Determination of nuclear position by the arrangement of actin filaments using deep generative networks

The cell nucleus is a dynamic structure that changes locales during cellular processes such as proliferation, differentiation, or migration, and its mispositioning is a hallmark of several disorders. As with most mechanobiological activities of adherent cells, the repositioning and anchoring of the nucleus are presumed to be associated with the organization of the cytoskeleton, the network of protein filaments providing structural integrity to the cells. However, this correlation between cytoskeleton organization and nuclear position has not, to date, been demonstrated, as it would require the parameterization of the extraordinarily intricate cytoskeletal fiber arrangements. Here, we show that this parameterization and demonstration can be achieved outside the limits of human conceptualization, using generative network and raw microscope images, relying on machine-driven interpretation and selection of parameterizable features. The developed transformer-based architecture was able to generate high-quality, completed images of more than 8,000 cells, using only information on actin filaments, predicting the presence of a nucleus and its exact localization in more than 70 per cent of instances. Our results demonstrate one of the most basic principles of mechanobiology with a remarkable level of significance. They also highlight the role of deep learning as a powerful tool in biology beyond data augmentation and analysis, capable of interpreting -unconstrained by the principles of human reasoning- complex biological systems from qualitative data.

command intonation in Brazilian Portuguese: a dialectal description from ALiB corpus

In this paper, we described the command intonational contours in the twenty-five Brazilian capitals included in the corpus “Linguistic Atlas of Brazil” (ALiB). This work aims at: (i) describing the intonational contour of twenty-five capitals from the corpus ALiB; (ii) comparing the intonation of the directive speech acts in the five Brazilian regions and (iii) proposing a phonological representation of the variation of this contour. Our corpus is composed of fifty imperative utterances produced by male and female speakers of the analyzed capitals. We observed that there is a predominance of a rising F0 movement in the prenucleus of the command contours with the phonological notation L*+H or L+H* in the twentyfive Brazilian capitals. In the nuclear position, the pitch accent can be defined for the majority of the capitals as H+L*L%, a falling F0 movement, with the variant H*L% for the capital Belém (PA). The capital that presented a different F0 movement in the nucleus was Florianópolis (SC) that showed the predominance of a rising-falling F0 movement represented as L+H*L%.

Gemination in Northern versus Central and Southern Varieties of Italian: A Corpus-based Investigation

It is often claimed that patterns of gemination are different across varieties of Italian. In particular, northern speakers are sometimes said to degeminate, or to produce shorter geminates than central and southern speakers. However, experimental data proving such claims is largely missing. In this article, we perform an analysis of the CLIPS corpus with the aim of comparing gemination for northern versus central and southern speakers of Italian. The analysis of different data types (target words in isolated position, read sentences, dialogues, local radio and TV broadcasts) revealed that: (a) geminate consonants are produced by all speakers, incl. northern speakers; (b) differences in the magnitude of consonant lengthening are small (< 19 ms) and reach significance only for some data types; (c) the shortening of vowels preceding geminate consonants is mainly restricted to isolated target words in nuclear position, with no significant differences between northern and central/southern speakers. We argue that regional differences in Italian gemination have been overestimated and overemphasized in the literature. In fact, the evidence suggests that they are not as sizeable as previously thought, probably because of the progressive standardization of the language.

Analysis of the contribution of phosphoinositides to medial septation in fission yeast highlights the importance of PI(4,5)P2 for medial contractile ring anchoring

In Schizosaccharomyces pombe, loss of the plasma membrane PI4-kinase scaffold Efr3 leads to sliding of the cytokinetic ring (CR) away from the cell center during anaphase, implicating phosphoinositides (PIPs) in CR anchoring. However, whether other PIP regulators contribute to CR anchoring has not been investigated. Here we report that mutants of other PIP kinases and their regulators divide with off-center septa, similar to efr3∆. Using new biosensors for S. pombe PIPs, we confirm that these mutants have disrupted PIP composition. We extend a previous finding that a mutant known to decrease PI(3,5)P2 levels indirectly affects CR positioning by increasing vacuole size which disrupts nuclear position at the onset of mitosis. Indeed, we found that other mutants with increased vacuole size also disrupt medial division via this mechanism. Although elevated plasma membrane PI(4,5)P2 levels do not affect medial cytokinesis, mutants with decreased levels display CR sliding events indicating a specific role for PI(4,5)P2 in CR anchoring.

Emery–Dreifuss muscular dystrophy–linked genes and centronuclear myopathy–linked genes regulate myonuclear movement by distinct mechanisms

Muscle cells are a syncytium in which the many nuclei are positioned to maximize the distance between adjacent nuclei. Although mispositioned nuclei are correlated with many muscle disorders, it is not known whether this common phenotype is the result of a common mechanism. To answer this question, we disrupted the expression of genes linked to Emery–Dreifuss muscular dystrophy (EDMD) and centronuclear myopathy (CNM) in Drosophila and evaluated the position of the nuclei. We found that the genes linked to EDMD and CNM were each necessary to properly position nuclei. However, the specific phenotypes were different. EDMD-linked genes were necessary for the initial separation of nuclei into distinct clusters, suggesting that these factors relieve interactions between nuclei. CNM-linked genes were necessary to maintain the nuclei within clusters as they moved toward the muscle ends, suggesting that these factors were necessary to maintain interactions between nuclei. Together these data suggest that nuclear position is disrupted by distinct mechanisms in EDMD and CNM.

Nucleus-dependent sarcomere assembly is mediated by the LINC complex

Two defining characteristics of muscle cells are the many precisely positioned nuclei and the linearly arranged sarcomeres, yet the relationship between these two features is not known. We show that nuclear positioning precedes sarcomere formation. Furthermore, ZASP-GFP, a Z-line protein, colocalizes with F-actin in puncta at the cytoplasmic face of nuclei before sarcomere assembly. In embryos with mispositioned nuclei, ZASP-GFP is still recruited to the nuclei before its incorporation into sarcomeres. Furthermore, the first sarcomeres appear in positions close to the nuclei, regardless of nuclear position. These data suggest that the interaction between sarcomere proteins and nuclei is not dependent on properly positioned nuclei. Mechanistically, ZASP-GFP localization to the cytoplasmic face of the nucleus did require the linker of nucleoskeleton and cytoskeleton (LINC) complex. Muscle-specific depletion of klarsicht (nesprin) or klariod (SUN) blocked the recruitment of ZASP-GFP to the nucleus during the early stages of sarcomere assembly. As a result, sarcomeres were poorly formed and the general myofibril network was less stable, incomplete, and/or torn. These data suggest that the nucleus, through the LINC complex, is crucial for the proper assembly and stability of the sarcomere network.