Top PDF Dorsal Ventral Patterning and Gene Regulation in the Early Embryo of Drosophila melanogaster

Dorsal Ventral Patterning and Gene Regulation in the Early Embryo of Drosophila melanogaster

Dorsal Ventral Patterning and Gene Regulation in the Early Embryo of Drosophila melanogaster

Additional evidence also suggests that TGF-ß signaling may also regulate the ind expression domains, but whether or not this signaling pathway functions through the A- box element was not known. Decapentaplegic (Dpp) is a TGFß/BMP homolog that is limited in its expression to dorsal regions of the embryo and functions as a morphogen to support patterning of the amnioserosa, at higher levels in dorsal-most regions of the embryo, and the non-neurogenic ectoderm, at lower levels in dorsal-lateral regions of the embryo (Ferguson and Anderson, 1992). A previous study found that in mutants in which Dpp signaling is expanded into lateral regions of the embryo, ind expression is lost (Von Ohlen and Doe, 2000). Likewise, ectopic expression of dpp in lateralized embryos that exhibit expanded ind expression throughout the embryo was able to repress ind in the domain where Dpp signaling was presented (Mizutani et al., 2006). Also, the ind CRM contains a 15 bp DNA sequence implicated in TGF- β signaling-mediated repression (Stathopoulos and Levine, 2005). Similar sites have been shown to mediate repression by recruiting a Dpp-dependent Schnurri/Mad/Medea (SMM) protein complex, but SMM dependent repression of ind has never been shown and in fact this mechanism of repression has only been shown to act at later stages of development (Dai et al., 2000; Pyrowolakis et al., 2004).
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Evolution of the dorsal ventral patterning network in the mosquito,
Anopheles gambiae

Evolution of the dorsal ventral patterning network in the mosquito, Anopheles gambiae

The dorsal-ventral patterning of the Drosophila embryo is controlled by a well-defined gene regulation network. We wish to understand how changes in this network produce evolutionary diversity in insect gastrulation. The present study focuses on the dorsal ectoderm in two highly divergent dipterans, the fruitfly Drosophila melanogaster and the mosquito Anopheles gambiae. In D. melanogaster, the dorsal midline of the dorsal ectoderm forms a single extra-embryonic membrane, the amnioserosa. In A. gambiae, an expanded domain forms two distinct extra-embryonic tissues, the amnion and serosa. The analysis of approximately 20 different dorsal-ventral patterning genes suggests that the initial specification of the mesoderm and ventral neurogenic ectoderm is highly conserved in flies and mosquitoes. By contrast, there are numerous differences in the expression profiles of genes active in the dorsal ectoderm. Most notably, the subdivision of the extra-embryonic domain into separate amnion and serosa lineages in A. gambiae correlates with novel patterns of gene expression for several segmentation repressors. Moreover, the expanded amnion and serosa anlage correlates with a broader domain of Dpp signaling as compared with the D. melanogaster embryo. Evidence is presented that this expanded signaling is due to altered expression of the sog gene.
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The CNS midline cells and spitz class genes are required for proper patterning of Drosophila ventral neuroectoderm

The CNS midline cells and spitz class genes are required for proper patterning of Drosophila ventral neuroectoderm

The CNS midline cells may help each NB obtain unique identity and then delaminate from the proneural clusters by sending out signal(s) throughout the VNE. It was reported that EGF receptor signaling pathway is required in the initial patterning of the entire VNE before gastrulation and later in the vicinity of the CNS midline cells during neurogenesis (Skeath, 1998; Udolph et al., 1998; Yagi et al., 1998). It was also shown that Rho and Vein expressed in the VNE activate Egfr during stage 5-6 before gastrulation. They were shown to play important roles in the specification and formation of medial and intermediate NBs by repression of proneural gene expression and promotion of NB formation in the intermediate column. In addition, they are also independently involved in the regulation of separate sets of genes, esg and msh that help medial and lateral NBs establish their unique identity, finally resulting in patterning of medial, intermediate, and lateral columns of the VNE along the D-V axis. Considering that the CNS midline cells are required for the proneural gene expression during the second stage of neurogenesis from this study, they may replace the roles of early–acting genes such as rho and vein by providing the VNE with additional ligand(s) including the secreted Spi that activates the Egfr in the second stage. This may provide the medial, intermediate and lateral NBs with additional positional information to generate diversified NB lineage from the VNE. It was reported that ac and sc expression in the VNE is necessary for the determination of NB identity as well as NB formation (Parras et al., 1996; Skeath and Doe, 1996), supporting the idea that the CNS midline cells may provide some signal(s) to generate the NBs that have unique identities along the D-V axis. In contrast to the result obtained with Egfr mutants, the CNS midline cells influence the proneural gene expression even in the Fig. 7. Expression of the aCC/pCC and
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Distinct functional specificities are associated with protein isoforms
encoded by the Drosophila dorsal ventral patterning gene
pipe

Distinct functional specificities are associated with protein isoforms encoded by the Drosophila dorsal ventral patterning gene pipe

The production of appropriately polarized, partially rescued embryos by females expressing Pipe-ST2 in an otherwise pipe-null background strongly suggests the existence of a second signal that can impart polarity, even in a situation in which Pipe-ST2 activity is not ventrally restricted. Carneiro et al. (Carneiro et al., 2006) have proposed a model in which maternally directed activation of the Decapentaplegic (Dpp) pathway facilitates degradation of the Cactus protein on the dorsal side of embryos in a Toll-independent manner, thus representing a second mechanism for polarizing the DV axis of the embryo. Although this pathway could, in principle, correspond to the second polarizing input, we do not favor this explanation. The findings of Carneiro et al. (Carneiro et al., 2006) are difficult to reconcile with the existence of mutant gain-of-function alleles of easter and Toll that cause uniform activation of Toll around the DV circumference of the embryo, and the consequent production of apolar lateralized or ventralized embryos. The production of such apolar embryos would not be expected were the Dpp pathway acting independently of Toll signaling to establish embryonic DV axis formation. Based on the existence of these unusual apolar alleles of easter and Toll, we favor Table 1. Cuticular phenotypes of embryos produced 18 to 30 hours after heat shock of adult females carrying hsp70-pipe-ST2 in various pipe mutant backgrounds
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Regulation of Gastrulation Through Dynamic Patterning in the Drosophila Embryo

Regulation of Gastrulation Through Dynamic Patterning in the Drosophila Embryo

In a developing organism, tissues have long been proposed to be patterned by spatially graded signals that specify cell fate in a concentration-dependent manner. Classically, these “morphogens” have been defined as originating from a defined source and forming a graded distribution by diffusion and degradation; however, in recent years it has become clear that morphogens can become spatially organized by a variety of mechanisms. Two of the best-characterized morphogen gradients pattern the anterior-posterior (AP) and dorsal- ventral (DV) axes of the Drosophila early embryo: the Bicoid and Dorsal transcription factor gradients (rev. in Porcher and Dostatni, 2010; Reeves and Stathopoulos, 2009). Their graded distributions are established using very different mechanisms. Bicoid is locally translated because its mRNA contains a localization sequence; whereas, Dorsal is localized to the nucleus more strongly in the ventral regions of the embryo because of localized Toll- receptor associated signaling. Live imaging has revealed significant dynamics in the exact levels of Bicoid (e.g., Gregor et al., 2007b; Little et al., 2011); however, the dynamics of target gene expression examined in fixed embryos suggest that the levels of Bicoid are important, but not the only defining factor in the expression of target genes (e.g., Jaeger et al., 2004; Ochoa-Espinosa et al., 2009). In contrast, no study to date has investigated systematically temporal features of the Dorsal gradient and its relationship to the expression of its target genes.
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Toll signals regulate dorsal–ventral patterning and anterior–posterior placement of the embryo in the hemipteran Rhodnius prolixus

Toll signals regulate dorsal–ventral patterning and anterior–posterior placement of the embryo in the hemipteran Rhodnius prolixus

Rhodnius Toll signals play a novel role in defining the embryo ’ s position along the anterior-posterior axis Interestingly, our functional assays reveal that Rp-dl pRNAi leads to a severe defect in the positioning of the developing embryo, which is found at the anterior of the egg instead of being placed at the posterior. This obser- vation strongly suggests that the Toll pathway exerts a role not only in the establishment of the DV axis, but also in the AP axis. The embryo’s anterior placement could result from incorrect specification of extraembry- onic membranes, since we observed a small number of amniotic cells in Rp-dl RNAi embryos. However, we observed misplaced embryos as early as the syncytial blastoderm stages, before extracellular membranes are able to exert a tracking effect on the developing embryo. Therefore, an alternative hypothesis is that specification of the AP and DV axes are interdependent and that Rp- dl RNAi interferes with the expression of AP patterning genes. A recent study reported that patterning of the two major body axes is co-dependent in Apis mellifera. Considering that we found Rp-dl pRNAi embryos mislo- calized along the AP axis, a similar mechanism may play a role during axis specification in Rhodnius [10].
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Twisted gastrulation promotes BMP signaling in zebrafish dorsal ventral axial patterning

Twisted gastrulation promotes BMP signaling in zebrafish dorsal ventral axial patterning

In Drosophila, Tsg also modulates BMP signaling during DV axial patterning. Tsg functions similarly to the Chordin ortholog Short gastrulation (Sog) in specifying the dorsal-most tissue, the amnioserosa, which requires the highest levels of BMP signaling in the fly embryo (Ashe and Levine, 1999; Francois et al., 1994; Mason et al., 1994; Ross et al., 2001; Zusman and Wieschaus, 1985). In addition to this pro-BMP activity, both Tsg and Sog exhibit anti-BMP activity in dorsolateral regions of the embryo (Ross et al., 2001). Current models suggest that Sog and Tsg bind to and transport BMP ligands toward dorsal regions of the embryo, where they are released from Sog by the activity of Tolloid, thereby generating the highest levels of BMP signal dorsally (Decotto and Ferguson, 2001; Eldar et al., 2002; Shimmi and O’Connor, 2003). In this model, the activity of Tsg relies on the presence of Sog and Tolloid. In vertebrates, there is no evidence for a role for Chordin in promoting gastrula BMP signaling, although it is possible it plays such a role at later stages in tail patterning (Hammerschmidt and Mullins, 2002; Wagner and Mullins, 2002). Thus, all aspects of how Sog/Chordin and Tsg function in DV patterning in vertebrates and invertebrates may not be conserved.
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Dorsal ventral patterning in amphioxus: current understanding, unresolved issues, and future directions

Dorsal ventral patterning in amphioxus: current understanding, unresolved issues, and future directions

of the Wnt/ b -catenin signaling pathway in the amphioxus DV patterning. In addition to determining how the signaling pathways specify the dorsal and ventral signaling territories, it is also important to identify the corresponding downstream target genes and study their complex regulatory roles during the amphioxus early devel- opment. Such a study has previously only been performed for the Vent1 homeobox gene. Bmp signaling has been shown to directly regulate the Vent1 gene through Smad1/5/8 signaling and Smad binding sites in the Vent1 promoter (Kozmikova et al., 2011), and in turn, Vent1 to directly repress the Chordin and Goosecoid genes via the homeodomain binding sites in their promoters (Kozmikova et al., 2013; Kozmikova et al., 2011). With the recent availability of high-quality genome assembly for B. lanceolatum (Acemel et al., 2016) and the advances in next-generation sequencing technolo- gies, we anticipate that further implementation of genome-wide approaches in the amphioxus model will allow us to study the gene regulatory networks underlying its body plan development. This kind of genome-wide unbiased approaches that combine differential RNA-seq of control and pharmacologically treated embryos with chromatin immunoprecipitation-sequencing (ChIP-seq) would be highly useful for deciphering the gene regulatory networks involved in the amphioxus early development.
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Dorsoventral Patterning of the Drosophila melanogaster Embryo by the Dorsal/NF-κB Signaling Pathway

Dorsoventral Patterning of the Drosophila melanogaster Embryo by the Dorsal/NF-κB Signaling Pathway

While the downstream effects of Dorsal signaling have been well documented, less is known about the global gradient formation. We proposed a mechanism by which the inhibitory factor Cactus shuttles Dorsal to the ventral midline, where Toll signaling acts as a sink. First, we dispelled the myth that there is a counter gradient of free Dorsal present in the cytoplasm, leading us to ask how Dorsal could collect at the ventral midline when Fickian diffusion states that it should diffuse outwards and away. This question brought us to the idea of shuttling, by which a carrier essentially causes a molecule to diffuse against its own concentration gradient. Through experiments with fluorescently-tagged Dorsal, we found that increased protein size widened the Dorsal gradient when Fickian diffusion would indicate a narrowing. We could exacerbate this effect by using GFP, which forms weak dimers. We also expanded the domain of Toll signaling, leading to a double peak of nuclear Dorsal. Again, this phenomenon seems contrary to what would be expected in a simple diffusion model; however, in the context of a shuttling model, it can be explained.
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Quantitative Single-Embryo Profile of Drosophila Genome Activation and the Dorsal–Ventral Patterning Network

Quantitative Single-Embryo Profile of Drosophila Genome Activation and the Dorsal–Ventral Patterning Network

The TGF-b signaling pathway is one of the best-studied sig- naling pathways in Drosophila, and model organisms in gen- eral, and because the components are well known, presents an opportunity to observe how the MZT activates a complete signaling pathway (Wu and Hill 2009; Akhurst and Padgett 2015). We included 18 members of the TGF-b pathway, as well as others peripherally related. The two primary ligands are Dpp and Scw: both purely zygotically transcribed. While peak TGF-b signaling takes place in the dorsal ectoderm, both scw and dpp are initially expressed in broader regions of the embryo. The expression of dpp extends to the ventral midline during NC13 and the expression of scw is ubiquitous starting as early as NC11, and both genes refine to the dorsal ectoderm during NC14. Our NanoString data confirms this initial broad expression and subsequent refinement of both dpp and scw (Figure 5A). Furthermore, both scw and dpp de- crease at very similar rates from NC14B onwards, including a pause in decreasing from NC14C to 14D, when they are both in the last stage of refining to their final expression domain. We included six TGF-b targets in the study and found that they are all strongly activated beginning in NC14. We
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Extramacrochaetae functions in dorsal ventral patterning of Drosophila imaginal discs

Extramacrochaetae functions in dorsal ventral patterning of Drosophila imaginal discs

In nearly all imaginal discs, the D/V axis is laid down during the late first/early second larval instar (Bohn, 1967; Bryant, 1970; Garcia-Bellido and Merriam, 1971a,b; Lawrence and Morata, 1976; Williams et al., 1993). Prior to the imposition of dorsal identity, the entire eye disc expresses the ventral selector gene fringe ( fng). During the late first/early second instar, expression of pannier (pnr), which encodes a GATA transcription factor, is activated via an unknown mechanism in a small group of cells within the peripodial membrane along the dorsal margin (Heitzler et al., 1996; Maurel-Zaffran and Treisman, 2000; Oros et al., 2010). Pnr is then responsible for inducing the expression of wingless (wg) (Maurel-Zaffran and Treisman, 2000), which in turn activates expression of the Iroquois complex (Iro-C) genes within the dorsal half of the eye (McNeill et al., 1997; Heberlein et al., 1998). One member of Iro-C, mirror (mirr), represses the expression of fng in the dorsal half of the eye field (Cho and Choi, 1998; Cavodeassi et al., 1999; Yang et al., 1999; Sato and Tomlinson, 2007). In the ventral half of the eye, sloppy paired 1 (slp1) represses mirr, which in turn preserves fng expression and ventral identity (Sato and Tomlinson, 2007). The confrontation of fng − (dorsal) and fng+ (ventral) tissue leads to the differential activation of Delta (Dl) and Serrate (Ser) within the two compartments and the activation of Notch (N) signaling at the D/V midline (Panin et al., 1997; Cho and Choi, 1998; Dominguez and de Celis, 1998; Papayannopoulos et al., 1998). Notch signaling at the midline is necessary for the growth of the eye field and for the expression of four-jointed ( fj) (Zeidler et al., 1999; Chao et al., 2004; Reynolds-Kenneally and Mlodzik, 2005; Gutierrez-Aviño et al., 2009). Fj has been linked to planar cell polarity (PCP) and for Notch- and JAK/STAT-dependent growth (Zeidler et al., 1999; Gutierrez-Aviño et al., 2009). Thus, the early division of the eye into dorsal, ventral and midline zones is
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Dorsal/NF-κB exhibits a Dorsal-to-Ventral Mobility Gradient in the Drosophila Embryo

Dorsal/NF-κB exhibits a Dorsal-to-Ventral Mobility Gradient in the Drosophila Embryo

2 insect behind 6 Nobel prizes in Physiology and Medicine to date with the recent one being in 2017. This tiny fly was able to contribute to medicine because of the genes humans share with Drosophila. An astonishing 75% of human disease genes have equivalence in flies. In particular, the genes that tell the cells how to divide, develop, and function and what the basic body plan should look like are often the same between humans and flies. This understanding yielded a wealth of discoveries. For instance, the Hedgehog (Hh) gene that is important in wing formation in Drosophila has a direct relative gene in humans called the Sonic Hedgehog. Studying the wing development in flies helps explain what we see when people have extra fingers or toes, which is a condition known as Polydactyly [2]. Many human diseases have been modeled in Drosophila such as Huntington’s, addiction, and neurological diseases, including neuromuscular disease [3]. Tissue Patterning
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The hormonal coordination of behavior and physiology at adult ecdysis in Drosophila melanogaster

The hormonal coordination of behavior and physiology at adult ecdysis in Drosophila melanogaster

The extent of filling of the tracheae of the central nervous system (CNS) with gas was observed by dissecting animals in 4 % formaldehyde at room temperature. Maintaining the tissues at room temperature prevented the air trapped in the tracheal system from dissolving, as it will if the tissue is chilled. The central nervous systems were fixed for a minimum of 2 h, rinsed for 20–30 min in PBS and mounted on polylysine-coated coverslips in 100 % glycerol. The nervous systems were then allowed to equilibrate with the glycerol overnight before scoring. This treatment permitted us to visualize the extent of filling of the tracheae using light microscopy and differential interference contrast optics. Images were collected from a Sony CCD camera connected to a Nikon Optiphot microscope. On average, 30 focal planes of each region of the ventral nervous system were collected, and these were collapsed into a single image using the layering palette in Adobe Photoshop 3.0. Different regions were then assembled into a single montage. This method allowed us to produce single images containing information about the state of tracheal inflation through the entire ventral nervous system.
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The four aldehyde oxidases of Drosophila melanogaster have different gene expression patterns and enzyme substrate specificities

The four aldehyde oxidases of Drosophila melanogaster have different gene expression patterns and enzyme substrate specificities

To reconstruct the evolutionary history, we performed a phylogenetic analysis on the predicted structures of the AOX genes and corresponding protein products in Drosophila using the available genomic sequencing data covering a total of 12 distinct lineages. Our phylogenetic reconstruction suggests that Drosophila AOX1 originated from an ancient XOR duplication, distinct from the one giving rise to vertebrate AOXs (Fig. 2). It is likely that this duplication resulted in the appearance of AOX1, which, subsequently, duplicated into AOX2. A further duplication event involving AOX2 gave rise to AOX3. Drosophila willistoni and Drosophila mojavensis are endowed with a single XOR and three active AOX genes that are predicted to be the orthologs of D. melanogaster AOX1, AOX2 and AOX3 (see also supplementary material Fig. S1). These species are representative of the most ancient complement of AOXs in Drosophila. The subsequent evolutionary history of AOXs in the Drosophilidae is characterized by four distinct AOX3 duplications (Fig. 2). Drosophila virilis is endowed by a species-specific AOX3-D in addition to XOR, AOX1, AOX2 and AOX3 (Fig. 2, supplementary material Fig. S1). In Drosophila grimshawi, two distinct duplications giving rise to AOX2- D and AOX3-D2 are evident (Fig. 2, supplementary material Fig. S1). A major evolutionary event is represented by a third AOX3 duplication, which led to the origin of AOX4 and is conserved among downstream lineages. The duplication led to the extant complement of the predicted molybdo-flavoenzymes present in Drosophila simulans, Drosophila sechellia, D. melanogaster, Drosophila yakuba and Drosophila erecta, which consists of XOR, AOX1, AOX2, AOX3 and AOX4 genes (Fig. 2, supplementary material Fig. S1). In Drosophila ananassae, a further AOX3 duplication gave rise to AOX3-D3 (Fig. 2, supplementary material List of abbreviations
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Dorsal ventral midline signaling in the developing Drosophila
eye

Dorsal ventral midline signaling in the developing Drosophila eye

Development is a stepwise process in which new information is generated through the interactions of previously specified cell types. The place where different cell types abut often defines the position from which secreted molecules are released, and these signals then direct further elaboration of patterning (Lawrence and Struhl, 1996). The cell types at the interface not only define the position from which the signal will be released, but they also carry the molecular information that directs which type of signal will be expressed, and the modes of response of the cells. Interfaces between different cell types can be established by a number of mechanisms. In the fly wing, the dorsal-ventral (D-V) boundary is established by a compartment mechanism, whereby cells on either side of the border are clonally isolated from one another: dorsal cells express the Apterous (Ap) transcription factor and share a lineage ancestry isolated from the ventral cells that do not express Ap (Blair et al., 1994; Diaz-Benjumea and Cohen, 1993). Differential adhesion between the two cell types leads to the formation of a long interface (the D-V border). Borders between distinct cell types can be generated by non-compartment mechanisms. For example, in the vertebrate neural tube, Sonic Hedgehog released from the ventral floorplate diffuses dorsally to elicit the expression of an array of different transcription factors, each expression domain depending on its distance from the source (Jessell, 2000). This first step establishes a relatively crude array of expression domains with many cells expressing more than one transcription factor. The transcription factors, however, are autoregulatory and mutually repressive, and if a cell initially expresses two, the action of one will force the extinction of the other. As with the compartment mechanism, the transcription factors also provide a miscibility code, such that like- cells mix and unlike-cells repel, and sharply defined interfaces are formed.
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Regulation of ventral midbrain patterning by Hedgehog signaling

Regulation of ventral midbrain patterning by Hedgehog signaling

A role for HH signaling in the regulation of cell affinities has been found in the fly wing imaginal disc and abdominal ectoderm (Blair and Ralston, 1997; Lawrence et al., 1999; Rodriguez and Basler, 1997). In each tissue, differential HH signaling creates two compartments that display distinct and inheritable affinities. Thus, cells of a compartment and their lineal relatives cohere with each other and do not intermix with those of the other compartment. As a result, the compartments become separated by a sharp, lineage restriction boundary exhibiting signaling properties (Blair, 1992; Garcia-Bellido et al., 1973; Lawrence et al., 1999; Morata and Lawrence, 1975). These results implicate HH signaling in the establishment of tissue boundaries and in the maintenance of a spatially coherent pattern (Dahmann and Basler, 1999). A loss of spatial organization has also been reported in several HH-pathway mutants in mouse (Shh –/– ;Gli3 –/– , Smo –/– ;Gli3 –/– , Gli2 –/– ;Gli3 –/– ) and
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Microbiota Induced Changes in Drosophila melanogaster Host Gene Expression and Gut Morphology

Microbiota Induced Changes in Drosophila melanogaster Host Gene Expression and Gut Morphology

In addition to geographic variation, we and others have shown that bacterial density increases as flies age (14, 16), a finding also confirmed by this study. Accordingly, most gut immune genes are induced with aging, suggesting that increased bacterial density triggers a higher immune response. Contrary to most immune genes, we identified a number of immune and metabolic genes that are dysregulated in older flies. These genes are potentially markers of immune senescence and could explain how microbiota titers increase despite a general increased immune and stress re- sponse. These results are largely in agreement with those of a re- cent study examining the impact of microbiota on the gut tran- scriptome of aging flies (30). However, while we observed many of the same immune genes deregulated in the guts of old flies, there were distinct differences. Specifically, in both wild-type lines we examined, the expression of PGRP-SC1 but not PGRP-SC2 was increased by the presence of microbiota in the guts of young flies, a phenomenon that was lost in older flies. In contrast, we identi- fied PGRP-SC2 as a gene upregulated in nongut carcass tissue of young flies when reared in the presence of microbiota. Further FIG 5 Impact of microbiota on cell identity of the gut. (A) The mitotic activity of the guts of conventionally reared flies is significantly higher than that of axenically reared flies, as measured by immunostaining with anti-Ph3 antibody. The impacts of microbiota on mitotic activity are more pronounced in the posterior region of the gut. Mean values from four experiments (n ⫽ 10 guts each) ⫾ SE are shown; anterior, P ⫽ 0.04; middle, P ⫽ 0.39; posterior, P ⫽ 0.0019. Results from Oregon R are shown; similar results were obtained with Canton S . (B) There is no significant difference in the number of midgut enterocytes in axenic
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The maternal to zygotic transition revisited

The maternal to zygotic transition revisited

methylation poises genes for expression (Blythe et al., 2010). Similarly, Histone 3 Lysine 4 trimethylation (H3K4me3), a mark that is generally associated with active transcription, appears on promoters during genome activation in Drosophila (Chen et al., 2013; Li et al., 2014), X. tropicalis (Hontelez et al., 2015; Lindeman et al., 2011), zebrafish (Vastenhouw et al., 2010; Zhang et al., 2014b) and mouse (Dahl et al., 2016; Zhang et al., 2016) embryos, often prior to transcription. Although in most cases the relevance of H3K4me3 has not yet been investigated directly, studies in mouse have revealed that it is required for the onset of transcription (Aoshima et al., 2015; Dahl et al., 2016; Liu et al., 2016; Zhang et al., 2016), which supports the observation that Brg1, which is required for H3K4 methylation, is necessary for ZGA (Bultman et al., 2006). Finally, acetylation of Histone 3 Lysine 27 (H3K27Ac) precedes ZGA in zebrafish (Chan et al., 2018 preprint; Sato et al., 2019 preprint; Zhang et al., 2018), and is required for the transcription of – at least – miR-430, which is one of the first genes to be transcribed. Although there is clearly a role for local histone modifications in ZGA, no local DNA methylation changes have been observed that coincide with the onset of transcription (Jiang et al., 2013; Kaaij et al., 2016; Potok et al., 2013), arguing against a role for DNA methylation in regulating ZGA. DNA methylation patterns, however, do play a role in the regulation of transcription during embryogenesis. In zebrafish, for example, hypermethylation at enhancers predicts transcription factor binding and enhancer activity (Kaaij et al., 2016; Liu et al., 2018b), whereas low levels of DNA methylation at promoters predict H3K4me3 and promoter activity (Andersen et al., 2012; Liu et al., 2018b). Finally, ZGA coincides with a significant increase in both the repressive histone modification H3K27me3 (Akkers et al., 2009; Hontelez et al., 2015; Li et al., 2014; Lindeman et al., 2011; Liu et al., 2016; van Heeringen et al., 2014; Vastenhouw et al., 2010) and DNA methylation (Potok et al., 2013), which may help to ensure the onset of gene-specific transcription (Potok et al., 2013; Zenk et al., 2017).
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A role for Shh and Bmp4 in regulating the dorsal-ventral patterning of the developing pharyngeal region

A role for Shh and Bmp4 in regulating the dorsal-ventral patterning of the developing pharyngeal region

Sonic hedgehog (Shh) is one of the three Hedgehog signalling proteins (the other two are Indian and Desert hedgehog) and has been implicated in many biological processes throughout an organism’s lifespan including events in early development, tissue regeneration, stem cell renewal and cancer (Bailey et al., 2008; Ericson et al., 1995; Machold et al., 2003). In addition to its role in patterning the neural tube, Shh is required for many critical patterning events in invertebrates and vertebrates (Ericson et al., 1995; Laufer et al., 1994; Rankin et al., 2016). One such place that Shh plays a critical role is during the development of the limb (Laufer et al., 1994; Tickle and Towers, 2017). Here Shh not only provides positional information for cells along the anteroposterior axis (thumb to little finger) but also stimulates mesenchymal cell proliferation to control the width of the limb and regulates the anteroposterior length of the apical ectodermal ridge which is important for developing the correct structures along the proximo-distal axis of the developing limb (Laufer et al., 1994; Tickle and Towers, 2017). With respect to Xenopus, Shh is expressed in defined locations during specific stages of development such as ventral to the neural tube, in the floor plate, in the limb bud, and dorsal to the pharyngeal region (Ericson et al., 1995; Koide et al., 2006; Laufer et al., 1994).
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Temporal and spacial control of RNA stability in the early embryo of Drosophila melanogaster

Temporal and spacial control of RNA stability in the early embryo of Drosophila melanogaster

In addition, oskar and Pgc transcripts move back to the posterior pole of the oocyte at stage 9, whereas the bicoid and Add-hts RNAs never show the early posterior localization but are e[r]

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