A novel protein Moat prevents ectopic epithelial folding by limiting Bazooka/Par3-dependent adherens junctions.

Contractile myosin and cell adhesion work together to induce tissue shape changes, but how they are patterned to achieve diverse morphogenetic outcomes remains unclear. Epithelial folding occurs via apical constriction, mediated by apical contractile myosin engaged with adherens junctions, as in Drosophila ventral furrow formation. While it has been shown that a multicellular gradient of myosin contractility determines folding shape, the impact of multicellular patterning of adherens junction levels on tissue folding is unknown. We identified a novel Drosophila gene moat essential for differential apical constriction and folding behaviors across the ventral epithelium which contains both folding ventral furrow and non-folding ectodermal anterior midgut (ectoAMG). We show that Moat functions to downregulate polarity-dependent adherens junctions through inhibiting cortical clustering of Bazooka/Par3 proteins. Such downregulation of polarity-dependent junctions is critical for establishing a myosin-dependent pattern of adherens junctions, which in turn mediates differential apical constriction in the ventral epithelium. In moat mutants, abnormally high levels of polarity-dependent junctions promote ectopic apical constriction in cells with low-level contractile myosin, resulting in expansion of infolding from ventral furrow to ectoAMG, and flattening of ventral furrow constriction gradient. Our results demonstrate that tissue-scale distribution of adhesion levels patterns apical constriction and establishes morphogenetic boundaries. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text].

A novel protein Moat prevents ectopic epithelial folding by limiting Bazooka/Par3-dependent adherens junctions.

Cortical myosin contraction and cell adhesion work together to promote tissue shape changes, but how they are modulated to achieve diverse morphogenetic outcomes remains unclear. Epithelial folding occurs via apical constriction, mediated by apical accumulation of contractile myosin engaged with adherens junctions, as in Drosophila ventral furrow formation. While levels of contractile myosin correlate with apical constriction, whether levels of adherens junctions modulate apical constriction is unknown. We identified a novel Drosophila gene moat that maintains low levels of Bazooka/Par3-dependent adherens junctions and thereby restricts apical constriction to ventral furrow cells with high-level contractile myosin. In moat mutants, abnormally high levels of Bazooka/Par3-dependent adherens junctions promote ectopic apical constriction in cells with low-level contractile myosin, insufficient for apical constriction in wild type. Such ectopic apical constriction expands infolding behavior from ventral furrow to ectodermal anterior midgut, which normally forms a later circular invagination. In moat mutant ventral furrow, a perturbed apical constriction gradient delays infolding. Our results indicate that levels of adherens junctions can modulate the outcome of apical constriction, providing an additional mechanism to define morphogenetic boundaries.

Digitally predicting protein localization and manipulating protein activity in fluorescence images using 4D reslicing GAN.

MOTIVATION: While multi-channel fluorescence microscopy is a vital imaging method in biological studies, the number of channels that can be imaged simultaneously is limited by technical and hardware limitations such as emission spectra cross-talk. One solution is using deep neural networks to model the localization relationship between two proteins so that the localization of one protein can be digitally predicted. Furthermore, the input and predicted localization implicitly reflect the modeled relationship. Accordingly, observing the response of the prediction via manipulating input localization could provide an informative way to analyze the modeled relationships between the input and the predicted proteins. RESULTS: We propose a protein localization prediction (PLP) method using a cGAN named 4D Reslicing Generative Adversarial Network (4DR-GAN) to digitally generate additional channels. 4DR-GAN models the joint probability distribution of input and output proteins by simultaneously incorporating the protein localization signals in four dimensions including space and time. Because protein localization often correlates with protein activation state, based on accurate PLP, we further propose two novel tools: digital activation (DA) and digital inactivation (DI) to digitally activate and inactivate a protein, in order to observing the response of the predicted protein localization. Compared with genetic approaches, these tools allow precise spatial and temporal control. A comprehensive experiment on six pairs of proteins shows that 4DR-GAN achieves higher-quality PLP than Pix2Pix, and the DA and DI responses are consistent with the known protein functions. The proposed PLP method helps simultaneously visualize additional proteins, and the developed DA and DI tools provide guidance to study localization-based protein functions. AVAILABILITY AND IMPLEMENTATION: The open-source code is available at https://github.com/YangJiaoUSA/4DR-GAN. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Live Imaging of Epithelial-Mesenchymal Transition in Mesoderm Cells of Gastrulating Drosophila Embryos.

Epithelial-mesenchymal transitions (EMTs) drive the generation of cell diversity during both evolution and development. More and more evidence has pointed to a model where EMT is not a binary switch but a reversible process that can be stabilized at intermediate states. Despite our vast knowledge on the signaling pathways that trigger EMT, we know very little about how EMT happens in a step-wise manner. Live imaging of cells that are undergoing EMT in intact, living, animals will provide us valuable insights into how EMT is executed at both the cellular and molecular levels and help us identify and understand the intermediate states. Here, we describe how to image early stages of EMT in the mesoderm cells of live Drosophila melanogaster embryos and how to image contractile myosin that suspends EMT progression.

Multi-Object Portion Tracking in 4D Fluorescence Microscopy Imagery with Deep Feature Maps.

3D fluorescence microscopy of living organisms has increasingly become an essential and powerful tool in biomedical research and diagnosis. An exploding amount of imaging data has been collected, whereas efficient and effective computational tools to extract information from them are still lagging behind. This is largely due to the challenges in analyzing biological data. Interesting biological structures are not only small, but are often morphologically irregular and highly dynamic. Although tracking cells in live organisms has been studied for years, existing tracking methods for cells are not effective in tracking subcellular structures, such as protein complexes, which feature in continuous morphological changes including split and merge, in addition to fast migration and complex motion. In this paper, we first define the problem of multi-object portion tracking to model the protein object tracking process. A multi-object tracking method with portion matching is proposed based on 3D segmentation results. The proposed method distills deep feature maps from deep networks, then recognizes and matches objects' portions using an extended search. Experimental results confirm that the proposed method achieves 2.96% higher on consistent tracking accuracy and 35.48% higher on event identification accuracy than the state-of-art methods.

Polarity protein Par3/Bazooka follows myosin-dependent junction repositioning.

The polarity protein Par3/Bazooka (Baz) has been established as a central component of the apical basal polarity system that determines the position of cell-cell junctions in epithelial cells. Consistent with that view, we show that shortly before gastrulation in Drosophila, Baz protein in the mesoderm is down-regulated from junctional sites in response to Snail (Sna) expression. This down-regulation leads to a specific decrease in adherens junctions without affecting other E-Cadherin pools. However, we further show that, interactions between Baz and junctions are not unidirectional. During apical constriction and the internalization of the mesoderm, down-regulation of Baz is transiently blocked as adherens junctions shift apically and are strengthened in response to tension generated by contractile actomyosin. When such junction remodeling is prevented by down-regulating myosin, Baz is lost prematurely in mesodermal epithelium. During such apical shifts, Baz is initially left behind as the junction shifts position, but then re-accumulates at the new location of the junctions. On the dorsal side of the embryo, a similar pattern of myosin activity appears to limit the basal shift in junctions normally driven by Baz that controls epithelium folding. Our results suggest a model where the sensitivity of Baz to Sna expression leads to the Sna-dependent junction disassembly required for a complete epithelium-mesenchymal transition. Meanwhile this loss of Baz-dependent junction maintenance is countered by the myosin-based mechanism which promotes an apical shift and strengthening of junctions accompanied by a transient re-positioning and maintenance of Baz proteins.

Myosin-dependent remodeling of adherens junctions protects junctions from Snail-dependent disassembly.

Although Snail is essential for disassembly of adherens junctions during epithelial-mesenchymal transitions (EMTs), loss of adherens junctions in Drosophila melanogaster gastrula is delayed until mesoderm is internalized, despite the early expression of Snail in that primordium. By combining live imaging and quantitative image analysis, we track the behavior of E-cadherin-rich junction clusters, demonstrating that in the early stages of gastrulation most subapical clusters in mesoderm not only persist, but move apically and enhance in density and total intensity. All three phenomena depend on myosin II and are temporally correlated with the pulses of actomyosin accumulation that drive initial cell shape changes during gastrulation. When contractile myosin is absent, the normal Snail expression in mesoderm, or ectopic Snail expression in ectoderm, is sufficient to drive early disassembly of junctions. In both cases, junctional disassembly can be blocked by simultaneous induction of myosin contractility. Our findings provide in vivo evidence for mechanosensitivity of cell-cell junctions and imply that myosin-mediated tension can prevent Snail-driven EMT.

Identification of neural stem cells in the Drosophila larval brain.

The balance between self-renewal and differentiation must be tightly regulated in somatic stem cells to ensure proper tissue generation and to prevent tumorlike overgrowth. A Drosophila larval brain lobe consists of the central brain and the optic lobe and possesses three well-defined neural stem cell lineages that generate differentiated cells in a highly reproducible pattern. Unambiguous identification of various cell types in these stem cell lineages is pivotal for studying the regulation of neural stem cells and progenitor cells at a single-cell resolution. This chapter will describe the methodology for collection and processing of larval brains for examination by fluorescence confocal microscopy.

Changes in Notch signaling coordinates maintenance and differentiation of the Drosophila larval optic lobe neuroepithelia.

A dynamic balance between stem cell maintenance and differentiation paces generation of post-mitotic progeny during normal development and maintenance of homeostasis. Recent studies show that Notch plays a key role in regulating the identity of neuroepithelial stem cells, which generate terminally differentiated neurons that populate the adult optic lobe via the intermediate progenitor cell type called neuroblast. Thus, understanding how Notch controls neuroepithelial cell maintenance and neuroblast formation will provide critical insight into the intricate regulation of stem cell function during tissue morphogenesis. Here, we showed that a low level of Notch signaling functions to maintain the neuroepithelial cell identity by suppressing the expression of pointedP1 gene through the transcriptional repressor Anterior open. Increased Notch signaling, which coincides with transient cell cycle arrest but precedes the expression of PointedP1 in cells near the medial edge of neuroepithelia, defines transitioning neuroepithelial cells that are in the process of acquiring the neuroblast identity. Transient up-regulation of Notch signaling in transitioning neuroepithelial cells decreases their sensitivity to PointedP1 and prevents them from becoming converted into neuroblasts prematurely. Down-regulation of Notch signaling combined with a high level of PointedP1 trigger a synchronous conversion from transitioning neuroepithelial cells to immature neuroblasts at the medial edge of neuroepithelia. Thus, changes in Notch signaling orchestrate a dynamic balance between maintenance and conversion of neuroepithelial cells during optic lobe neurogenesis.

Keeping neural progenitor cells on a short leash during Drosophila neurogenesis.

The developmental potential of stem cells and progenitor cells must be functionally distinguished to ensure the generation of diverse cell types while maintaining the stem cell pool throughout the lifetime of an organism. In contrast to stem cells, progenitor cells possess restricted developmental potential, allowing them to give rise to only a limited number of post-mitotic progeny. Failure to establish or maintain restricted progenitor cell potential can perturb tissue development and homeostasis, and probably contributes to tumor initiation. Recent studies using the developing fruit fly Drosophila larval brain have provided molecular insight into how the developmental potential is restricted in neural progenitor cells.

dFezf/Earmuff maintains the restricted developmental potential of intermediate neural progenitors in Drosophila.

To ensure normal development and maintenance of homeostasis, the extensive developmental potential of stem cells must be functionally distinguished from the limited developmental potential of transit amplifying cells. Yet the mechanisms that restrict the developmental potential of transit amplifying cells are poorly understood. Here we show that the evolutionarily conserved transcription factor dFezf/Earmuff (Erm) functions cell-autonomously to maintain the restricted developmental potential of the intermediate neural progenitors generated by type II neuroblasts in Drosophila larval brains. Although erm mutant intermediate neural progenitors are correctly specified and show normal apical-basal cortical polarity, they can dedifferentiate back into a neuroblast state, functionally indistinguishable from normal type II neuroblasts. Erm restricts the potential of intermediate neural progenitors by activating Prospero to limit proliferation and by antagonizing Notch signaling to prevent dedifferentiation. We conclude that Erm dependence functionally distinguishes intermediate neural progenitors from neuroblasts in the Drosophila larval brain, balancing neurogenesis with stem cell maintenance.

Optimization of reporter gene assay: several factors influencing detection of promoter activity.

BACKGROUND: Promoter analysis is currently applied to detect the expression of the targeted gene in studies of signal transduction and transcriptional regulation. As a reporter gene, luciferase plays an important role and has been used widely in the promoter assay. METHODS: Human embryonic lung fibroblast cells (2BS), HeLa cells and MCF-7 cells were transfected with various genes embedded by lipofectamine. This study determined various factors that affect promoter activity determination, such as the selection of the reporter genes and internal references, the dose and the type of the vectors carrying the transcription factors, the host cells and the instruments. RESULTS: The sensitivity of the luciferase assay was much higher than that of enhanced green fluorescence protein (EGFP). Moreover, promoter activity is increased in a dose-related manner only in certain ranges outside of which the results may be reversed and the promoter activity is related to the expression vector which is carrying the cDNA. Otherwise, the length of the promoter, internal references and the host cell can also influence the promoter activity. CONCLUSIONS: To detect the promoter activity accurately, a few factors including dose, vector, length and host cell which influence reporter gene assay aforementioned should be considered.

Sp1 is essential for p16 expression in human diploid fibroblasts during senescence.

BACKGROUND: p16(INK4a) tumor suppressor protein has been widely proposed to mediate entrance of the cells into the senescent stage. Promoter of p16(INK4a) gene contains at least five putative GC boxes, named GC-I to V, respectively. Our previous data showed that a potential Sp1 binding site, within the promoter region from -466 to -451, acts as a positive transcription regulatory element. These results led us to examine how Sp1 and/or Sp3 act on these GC boxes during aging in cultured human diploid fibroblasts. METHODOLOGY/PRINCIPAL FINDINGS: Mutagenesis studies revealed that GC-I, II and IV, especially GC-II, are essential for p16(INK4a) gene expression in senescent cells. Electrophoretic mobility shift assays (EMSA) and ChIP assays demonstrated that both Sp1 and Sp3 bind to these elements and the binding activity is enhanced in senescent cells. Ectopic overexpression of Sp1, but not Sp3, induced the transcription of p16(INK4a). Both Sp1 RNAi and Mithramycin, a DNA intercalating agent that interferes with Sp1 and Sp3 binding activities, reduced p16(INK4a) gene expression. In addition, the enhanced binding of Sp1 to p16(INK4a) promoter during cellular senescence appeared to be the result of increased Sp1 binding affinity, not an alteration in Sp1 protein level. CONCLUSIONS/SIGNIFICANCE: All these results suggest that GC- II is the key site for Sp1 binding and increase of Sp1 binding activity rather than protein levels contributes to the induction of p16(INK4a) expression during cell aging.