Nfinder: automatic inference of cell neighborhood in 2D and 3D using nuclear markers.

BACKGROUND: In tissues and organisms, the coordination of neighboring cells is essential to maintain their properties and functions. Therefore, knowing which cells are adjacent is crucial to understand biological processes that involve physical interactions among them, e.g. cell migration and proliferation. In addition, some signaling pathways, such as Notch or extrinsic apoptosis, are highly dependent on cell-cell communication. While this is straightforward to obtain from membrane images, nuclei labelling is much more ubiquitous for technical reasons. However, there are no automatic and robust methods to find neighboring cells based only on nuclear markers. RESULTS: In this work, we describe Nfinder, a method to assess the cell's local neighborhood from images with nuclei labeling. To achieve this goal, we approximate the cell-cell interaction graph by the Delaunay triangulation of nuclei centroids. Then, links are filtered by automatic thresholding in cell-cell distance (pairwise interaction) and the maximum angle that a pair of cells subtends with shared neighbors (non-pairwise interaction). We systematically characterized the detection performance by applying Nfinder to publicly available datasets from Drosophila melanogaster, Tribolium castaneum, Arabidopsis thaliana and C. elegans. In each case, the result of the algorithm was compared to a cell neighbor graph generated by manually annotating the original dataset. On average, our method detected 95% of true neighbors, with only 6% of false discoveries. Remarkably, our findings indicate that taking into account non-pairwise interactions might increase the Positive Predictive Value up to + 11.5%. CONCLUSION: Nfinder is the first robust and automatic method for estimating neighboring cells in 2D and 3D based only on nuclear markers and without any free parameters. Using this tool, we found that taking non-pairwise interactions into account improves the detection performance significantly. We believe that using our method might improve the effectiveness of other workflows to study cell-cell interactions from microscopy images. Finally, we also provide a reference implementation in Python and an easy-to-use napari plugin.

Compact and reflective light-sheet microscopy for long-term imaging of living embryos.

The development of light-sheet fluorescence microscopy has been a revolution for developmental biology as it allows long-term imaging during embryonic development. An important reason behind the quick adoption has been the availability of open hardware alternatives. In this work, we present a robust and compact version of a light-sheet fluorescence microscope that is easy to assemble and requires little to no maintenance. An important aspect of the design is that the illumination unit consists of reflective elements, thereby reducing chromatic aberrations an order of magnitude as compared to refractive counterparts.

Single-cell transcriptional dynamics in a living vertebrate.

The ability to quantify transcriptional dynamics in individual cells via live imaging has revolutionized our understanding of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling to the quantification of transcription in zebrafish, a model vertebrate. We developed a platform of transgenic organisms, light sheet fluorescence microscopy, and optimized image analysis that enables visualization and quantification of MS2 reporters. We used these tools to obtain the first single-cell, real-time measurements of transcriptional dynamics of the segmentation clock. Our measurements challenge the traditional view of smooth clock oscillations and instead suggest a model of discrete transcriptional bursts that are organized in space and time. Together, these results highlight how measuring single-cell transcriptional activity can reveal unexpected features of gene regulation and how this data can fuel the dialogue between theory and experiment.

Furry is required for cell movements during gastrulation and functionally interacts with NDR1.

Gastrulation is a key event in animal embryogenesis during which germ layer precursors are rearranged and the embryonic axes are established. Cell polarization is essential during gastrulation, driving asymmetric cell division, cell movements, and cell shape changes. The furry (fry) gene encodes an evolutionarily conserved protein with a wide variety of cellular functions, including cell polarization and morphogenesis in invertebrates. However, little is known about its function in vertebrate development. Here, we show that in Xenopus, Fry plays a role in morphogenetic processes during gastrulation, in addition to its previously described function in the regulation of dorsal mesoderm gene expression. Using morpholino knock-down, we demonstrate a distinct role for Fry in blastopore closure and dorsal axis elongation. Loss of Fry function drastically affects the movement and morphological polarization of cells during gastrulation and disrupts dorsal mesoderm convergent extension, responsible for head-to-tail elongation. Finally, we evaluate a functional interaction between Fry and NDR1 kinase, providing evidence of an evolutionarily conserved complex required for morphogenesis.

O futuro do SUS: impactos das reformas neoliberais na saúde pública - austeridade versus universalidade / The future of the SUS: impacts of neoliberal reforms on public health - austerity versus universality

RESUMO O ensaio analisa os efeitos da política de austeridade sobre o Sistema Único de Saúde (SUS). Dados orçamentários e fiscais indicam que o Novo Regime Fiscal (NRF), criado pela Emenda Constitucional nº 95/2016 (EC 95), transformou o subfinanciamento crônico da saúde em desfinanciamento do SUS. Ademais, o NRF altera as relações entre as dimensões fiscal e social, uma vez que a despesa passa a ser avaliada a partir da pressão que exerce sobre o teto. Particularmente, o sistema de saúde universal se torna um excesso em relação ao limite estabelecido pela EC 95, pois os direitos sociais passam a aparecer como objeto de ajuste à fronteira fiscal, a partir da qual o gasto é tomado como irregular. Será mostrado que tais mudanças já implicam redução do orçamento disponível de saúde.

ABSTRACT The essay analyzes the effects of the austerity policy on the Unified Health System (SUS). Budgetary and fiscal data indicate that the New Tax Regime (NTR), created by Constitutional Amendment nº 95/2016 (CA 95), has transformed chronic underfunding into reduction of the health budget. In addition, the NTR alters the relations between the fiscal and social dimensions, since the expense is now evaluated from the pressure exerted on the cap. Particularly, the universal health care system becomes an excess in relation to the limit established by CA 95, since social rights begin to appear as an object of adjustment to the fiscal frontier, from which the expense is taken as irregular. The article shows that such changes already imply reduction of the available health budget.