the Coma cluster is the result of turbulent amplification of the magnetic field during build-up of the cluster. The magnetic seed field originates from star-burst driven, galactic outflows. The synchrotron emission is calculated assuming a hadronic model. We follow four approaches with different distributions for the cosmic-ray proton (CRp) population within galaxy clusters. The radial profile the radio halo can only be reproduced with a radially increasing energy fraction within the cosmic ray proton population, reaching $>$100% of the thermal energy content at $\approx$ 1Mpc, e.g. the edge of the radio emitting region. Additionally the spectral steepening of the observed radio halo in Coma cannot be reproduced, even when accounting for the negative flux from the thermal SZ effect at high frequencies. Therefore the hadronic models are disfavored from present analysis. The emission of $\gamma$-rays expected from our simulated coma is still below the current observational limits (by a factor of $\sim$6) but would be detectable in the near future.Comment: Submitted to MNRAS, 5pages, 3 figures, 1 tabl

On the evolution of giant radio halos and their connection with cluster mergers

Giant radio halos are diffuse, Mpc-scale, synchrotron sources located in the central regions of galaxy clusters and provide the most relevant example of cluster non-thermal activity. Radio and X-ray surveys allow to investigate the statistics of halos and may contribute to constrain their origin and evolution. We investigate the distribution of clusters in the plane X-ray (thermal, L_X) vs synchrotron (P_{1.4})luminosity, where clusters hosting giant radio halos trace the P_{1.4}--L_X correlation and clusters without radio halos populate a region that is well separated from that spanned by the above correlation. The connection between radio halos and cluster mergers suggests that the cluster Mpc-scale synchrotron emission is amplified during these mergers and then suppressed when clusters become more dynamically relaxed. In this context, by analysing the distribution in the P_{1.4}--L_X plane of clusters from X-ray selected samples with adequate radio follow up, we constrain the typical time-scale of evolution of diffuse radio emission in clusters and discuss the implications for the origin of radio halos. We conclude that cluster synchrotron emission is suppressed (and amplified) in a time-scale significantly smaller than 1 Gyr. We show that this constraint appears difficult to reconcile with the hypothesis that the halo's radio power is suppressed due to dissipation of magnetic field in galaxy clusters. On the other hand, in agreement with models where turbulent acceleration plays a role, present constraints suggest that relativistic electrons are accelerated in Mpc-scale regions, in connection with cluster mergers and for a time-interval of about 1 Gyr, and then they cool in a relatively small time-scale, when the hosting cluster becomes more dynamically relaxed.Comment: 11 pages, 5 figure, to appear in Astronomy & Astrophysics, 2 typos in references corrected, last sentence at the end of Sect.2 modifie

Low aerobic mitochondrial energy metabolism in poorly- or undifferentiated neuroblastoma

<p>Abstract</p> <p>Background</p> <p>Succinate dehydrogenase (SDH) has been associated with carcinogenesis in pheochromocytoma and paraganglioma. In the present study we investigated components of the oxidative phosphorylation system in human neuroblastoma tissue samples.</p> <p>Methods</p> <p>Spectrophotometric measurements, immunohistochemical analysis and Western blot analysis were used to characterize the aerobic mitochondrial energy metabolism in neuroblastomas (NB).</p> <p>Results</p> <p>Compared to mitochondrial citrate synthase, SDH activity was severely reduced in NB (n = 14) versus kidney tissue. However no pathogenic mutations could be identified in any of the four subunits of SDH. Furthermore, no genetic alterations could be identified in the two novel SDH assembly factors SDHAF1 and SDH5. Alterations in genes encoding nfs-1, frataxin and isd-11 that could lead to a diminished SDH activity have not been detected in NB.</p> <p>Conclusion</p> <p>Because downregulation of other complexes of the oxidative phosphorylation system was also observed, a more generalized reduction of mitochondrial respiration seems to be present in neuroblastoma in contrast to the single enzyme defect found in hereditary pheochromocytomas.</p

Altered gene expression and DNA damage in peripheral blood cells from Friedreich's ataxia patients: Cellular model of pathology

The neurodegenerative disease Friedreich's ataxia (FRDA) is the most common autosomal-recessively inherited ataxia and is caused by a GAA triplet repeat expansion in the first intron of the frataxin gene. In this disease, transcription of frataxin, a mitochondrial protein involved in iron homeostasis, is impaired, resulting in a significant reduction in mRNA and protein levels. Global gene expression analysis was performed in peripheral blood samples from FRDA patients as compared to controls, which suggested altered expression patterns pertaining to genotoxic stress. We then confirmed the presence of genotoxic DNA damage by using a gene-specific quantitative PCR assay and discovered an increase in both mitochondrial and nuclear DNA damage in the blood of these patients (p<0.0001, respectively). Additionally, frataxin mRNA levels correlated with age of onset of disease and displayed unique sets of gene alterations involved in immune response, oxidative phosphorylation, and protein synthesis. Many of the key pathways observed by transcription profiling were downregulated, and we believe these data suggest that patients with prolonged frataxin deficiency undergo a systemic survival response to chronic genotoxic stress and consequent DNA damage detectable in blood. In conclusion, our results yield insight into the nature and progression of FRDA, as well as possible therapeutic approaches. Furthermore, the identification of potential biomarkers, including the DNA damage found in peripheral blood, may have predictive value in future clinical trials

Nonthermal phenomena in clusters of galaxies

Recent observations of high energy (> 20 keV) X-ray emission in a few clusters of galaxies broaden our knowledge of physical phenomena in the intracluster space. This emission is likely to be nonthermal, probably resulting from Compton scattering of relativistic electrons by the cosmic microwave background (CMB) radiation. Direct evidence for the presence of relativistic electrons in some 50 clusters comes from measurements of extended radio emission in their central regions. We briefly review the main results from observations of extended regions of radio emission, and Faraday rotation measurements of background and cluster radio sources. The main focus of the review are searches for nonthermal X-ray emission conducted with past and currently operating satellites, which yielded appreciable evidence for nonthermal emission components in the spectra of a few clusters. This evidence is clearly not unequivocal, due to substantial observational and systematic uncertainties, in addition to virtually complete lack of spatial information. If indeed the emission has its origin in Compton scattering of relativistic electrons by the CMB, then the mean magnetic field strength and density of relativistic electrons in the cluster can be directly determined. Knowledge of these basic nonthermal quantities is valuable for the detailed description of processes in intracluster gas and for the origin of magnetic fields.Comment: 23 pages, 7 figures, accepted for publication in Space Science Reviews, special issue "Clusters of galaxies: beyond the thermal view", Editor J.S. Kaastra, Chapter 5; work done by an international team at the International Space Science Institute (ISSI), Bern, organised by J.S. Kaastra, A.M. Bykov, S. Schindler & J.A.M. Bleeke