Morphogens and pattern formation

Molecular evidence supports the functionality of a protein-trapped endogenous allele of Dally-like protein

The Drosophila glypican Dally-like protein (Dlp) is an evolutionarily-conserved cell-surface protein that modulates extracellular distribution of several secreted ligands for cell signaling. Several fly lines expressing tagged dlp have been used to study the role of Dlp in vivo including the PBac{602.P.SVS-1}dlp [CPTI000445] protein-trap line, which encodes StrepII-Venus-StrepII (SVS)-tagged Dlp from the endogenous locus. dlp is essential for embryonic development, and the SVS-dlp line is homozygous viable. Although this suggests that the SVS-tagged Dlp is functional, it is possible that that the SVS-dlp flies produce wild-type dlp isoform through alternative splicing, contributing to their survival. Here, we used a molecular analysis approach to show that the SVS-dlp flies do not produce wild-type isoform, confirming that the SVS-tagged Dlp is indeed functional.

Numerous Serine/Threonine Kinases Affect Blood Cell Homeostasis in Drosophila melanogaster

Blood cells in Drosophila serve primarily innate immune responses. Various stressors influence blood cell homeostasis regarding both numbers and the proportion of blood cell types. The principle molecular mechanisms governing hematopoiesis are conserved amongst species and involve major signaling pathways like Notch, Toll, JNK, JAK/Stat or RTK. Albeit signaling pathways generally rely on the activity of protein kinases, their specific contribution to hematopoiesis remains understudied. Here, we assess the role of Serine/Threonine kinases with the potential to phosphorylate the transcription factor Su(H) in crystal cell homeostasis. Su(H) is central to Notch signal transduction, and its inhibition by phosphorylation impedes crystal cell formation. Overall, nearly twenty percent of all Drosophila Serine/Threonine kinases were studied in two assays, global and hemocyte-specific overexpression and downregulation, respectively. Unexpectedly, the majority of kinases influenced crystal cell numbers, albeit only a few were related to hematopoiesis so far. Four kinases appeared essential for crystal cell formation, whereas most kinases restrained crystal cell development. This group comprises all kinase classes, indicative of the complex regulatory network underlying blood cell homeostasis. The rather indiscriminative response we observed opens the possibility that blood cells measure their overall phospho-status as a proxy for stress-signals, and activate an adaptive immune response accordingly.

Signaling oscillations in embryonic development

Tight spatiotemporal control of cellular behavior and cell fate decisions is paramount to the formation of multicellular organisms during embryonic development. Intercellular communication via signaling pathways mediates this control. Interestingly, these signaling pathways are not static, but dynamic and change in activity over time. Signaling oscillations as a specific type of dynamics are found in various signaling pathways and model systems. Functions of oscillations include the regulation of periodic events or the transmission of information by encoding signals in the dynamic properties of a signaling pathway. For instance, signaling oscillations in neural or pancreatic progenitor cells modulate their proliferation and differentiation. Oscillations between neighboring cells can also be synchronized, leading to the emergence of waves traveling through the tissue. Such population-wide signaling oscillations regulate for example the consecutive segmentation of vertebrate embryos, a process called somitogenesis. Here, we outline our current understanding of signaling oscillations in embryonic development, how signaling oscillations are generated, how they are studied and how they contribute to the regulation of embryonic development.

The many bits of positional information

Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?

Essential long-range action of Wingless/Wnt in adult intestinal compartmentalization

Signal transduction activated by Wingless/Wnt ligands directs cell proliferation and fate specification in metazoans, and its overactivation underlies the development of the vast majority of colorectal cancers. In the conventional model, the secretion and movement of Wingless to cells distant from its source of synthesis are essential for long-range signaling in tissue patterning. However, this model was upended recently by an unanticipated finding: replacement of wild-type Drosophila Wingless with a membrane-tethered form produced viable adults with largely normal external morphology, which suggested that Wingless secretion and movement are dispensable for tissue patterning. Herein, we tested this foundational principle in the adult intestine, where Wingless signaling gradients coincide with all major boundaries between compartments. We find that the critical roles of Wingless during adult intestinal development, which include regulation of target gene activation, boundary formation, stem cell proliferation, epithelial cell fate specification, muscle differentiation, gut folding, and signaling crosstalk with the Decapentaplegic pathway, are all disrupted by Wingless tethering. These findings provide new evidence that supports the requirement for the direct, long-range action of Wingless in tissue patterning, with relevance for animal development, tissue homeostasis and Wnt-driven disease.

Comparative Transcriptome Analyses Uncover Key Candidate Genes Mediating Flight Capacity in Bactrocera dorsalis (Hendel) and Bactrocera correcta (Bezzi) (Diptera: Tephritidae)

Flight capacity is important for invasive pests during entry, establishment and spreading. Both Bactroceradorsalis Hendel and Bactroceracorrecta Bezzi are invasive fruit flies but their flight capacities differ. Here, a tethered flight mill test demonstrated that B. dorsalis exhibits a greater flight capacity than B. correcta. RNA-Seq was used to determine the transcriptomic differences associated with the flight capacity of two Bactrocera species. Transcriptome data showed that 6392 unigenes were differentially expressed between the two species in the larval stage, whereas in the adult stage, 4104 differentially expressed genes (DEGs) were identified in females, and 3445 DEGs were observed in males. The flight capacity appeared to be correlated with changes in the transcriptional levels of genes involved in wing formation, flight muscle structure, energy metabolism, and hormonal control. Using RNA interference (RNAi) to verify the function of one DEG, the epidermal growth factor receptor (EGFR), we confirmed the role of this gene in regulating wing development, and thereby flight capacity, in both species. This work reveals the flight mechanism of fruit flies and provides insight into fundamental transcriptomics for further studies on the flight performance of insects.

Decoding temporal interpretation of the morphogen Bicoid in the early Drosophila embryo

Morphogen gradients provide essential spatial information during development. Not only the local concentration but also duration of morphogen exposure is critical for correct cell fate decisions. Yet, how and when cells temporally integrate signals from a morphogen remains unclear. Here, we use optogenetic manipulation to switch off Bicoid-dependent transcription in the early Drosophila embryo with high temporal resolution, allowing time-specific and reversible manipulation of morphogen signalling. We find that Bicoid transcriptional activity is dispensable for embryonic viability in the first hour after fertilization, but persistently required throughout the rest of the blastoderm stage. Short interruptions of Bicoid activity alter the most anterior cell fate decisions, while prolonged inactivation expands patterning defects from anterior to posterior. Such anterior susceptibility correlates with high reliance of anterior gap gene expression on Bicoid. Therefore, cell fates exposed to higher Bicoid concentration require input for longer duration, demonstrating a previously unknown aspect of Bicoid decoding.

DOI:http://dx.doi.org/10.7554/eLife.26258.001

GENETICS OF FLUCTUATING ASYMMETRY: A DEVELOPMENTAL MODEL OF DEVELOPMENTAL INSTABILITY

Although numerous studies have found that fluctuating asymmetry (FA) can have a heritable component, the genetic and developmental basis of FA is poorly understood. We used a developmental model of a trait, according to a diffusion-threshold process, whose parameters are under genetic control. We added a small amount of random variation to the parameter values of this model to simulate developmental noise. As a result of the nonlinearity of the model, different genotypes differed in their sensitivity to developmental noise, even though the noise is completely random and independent of the genotype. The heritable component of FA can thus be understood as genetically modulated expression of variation that is itself entirely nongenetic. The loci responsible for this genetic variation of FA are the same that affect the left/right mean of the trait, showing that genetic variation for FA does not require genes that specifically control FA. Furthermore, the model offers alternative explanations for phenomena widely discussed in the literature on FA, for instance, the correlations between FA and heterozygosity and between FA and trait size. The model underscores the importance of dominance and epistasis, and therefore unites the study of FA with the classical theory of quantitative genetics.

Wnt-Frizzled/planar cell polarity signaling: cellular orientation by facing the wind (Wnt)

The establishment of planar cell polarity (PCP) in epithelial and mesenchymal cells is a critical, evolutionarily conserved process during development and organogenesis. Analyses in Drosophila and several vertebrate model organisms have contributed a wealth of information on the regulation of PCP. A key conserved pathway regulating PCP, the so-called core Wnt-Frizzled PCP (Fz/PCP) signaling pathway, was initially identified through genetic studies of Drosophila. PCP studies in vertebrates, most notably mouse and zebrafish, have identified novel factors in PCP signaling and have also defined cellular features requiring PCP signaling input. These studies have shifted focus to the role of Van Gogh (Vang)/Vangl genes in this molecular system. This review focuses on new insights into the core Fz/Vangl/PCP pathway and recent advances in Drosophila and vertebrate PCP studies. We attempt to integrate these within the existing core Fz/Vangl/PCP signaling framework.

The morphogen Decapentaplegic employs a two-tier mechanism to activate target retinal determining genes during ectopic eye formation in Drosophila

Understanding the role of morphogen in activating its target genes, otherwise epigenetically repressed, during change in cell fate specification is a very fascinating yet relatively unexplored domain. Our in vivo loss-of-function genetic analyses reveal that specifically during ectopic eye formation, the morphogen Decapentaplegic (Dpp), in conjunction with the canonical signaling responsible for transcriptional activation of retinal determining (RD) genes, triggers another signaling cascade. Involving dTak1 and JNK, this pathway down-regulates the expression of polycomb group of genes to do away with their repressive role on RD genes. Upon genetic inactivation of members of this newly identified pathway, the canonical Dpp signaling fails to trigger RD gene expression beyond a threshold, critical for ectopic photoreceptor differentiation. Moreover, the drop in ectopic RD gene expression and subsequent reduction in ectopic photoreceptor differentiation resulting from inactivation of dTak1 can be rescued by down-regulating the expression of polycomb group of genes. Our results unravel an otherwise unknown role of morphogen in coordinating simultaneous transcriptional activation and de-repression of target genes implicating its importance in cellular plasticity.

Coordination of patterning and growth by the morphogen DPP

The elegance of animal body plans derives from an intimate connection between function and form, which during organ formation is linked to patterning and growth. Yet, how patterning and growth are coordinated still remains largely a mystery. To study this question the Drosophila wing imaginal disc, an epithelial primordial organ that later forms the adult wing, has proven to be an invaluable and versatile model. Wing disc development is organized around a coordinate system provided by morphogens such as the TGF-β homolog Decapentaplegic (DPP). The function of DPP has been studied at multiple levels: ranging from the kinetics of gradient formation to the establishment and maintenance of target gene domains as well as DPP's role in growth control. Here, we focus on recent publications that both enrich our view of DPP signaling but also highlight outstanding questions of how DPP coordinates patterning and growth during development.

Dynamic signal encoding--from cells to organisms

Encoding information at the level of signal dynamics is characterized by distinct features, such as robustness to noise and high information content. Currently, a growing number of studies are unravelling the functional importance of signalling dynamics at the single cell level. In addition, first insights are emerging into how the principles of dynamic signal encoding apply to a multicellular context, such as development. In this review, we will first discuss general concepts of information transmission via signalling dynamics and recent experimental examples focusing on underlying principles, including the role of intracellular network topologies. How multicellular organisms use temporal modulation of specific signalling pathways, such as signalling gradients or oscillations, to faithfully control cell fate decisions and pattern formation will also be addressed. Finally, we will consider how technical advancements in the detection and perturbation of signalling dynamics contribute to reshaping our understanding of dynamic signalling in developing organisms.

Wnt and lithium: a common destiny in the therapy of nervous system pathologies?

Wnt signaling is required for neurogenesis, the fate of neural progenitors, the formation of neuronal circuits during development, neuron positioning and polarization, axon and dendrite development and finally for synaptogenesis. This signaling pathway is also implicated in the generation and differentiation of glial cells. In this review, we describe the mechanisms of action of Wnt signaling pathways and their implication in the development and correct functioning of the nervous system. We also illustrate how a dysregulated Wnt pathway could lead to psychiatric, neurodegenerative and demyelinating pathologies. Lithium, used for the treatment of bipolar disease, inhibits GSK3β, a central enzyme of the Wnt/β-catenin pathway. Thus, lithium could, to some extent, mimic Wnt pathway. We highlight the possible dialogue between lithium therapy and modulation of Wnt pathway in the treatment of the diseases of the nervous system.

Wnt6 is required for maxillary palp formation in Drosophila

Background

Wnt6 is an evolutionarily ancient member of the Wnt family. In Drosophila, Wnt6 loss-of-function animals have not yet been reported, hence information about fly Wnt6 function is lacking. In wing discs, Wnt6 is expressed at the dorsal/ventral boundary in a pattern similar to that of wingless, an important regulator of wing size. To test whether Wnt6 also contributes towards wing size regulation, we generated Wnt6 knockout flies.

Results

Wnt6 knockout flies are viable and have no obvious defect in wing size or planar cell polarity. Surprisingly, Wnt6 knockouts lack maxillary palps. Interestingly, Wnt6 is absent from the genome of hemipterans, correlating with the absence of maxillary palps in these insects.

Conclusions

Wnt6 is important for maxillary palp development in Drosophila, and phylogenetic analysis indicates that loss of Wnt6 may also have led to loss of maxillary palps on an evolutionary time scale.

Chemistry with spatial control using particles and streams()

Spatial control of chemical reactions, with micro- and nanometer scale resolution, has important consequences for one pot synthesis, engineering complex reactions, developmental biology, cellular biochemistry and emergent behavior. We review synthetic methods to engineer this spatial control using chemical diffusion from spherical particles, shells and polyhedra. We discuss systems that enable both isotropic and anisotropic chemical release from isolated and arrayed particles to create inhomogeneous and spatially patterned chemical fields. In addition to such finite chemical sources, we also discuss spatial control enabled with laminar flow in 2D and 3D microfluidic networks. Throughout the paper, we highlight applications of spatially controlled chemistry in chemical kinetics, reaction-diffusion systems, chemotaxis and morphogenesis.

The WIF domain of the human and Drosophila Wif-1 secreted factors confers specificity for Wnt or Hedgehog

The Hedgehog (Hh) and Wnt signaling pathways are crucial for development as well as for adult stem cell maintenance in all organisms from Drosophila to humans. Aberrant activation of these pathways has been implicated in many types of human cancer. During evolution, organisms have developed numerous ways to fine-tune Wnt and Hh signaling. One way is through extracellular modulators that directly interact with Wnt or Hh, such as the Wnt inhibitory factor (Wif-1) family of secreted factors. Interestingly, Wif-1 family members have divergent functions in the Wnt and Hh pathways in different organisms. Whereas vertebrate Wif-1 blocks Wnt signaling, Drosophila Wif-1 [Shifted (Shf)] regulates only Hh distribution and spreading through the extracellular matrix. Here, we investigate which parts of the Shf and human Wif-1 (WIF1) proteins are responsible for functional divergence. We analyze the behavior of domain-swap (the Drosophila and human WIF domain and EGF repeats) chimeric constructs during wing development. We demonstrate that the WIF domain confers the specificity for Hh or Wg morphogen. The EGF repeats are important for the interaction of Wif-1 proteins with the extracellular matrix; Drosophila EGF repeats preferentially interact with the glypican Dally-like (Dlp) when the WIF domain belongs to human WIF1 and with Dally when the WIF domain comes from Shf. These results are important both from the evolutionary perspective and for understanding the mechanisms of morphogen distribution in a morphogenetic field.

COLONY FORMATION AND SEXUAL MORPHOGENESIS IN THE COCCOLITHOPHORE PLEUROCHRYSIS SP. (HAPTOPHYTA)(1)

Pleurochrysis sp. formed two types of symmetrical, diploid colonies on solid media: (i) single-cell lineage (SCL) colonies and (ii) aggregation (AG) colonies. The first division of a single mother cell was asymmetric in ∼54% of SCL colonies. These colonies developed at a slower rate than AG colonies. Diffusible molecules released from the cells acted like morphogens enhancing formation of AG colonies; their influence on chemotaxis of aggregating cells was dependent on concentration of the inoculum. Nitrogen depletion of diploid colonies induced sexual morphogenesis and colony patterning into inner and outer regions. The smaller innermost cells were surrounded by outer larger cells. Developmental mechanisms of colony formation were examined in relation to the heteromorphic, haplo-diploid life cycle.

A secreted BMP antagonist, Cer1, fine tunes the spatial organization of the ureteric bud tree during mouse kidney development

The epithelial ureteric bud is critical for mammalian kidney development as it generates the ureter and the collecting duct system that induces nephrogenesis in dicrete locations in the kidney mesenchyme during its emergence. We show that a secreted Bmp antagonist Cerberus homologue (Cer1) fine tunes the organization of the ureteric tree during organogenesis in the mouse embryo. Both enhanced ureteric expression of Cer1 and Cer1 knock out enlarge kidney size, and these changes are associated with an altered three-dimensional structure of the ureteric tree as revealed by optical projection tomography. Enhanced Cer1 expression changes the ureteric bud branching programme so that more trifid and lateral branches rather than bifid ones develop, as seen in time-lapse organ culture. These changes may be the reasons for the modified spatial arrangement of the ureteric tree in the kidneys of Cer1+ embryos. Cer1 gain of function is associated with moderately elevated expression of Gdnf and Wnt11, which is also induced in the case of Cer1 deficiency, where Bmp4 expression is reduced, indicating the dependence of Bmp expression on Cer1. Cer1 binds at least Bmp2/4 and antagonizes Bmp signalling in cell culture. In line with this, supplementation of Bmp4 restored the ureteric bud tip number, which was reduced by Cer1+ to bring it closer to the normal, consistent with models suggesting that Bmp signalling inhibits ureteric bud development. Genetic reduction of Wnt11 inhibited the Cer1-stimulated kidney development, but Cer1 did not influence Wnt11 signalling in cell culture, although it did inhibit the Wnt3a-induced canonical Top Flash reporter to some extent. We conclude that Cer1 fine tunes the spatial organization of the ureteric tree by coordinating the activities of the growth-promoting ureteric bud signals Gndf and Wnt11 via Bmp-mediated antagonism and to some degree via the canonical Wnt signalling involved in branching.

Secreted, receptor-associated bone morphogenetic protein regulators reduce stochastic noise intrinsic to many extracellular morphogen distributions

Morphogens are secreted molecules that specify cell-fate organization in developing tissues. Patterns of gene expression or signalling immediately downstream of many morphogens such as the bone morphogenetic protein (BMP) decapentaplegic (Dpp) are highly reproducible and robust to perturbations. This contrasts starkly with our expectation of a noisy interpretation that would arise out of the experimentally determined low concentration (approximately picomolar) range of Dpp activity, tight receptor binding and very slow kinetic rates. To investigate mechanisms by which the intrinsic noise can be attenuated in Dpp signalling, we focus on a class of secreted proteins that bind to Dpp in the extracellular environment and play an active role in regulating Dpp/receptor interactions. We developed a stochastic model of Dpp signalling in Drosophila melanogaster and used the model to quantify the extent that stochastic fluctuations would lead to errors in spatial patterning and extended the model to investigate how a surface-associated BMP-binding protein (SBP) such as Crossveinless-2 (Cv-2) may buffer out signalling noise. In the presence of SBPs, fluctuations in the level of ligand-bound receptor can be reduced by more than twofold depending on parameter values for the intermediate transition states. Regulation of receptor-ligand interactions by SBPs may also increase the frequency of stochastic fluctuations providing a separation of timescales between high-frequency receptor equilibration and slower morphogen patterning. High-frequency noise generated by SBP regulation is easily attenuated by the intracellular network creating a system that imitates the performance of a simple low-pass filter common in audio and communication applications. Together, these data indicate that one of the benefits of receptor-ligand regulation by secreted non-receptors may be greater reliability of morphogen patterning mechanisms.

The sleeping brain as a complex system

'Complexity science' is a rapidly developing research direction with applications in a multitude of fields that study complex systems consisting of a number of nonlinear elements with interesting dynamics and mutual interactions. This Theme Issue 'The complexity of sleep' aims at fostering the application of complexity science to sleep research, because the brain in its different sleep stages adopts different global states that express distinct activity patterns in large and complex networks of neural circuits. This introduction discusses the contributions collected in the present Theme Issue. We highlight the potential and challenges of a complex systems approach to develop an understanding of the brain in general and the sleeping brain in particular. Basically, we focus on two topics: the complex networks approach to understand the changes in the functional connectivity of the brain during sleep, and the complex dynamics of sleep, including sleep regulation. We hope that this Theme Issue will stimulate and intensify the interdisciplinary communication to advance our understanding of the complex dynamics of the brain that underlies sleep and consciousness.

Cell-sorting at the A/P boundary in the Drosophila wing primordium: a computational model to consolidate observed non-local effects of Hh signaling

Non-intermingling, adjacent populations of cells define compartment boundaries; such boundaries are often essential for the positioning and the maintenance of tissue-organizers during growth. In the developing wing primordium of Drosophila melanogaster, signaling by the secreted protein Hedgehog (Hh) is required for compartment boundary maintenance. However, the precise mechanism of Hh input remains poorly understood. Here, we combine experimental observations of perturbed Hh signaling with computer simulations of cellular behavior, and connect physical properties of cells to their Hh signaling status. We find that experimental disruption of Hh signaling has observable effects on cell sorting surprisingly far from the compartment boundary, which is in contrast to a previous model that confines Hh influence to the compartment boundary itself. We have recapitulated our experimental observations by simulations of Hh diffusion and transduction coupled to mechanical tension along cell-to-cell contact surfaces. Intriguingly, the best results were obtained under the assumption that Hh signaling cannot alter the overall tension force of the cell, but will merely re-distribute it locally inside the cell, relative to the signaling status of neighboring cells. Our results suggest a scenario in which homotypic interactions of a putative Hh target molecule at the cell surface are converted into a mechanical force. Such a scenario could explain why the mechanical output of Hh signaling appears to be confined to the compartment boundary, despite the longer range of the Hh molecule itself. Our study is the first to couple a cellular vertex model describing mechanical properties of cells in a growing tissue, to an explicit model of an entire signaling pathway, including a freely diffusible component. We discuss potential applications and challenges of such an approach.

In developing animal tissues, cells can often re-arrange locally and mix relatively freely. However, in some stereotypic and crucially important instances during body development, cells will strictly not intermingle, and instead form sharp boundaries along which they will sort out from each other. This mechanism helps organisms to establish signaling centers and to maintain distinct cellular identities. Often, cells at such boundaries will remain in close physical contact and are morphologically alike. Thus, the boundary itself can be difficult to observe unless the expression status of specific marker genes is monitored experimentally. How are these ‘compartment boundaries’ established? Here we devise a computational model that aims to describe one such boundary in a well-studied animal tissue: the developing wing primordium of Drosophila melanogaster. We model the production, diffusion and local sensing of an essential signaling molecule, the Hedgehog protein. We reveal one possible mechanism by which Hedgehog sensing can influence the mechanical properties of cells, and compare the simulated outcome to observations in experimentally perturbed, actual wing discs. Our relatively simple model suffices to establish a straight and stable compartment boundary.

Wnt signaling signaling at and above the receptor level

Wnt signaling is one of the most important developmental signaling pathways that controls cell fate decisions and tissue patterning during early embryonic and later development. It is activated by highly conserved Wnt proteins that are secreted as palmitoylated glycoproteins and act as morphogens to form a concentration gradient across a developing tissue. Wnt proteins regulate transcriptional and posttranscriptional processes depending on the distance of their origin and activate distinct intracellular cascades, commonly referred to as canonical (β-catenin-dependent) and noncanonical (β-catenin-independent) pathways. Therefore, the secretion and the diffusion of Wnt proteins needs to be tightly regulated to induce short- and long-range downstream signaling. Even though the Wnt signaling cascade has been studied intensively, key aspects and principle mechanisms, such as transport of Wnt growth factors or regulation of signaling specificity between different Wnt pathways, remain unresolved. Here, we introduce basic principles of Wnt/Wg signal transduction and highlight recent discoveries, such as the involvement of vacuolar ATPases and vesicular acidification in Wnt signaling. We also discuss recent findings regarding posttranslational modifications of Wnts, trafficking through the secretory pathway and developmental consequences of impaired Wnt secretion. Understanding the detailed mechanism and regulation of Wnt protein secretion will provide valuable insights into many human diseases based on overactivated Wnt signaling.

Generation of complex concentration profiles by partial diffusive mixing in multi-stream laminar flow

This paper proposes novel microfluidic concentration gradient generator (CGG) devices that are capable of constructing complex profiles of chemical concentrations by laterally combining the constituent profiles (e.g., linear and bell-shaped) generated in simple Y- or psi-shaped mixers. While the majority of currently existing CGG devices are based on complete mixing of chemical species, our design harnesses partial diffusive mixing in multi-stream laminar flow, and hence, features simple network structures and enhanced device reliability. An iterative simulation approach that incorporates our previous system-level models of CGG networks is developed to locate best-matched combinations of geometrical and operating parameters (e.g., inlet flow rates and inlet sample concentrations) for the device design. Microfluidic CGG chips are fabricated and experimentally characterized using optimal layout and operating conditions selected by the design process. The experimental results not only serve as a benchmark for model verification but also establish the feasibility of concentration gradient generation based on partial mixing for a variety of microfluidic applications.

Global analysis of alternative splicing regulation by insulin and wingless signaling in Drosophila cells

BACKGROUND

Despite the prevalence and biological relevance of both signaling pathways and alternative pre-mRNA splicing, our knowledge of how intracellular signaling impacts on alternative splicing regulation remains fragmentary. We report a genome-wide analysis using splicing-sensitive microarrays of changes in alternative splicing induced by activation of two distinct signaling pathways, insulin and wingless, in Drosophila cells in culture.

RESULTS

Alternative splicing changes induced by insulin affect more than 150 genes and more than 50 genes are regulated by wingless activation. About 40% of the genes showing changes in alternative splicing also show regulation of mRNA levels, suggesting distinct but also significantly overlapping programs of transcriptional and post-transcriptional regulation. Distinct functional sets of genes are regulated by each pathway and, remarkably, a significant overlap is observed between functional categories of genes regulated transcriptionally and at the level of alternative splicing. Functions related to carbohydrate metabolism and cellular signaling are enriched among genes regulated by insulin and wingless, respectively. Computational searches identify pathway-specific sequence motifs enriched near regulated 5' splice sites.

CONCLUSIONS

Taken together, our data indicate that signaling cascades trigger pathway-specific and biologically coherent regulatory programs of alternative splicing regulation. They also reveal that alternative splicing can provide a novel molecular mechanism for crosstalk between different signaling pathways.

Modular microfluidics for gradient generation

This paper describes a modular approach to constructing microfluidic systems for the generation of gradients of arbitrary profiles. Unlike most current microfluidic-based systems that have integrated architectures, we design several basic component modules such as distributors, combiners, resistors and collectors and connect them into networks that produce gradients of any profile at will. Using the system as a platform we can generate arbitrary gradient profiles that are tunable in real time. The key advantage of this system is that its operation is based on prefabricated components that are relatively simple. Particularly for non-specialists, the modular microfluidic system is easier to implement and more versatile compared to single, integrated gradient generators. The disadvantages associated with this system is that the total amount of liquids used is rather large compared with single chip-based systems. The system would be useful in simulating environments in vivo, e.g., studying how cells respond to temporal and spatial stimuli.

Review: cancer immunotherapy by exosome-based vaccines

Exosomes (EXOs) are nanometer-sized membrane vesicles secreted from epithelial and hematopoietic cells. They display a spectrum of molecules involved in immune responses and signal transductions. Previous studies showed that tumor antigen-loaded dendritic cell (DC)- and tumor cell-derived EXOs (Dexo and Texo) induce tumor antigen-specific CD8(+) cytotoxic T-lymphocyte responses and antitumor immunity in experimental animal models and human clinical trials. This review will present the main biologic features of Dexo and Texo as cell-free cancer vaccines with emphasis on their immunostimulatory properties and their potential efficacy in cancer immunotherapy.

Morphogens, morphostats, microarchitecture and malignancy

Morphogenetic fields organize tissue morphology in the embryo. By analogy, morphostatic fields maintain normal cell behaviour and normal tissue microarchitecture in the adult. The most prominent feature of cancer is the disruption of tissue microarchitecture. Cancer occurs much more frequently when morphostatic influences fail (metaplasia) or at the junction of two different morphostatic fields. This Review will describe what we know about morphostats and morphostasis, discuss the evidence for the role of disruption of morphostasis in malignancy, and address some testable hypotheses.

Dynamic decapentaplegic signaling regulates patterning and adhesion in the Drosophila pupal retina

The correct organization of cells within an epithelium is essential for proper tissue and organ morphogenesis. The role of Decapentaplegic/Bone morphogenetic protein (Dpp/BMP) signaling in cellular morphogenesis during epithelial development is poorly understood. In this paper, we used the developing Drosophila pupal retina--looking specifically at the reorganization of glial-like support cells that lie between the retinal ommatidia--to better understand the role of Dpp signaling during epithelial patterning. Our results indicate that Dpp pathway activity is tightly regulated across time in the pupal retina and that epithelial cells in this tissue require Dpp signaling to achieve their correct shape and position within the ommatidial hexagon. These results point to the Dpp pathway as a third component and functional link between two adhesion systems, Hibris-Roughest and DE-cadherin. A balanced interplay between these three systems is essential for epithelial patterning during morphogenesis of the pupal retina. Importantly, we identify a similar functional connection between Dpp activity and DE-cadherin and Rho1 during cell fate determination in the wing, suggesting a broader link between Dpp function and junctional integrity during epithelial development.

Transdetermination: Drosophila imaginal disc cells exhibit stem cell-like potency

Drosophila imaginal discs, the primordia of the adult fly appendages, are an excellent system for studying developmental plasticity. Cells in the imaginal discs are determined for their disc-specific fate (wingness, legness) during embryogenesis. Disc cells maintain their determination during larval development, a time of extensive growth and proliferation. Only when prompted to regenerate do disc cells exhibit lability in their determined identity. Regeneration in the disc is mediated by a localized region of cell division, known as the regeneration blastema. Most regenerating disc cells strictly adhere to their disc-specific identity; some cells however, switch fate in a phenomenon known as transdetermination. Similar regeneration and transdetermination events can be induced in situ by misexpression of the signaling molecule wingless. Recent studies indicate that the plasticity of disc cells during regeneration is associated with high morphogen activity and the reorganization of chromatin structure. Here we provide both a historical perspective of imaginal disc transdetermination, as well as discuss recent findings on how imaginal disc cells acquire developmental plasticity and multipotency. We also highlight how an understanding of imaginal disc transdetermination can enhance an understanding of developmental potency exhibited by stem cells.

Controlled overexpression of Pax6 in vivo negatively autoregulates the Pax6 locus, causing cell-autonomous defects of late cortical progenitor proliferation with little effect on cortical arealization

Levels of expression of the transcription factor Pax6 vary throughout corticogenesis in a rostro-lateral(high) to caudo-medial(low) gradient across the cortical proliferative zone. Previous loss-of-function studies have indicated that Pax6 is required for normal cortical progenitor proliferation, neuronal differentiation, cortical lamination and cortical arealization, but whether and how its level of expression affects its function is unclear. We studied the developing cortex of PAX77 YAC transgenic mice carrying several copies of the human PAX6 locus with its full complement of regulatory regions. We found that PAX77 embryos express Pax6 in a normal spatial pattern, with levels up to three times higher than wild type. By crossing PAX77 mice with a new YAC transgenic line that reports Pax6 expression (DTy54), we showed that increased expression is limited by negative autoregulation. Increased expression reduces proliferation of late cortical progenitors specifically, and analysis of PAX77<---->wild-type chimeras indicates that the defect is cell autonomous. We analyzed cortical arealization in PAX77 mice and found that, whereas the loss of Pax6 shifts caudal cortical areas rostrally, Pax6 overexpression at levels predicted to shift rostral areas caudally has very little effect. These findings indicate that Pax6 levels are stabilized by autoregulation, that the proliferation of cortical progenitors is sensitive to altered Pax6 levels and that cortical arealization is not.

On the dynamic nature of positional information

Morphogenetic fields are among the most fundamental concepts of embryology. However, they are also among the most ill-defined, since they consist of dynamic regulatory processes whose exact nature remains elusive. In order to achieve a more rigorous definition of a developmental field, Lewis Wolpert introduced the concept of positional information illustrated by his French Flag model. Here we argue that Wolpert's positional information - a static coordinate system defining a field - lacks essential properties of the original field concept. We show how data-driven mathematical modeling approaches now enable us to study regulatory processes in a way that is qualitatively different from our previous level of understanding. As an example, we review our recent analysis of segmentation gene expression in the blastoderm embryo of the fruit fly Drosophila melanogaster. Based on this analysis, we propose a revised French Flag, which incorporates the dynamic, feedback-driven nature of pattern formation in the Drosophila blastoderm.

The Hippo pathway regulates the bantam microRNA to control cell proliferation and apoptosis in Drosophila

The Hippo signaling pathway acts upon the Yorkie transcriptional activator to control tissue growth in Drosophila. Activated Yorkie drives growth by stimulating cell proliferation and inhibiting apoptosis, but how it achieves this is not understood. Yorkie is known to activate Cyclin E (CycE) and the apoptosis inhibitor DIAP1. However, overexpression of these targets is not sufficient to cause tissue overgrowth. Here we show that Yorkie also activates expression of the bantam microRNA, a known regulator of both proliferation and apoptosis. bantam overexpression mimics Yorkie activation while loss of bantam function slows the rate of cell proliferation. bantam is necessary for Yorkie-induced overproliferation and bantam overexpression is sufficient to rescue survival and proliferation of yorkie mutant cells. Finally, we show that bantam levels are regulated during both developmentally programmed proliferation arrest and apoptosis. In summary, the results show that the Hippo pathway regulates expression of bantam to control tissue growth in Drosophila.

Exosomes: from biogenesis and secretion to biological function

Exosomes are small microvesicles that are released from late endosomal compartments of cultured cells. Recent work has shown that exosome-like vesicles are also found in many body fluids such as blood, urine, ascites and amnionic fluid. Although the biological function of exosomes is far from being fully understood, exosomes may have general importance in cell biology and immunology. The present review aims to address some of the facets of exosome research with particular emphasis on the immunologist's perspective: (i) exosomes as a novel platform for the ectodomain shedding of membrane proteins by ADAMs and (ii) recent findings on the role of exosomes in tumor biology and immune regulation.

Strength of signal: a fundamental mechanism for cell fate specification

How equipotent cells develop into complex tissues containing many diverse cell types is still a mystery. However, evidence is accumulating from different tissue systems in multiple organisms that many of the specific receptor families known to regulate cell fate decisions target conserved signaling pathways. A mechanism for preserving specificity in the cellular response that has emerged from these studies is one in which quantitative differences in receptor signaling regulate the cell fate decision. A signal strength model has recently gained support as a means to explain alphabeta/gammadelta lineage commitment. In this review, we compare the alphabeta/gammadelta fate decision with other cell fate decisions that occur outside of the lymphoid system to attain a better picture of the quantitative signaling mechanism for cell fate specification.

Mutation of an upstream cleavage site in the BMP4 prodomain leads to tissue-specific loss of activity

ProBMP4 is initially cleaved at a site adjacent to the mature ligand (the S1 site) allowing for subsequent cleavage at an upstream (S2) site. Mature BMP4 synthesized from a precursor in which the S2 site cannot be cleaved remains in a complex with the prodomain that is targeted for lysosomal degradation, and is thus less active when overexpressed in Xenopus. Here we report that mice carrying a point mutation that prevents S2 processing show severe loss of BMP4 activity in some tissues, such as testes and germ cells, whereas other tissues that are sensitive to Bmp4 dosage, such as the limb, dorsal vertebrae and kidney, develop normally. In a haploinsufficient background, inability to cleave the S2 site leads to embryonic and postnatal lethality due to defects in multiple organ systems including the allantois, placental vasculature, ventral body wall, eye and heart. These data demonstrate that cleavage of the S2 site is essential for normal development and, more importantly, suggest that this site might be selectively cleaved in a tissue-specific fashion. In addition, these studies provide the first genetic evidence that BMP4 is required for dorsal vertebral fusion and closure of the ventral body wall.

Generation of Complex, Static Solution Gradients in Microfluidic Channels

A microfluidic device is used to generate a complex gradient of diffusible molecules in a static solution. The gradient is precise and steady both in space and in time. This device, made from poly(dimethylsiloxane), consists of three layers. The molecules in reservoirs on the top layer diffuse through the flat middle layer of hydrogel and reach an equilibrium distribution. Microfluidic channels on the bottom layer that are in close contact with the hydrogel contain free solution that has concentration gradients based on the gradient in the gel. The gradient profile in the channel can be designed to have an arbitrary form (within the range of the existing gradient in the hydrogel) by controlling the local direction of the channel at each point.

Filtering transcriptional noise during development: concepts and mechanisms

The assignation of cell fates during eukaryotic development relies on the coordinated and stable expression of cohorts of genes within cell populations. The precise and reproducible nature of this process is remarkable given that, at the single-cell level, the transcription of individual genes is associated with noise - random molecular fluctuations that create variability in the levels of gene expression within a cell population. Here we consider the implications of transcriptional noise for development and suggest the existence of molecular devices that are dedicated to filtering noise. On the basis of existing evidence, we propose that one such mechanism might depend on the Wnt signalling pathway.

In vivo cell biology: following the zebrafish trend

A deeper understanding of the mechanisms of cell behavior is essential if we want to comprehend how an organism develops and functions. Changes in cellular processes, including the orientation of cell divisions, cell shape, polarity, differentiation and migration, account for tissue rearrangements during development and homeostasis. The in vivo relevance of in vitro findings is being constantly debated and the need for in vivo systems becoming more pressing. The zebrafish (Danio rerio) might become the vertebrate system of choice for a wide spectrum of biological questions that need to be investigated in vivo at cellular and subcellular resolutions. Here, we discuss some recent studies in which the zebrafish was used to gain insight into cell-biological mechanisms. Although this model system has been predominantly appreciated for its amenability to forward genetics, current advances in imaging technology and an increasing number of transgenic lines are bringing it closer to its full potential.

The endocytic pathway and formation of the Wingless morphogen gradient

Controlling the spread of morphogens is crucial for pattern formation during development. In the Drosophila wing disc, Wingless secreted at the dorsal-ventral compartment boundary forms a concentration gradient in receiving tissue, where it activates short- and long-range target genes. The glypican Dally-like promotes Wingless spreading by unknown mechanisms, while Dynamin-dependent endocytosis is thought to restrict Wingless spread. We have utilized short-term expression of dominant negative Rab proteins to examine the polarity of endocytic trafficking of Wingless and its receptors and to determine the relative contributions of endocytosis, degradation and recycling to the establishment of the Wingless gradient. Our results show that Wingless is internalized via two spatially distinct routes: one on the apical, and one on the basal, side of the disc. Both restrict the spread of Wingless, with little contribution from subsequent degradation or recycling. As previously shown for Frizzled receptors, depleting Arrow does not prevent Wingless from entering endosomes. We find that both Frizzled and Arrow are internalized mainly from the apical membrane. Thus, the basal Wingless internalization route must be independent of these proteins. We find that Dally-like is not required for Wingless spread when endocytosis is blocked, and propose that Dally-like promotes the spread of Wingless by directing it to lateral membranes, where its endocytosis is less efficient. Thus, subcellular localization of Wingless along the apical-basal axis of receiving cells may be instrumental in shaping the Wingless gradient.

Ability of scalloped deletion constructs to rescue sd mutant wing phenotypes in Drosophila melanogaster

Scalloped (SD) and Vestigial (VG) proteins physically interact to form a selector complex that activates genes involved in wing development in Drosophila melanogaster. SD belongs to a conserved family of transcription factors containing the TEA/ATTS DNA-binding motif. VG is also a nuclear protein providing the activator function for the SD VG complex. The TEA DNA-binding domain and the VG interacting domain (VID) of SD have been previously identified and described. However, they, and possibly other functional domains of SD, have not been thoroughly characterized in vivo. Herein, transgenic constructs encoding various truncations of SD were used to assess their respective ability to rescue the mutant wing phenotype of two viable sd recessive mutations (sd(ETX4) and sd(58d)). The transgenic strains produced were also tested for the ability to induce further sd expression, an ability possessed by full length SD. The functional dissection of SD confirms that specific regions are necessary for wing development and provides further information as to how the SD VG complex functions to promote wing fate. Previous experiments have shown that expression of full length SD can cause a dominant negative wing phenotype. We show that expression of constructs that delete the SD DNA-binding domain can also cause a dominant negative phenotype in a background with either of the two tester sd strains. In contrast, SD constructs that delete the VID have no effect on the wing phenotype in either tester background. Finally, a significant portion of SD at the N-terminal end appears to be dispensable with respect to normal wing development, as this construct behaves the same as full length SD in our assays.

Regiospecific control of protein expression in cells cultured on two-component counter gradients of extracellular matrix proteins

This work describes the use of microfluidic tools to generate covalently immobilized counter gradients of extracellular matrix (ECM) proteins laminin and collagen I. Using these platforms, we demonstrate control of the expression levels of two proteins linked to cell cycle progression by virtue of the spatial location of cells on the gradients, and hence by the local ECM environments in these devices. In contrast to physisorbed gradients, covalently immobilized protein patterns preserved the gradient fidelity, making long term cell studies feasible. This method of precisely controlling local cell environments is simple and broadly portable to other cell types and to other ECM proteins or soluble factors. Our approach promises to enable new investigations in cell biology that will contribute to the establishment of biological design rules for controlling cell growth, differentiation, and function.

Effects of Wnt signaling on proliferation and differentiation of human mesenchymal stem cells

Mesenchymal stem cells are pluripotent cells from bone marrow, which can be differentiated into the osteogenic, chondrogenic, and adipogenic lineages in vitro and are a source of cells in bone and cartilage tissue engineering. An improvement in current tissue-engineering protocols requires more detailed insight into the molecular cues that regulate the distinct steps of osteochondral differentiation. Because Wnt signaling has been widely implicated in mesenchymal differentiation, we analyzed the role of Wnt signaling in human mesenchymal stem cell (hMSC) biology by stimulation of the pathway with lithium chloride and Wnt3A-conditioned medium. We demonstrate a role for low levels of Wnt signaling in proliferation of uncommitted hMSCs and confirm that Wnt signaling controls osteoprogenitor proliferation. On the other hand, at high Wnt levels we observed a block in adipogenic differentiation and an increase in the expression of alkaline phosphatase, suggesting a role in the initiation of osteogenesis. The results of this study suggest that bone tissue engineering could benefit from the activation of critical levels of Wnt signaling at defined stages of differentiation. Moreover, our data suggest that hMSCs provide a valid in vitro model to study the role of Wnt signaling in mesenchymal biology.

Sustained Wnt protein expression in chondral constructs from mesenchymal stem cells

Wnt genes encode a number of secreted glycoproteins which are closely associated with the cell surface and the extracellular matrix. Recently, members of Wnt family have been implicated in regulating chondrocyte differentiation, but their roles in the chondrogenic process are not fully understood. To contribute to an understanding of the roles of Wnts during chondrogenesis, we have analysed the spatiotemporal expression patterns of Wnt using in vitro models for chondrogenesis of human bone marrow-derived mesenchymal stem cells (hMSCs). In chondrogenic aggregate culture system, RT-PCR analysis revealed expression of Wnt5a and Wnt4 during late chondrogenesis (days 10 and 15). Immunohistochemical analysis showed widespread distribution of Wnt5a and Wnt4 throughout the aggregates at this late phase of culture (days 14 and 21). In addition, in this aggregate culture system, immunohistochemical staining of Wnt4 and Wnt5a showed similar spatiotemporal expression patterns to that of type II collagen or type X collagen. To confirm the results obtained by immunostaining, the specificity of the anti-Wnt4 or anti-Wnt5a antibody was assessed by Western blot analysis. Of Wnt4 and Wnt5a, only Wnt5a was immunodetectable by Western blot analysis. Western blot analysis showed that Wnt5a was expressed as two different molecular weight forms of 40 and 44 kDa. Treatment with PNGase F, which removes N-linked oligosaccharides, revealed that the mass difference between these two forms could be accounted for by the N-glycosylation status of the protein. When hMSCs were seeded on a porous gelatin sponge, immunolocalization studies showed that type II collagen and type X collagen were detected particularly at the periphery at day 7 of culture. In contrast, Wnt4 and Wnt5a showed even distribution throughout the hMSC/gelatin sponge constructs. Their different spatial expression patterns suggest that Wnt4 and Wnt5a proteins are not functionally linked to type II collagen and type X collagen synthesis in in vitro chondrogenic models of hMSCs.

Patterned cell determination in a plant tissue: The secondary phloem of trees

The secondary vascular tissues (xylem and phloem) of woody plants originate from a vascular cambium and develop as radially oriented files of cells. The secondary phloem is composed of three or four cell types, which are organised into characteristic recurrent cellular sequences within the radial cell files of this tissue. There is a gradient of auxin (indole acetic acid) across both the cambium and the immediately postmitotic cells within the xylem and phloem domains, and it is believed that this morphogen, probably in concert with other morphogenic factors, is closely associated with the determination and differentiation of the different cells types in each tissue. A hypothesis is developed that, in conjunction with the positional values conferred by the graded radial distribution of morphogen, cell divisions at particular positions within the cambium are sufficient to determine not only each of the phloem cell types but also their recurrent pattern of differentiation within each radial cell file.