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Current papers in developmental biology and gene function





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Friday, October 20 th

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Jewett, C. E., Vanderleest, T. E., Miao, H., Xie, Y., Madhu, R., Loerke, D. and Blankenship, J. T. (2017). Planar polarized Rab35 functions as an oscillatory ratchet during cell intercalation in the Drosophila epithelium. Nat Commun 8(1): 476. PubMed ID: 28883443
Summary:
The coordination between membrane trafficking and actomyosin networks is essential to the regulation of cell and tissue shape. This study examined Rab protein distributions during Drosophila epithelial tissue remodeling and show that Rab35 is dynamically planar polarized. Rab35 compartments are enriched at contractile interfaces of intercalating cells and provide the first evidence of interfacial monopolarity. When Rab35 function is disrupted, apical area oscillations still occur and contractile steps are observed. However, contractions are followed by reversals and interfaces fail to shorten, demonstrating that Rab35 functions as a ratchet ensuring unidirectional movement. Although actomyosin forces have been thought to drive interface contraction, initiation of Rab35 compartments does not require Myosin II function. However, Rab35 compartments do not terminate and continue to grow into large elongated structures following actomyosin disruption. Finally, Rab35 represents a common contractile cell-shaping mechanism, as mesoderm invagination fails in Rab35 compromised embryos and Rab35 localizes to constricting surfaces. Various stages of tissue morphogenesis involve the contraction of epithelial surfaces. This study identified the Rab GTPase Rab35 as an essential component of this contractile process, which functions as a membrane ratchet to ensure unidirectional movement of intercalating cells.
Iacobucci, G. J. and Gunawardena, S. (2017). Ethanol stimulates the in vivo axonal movement of neuropeptide dense core vesicles in Drosophila motor neurons. J Neurochem [Epub ahead of print]. PubMed ID: 28960313
Summary:
Proper neuronal function requires essential biological cargoes to be packaged within membranous vesicles and transported, intracellularly, through the extensive outgrowth of axonal and dendritic fibers. The precise spatiotemporal movement of these cargoes is vital for neuronal survival and, thus, is highly regulated. This study tested how the axonal movement of a neuropeptide containing dense core vesicle (DCV) responds to alcohol stressors. Ethanol was found to induce a strong anterograde bias in vesicle movement. Low doses of ethanol stimulate the anterograde movement of neuropeptide-DCV while high doses inhibit bidirectional movement. This process required the presence of functional kinesin-1 motors as reduction of kinesin prevented the ethanol-induced stimulation of the anterograde movement of neuropeptide-DCV. Furthermore, expression of inactive GSK-3beta also prevented ethanol-induced stimulation of neuropeptide-DCV movement, similar to pharmacological inhibition of GSK-3beta with lithium. Conversely, inhibition of PI3K/AKT signaling with wortmannin led to a partial prevention of ethanol-stimulated transport of neuropeptide-DCV. Taken together, it is concluded that GSK-3beta signaling mediates the stimulatory effects of ethanol. Therefore, this study provides new insight into the physiological response of the axonal movement of neuropeptide-DCV to exogenous stressors.
Jabrani, A., Makamte, S., Moreau, E., Gharbi, Y., Plessis, A., Bruzzone, L., Sanial, M. and Biou, V. (2017). Biophysical characterisation of the novel zinc binding property in Suppressor of Fused. Sci Rep 7(1): 11139. PubMed ID: 28894158
Summary:
Suppressor of Fused (SUFU) is a highly conserved protein that acts as a negative regulator of the Hedgehog (HH) signalling pathway, a major determinant of cell differentiation and proliferation. Therefore, SUFU deletion in mammals has devastating effects on embryo development. SUFU is part of a multi-protein cytoplasmic signal-transducing complex. Its partners include the Gli family of transcription factors that function either as repressors, or as transcription activators according to the HH activation state. The crystal structure of SUFU revealed a two-domain arrangement, which undergoes a closing movement upon binding a peptide from Gli1. There remains however, much to be discovered about SUFU's behaviour. To this end, recombinant, full-length SUFU from Drosophila, Zebrafish and Human were expressed. Guided by a sequence analysis that revealed a conserved potential metal binding site, it was discovered that SUFU binds zinc. This binding was found to occur with a nanomolar affinity to SUFU from all three species. Mutation of one histidine from the conserved motif induces a moderate decrease in affinity for zinc, while circular dichroism indicates that the mutant remains structured. These results reveal new metal binding affinity characteristics about SUFU that could be of importance for its regulatory function in HH.
Jeong, S., Yang, D. S., Hong, Y. G., Mitchell, S. P., Brown, M. P. and Kolodkin, A. L. (2017). Varicose and cheerio collaborate with pebble to mediate semaphorin-1a reverse signaling in Drosophila. Proc Natl Acad Sci U S A 114(39): E8254-e8263. PubMed ID: 28894005
Summary:
The transmembrane semaphorin Sema-1a acts as both a ligand and a receptor to regulate axon-axon repulsion during neural development. Pebble (Pbl), a Rho guanine nucleotide exchange factor, mediates Sema-1a reverse signaling through association with the N-terminal region of the Sema-1a intracellular domain (ICD), resulting in cytoskeletal reorganization. This study uncover two additional Sema-1a interacting proteins, varicose (Vari) and cheerio (Cher), each with neuronal functions required for motor axon pathfinding. Vari is a member of the membrane-associated guanylate kinase (MAGUK) family of proteins, members of which can serve as scaffolds to organize signaling complexes. Cher is related to actin filament cross-linking proteins that regulate actin cytoskeleton dynamics. The PDZ domain binding motif found in the most C-terminal region of the Sema-1a ICD is necessary for interaction with Vari, but not Cher, indicative of distinct binding modalities. Pbl/Sema-1a-mediated repulsive guidance is potentiated by both vari and cher Genetic analyses further suggest that scaffolding functions of Vari and Cher play an important role in Pbl-mediated Sema-1a reverse signaling. These results define intracellular components critical for signal transduction from the Sema-1a receptor to the cytoskeleton and provide insight into mechanisms underlying semaphorin-induced localized changes in cytoskeletal organization.

Thursday, October 19th

Imran Alsous, J., Villoutreix, P., Berezhkovskii, A. M. and Shvartsman, S. Y. (2017). Collective growth in a small cell network. Curr Biol 27(17): 2670-2676.e2674. PubMed ID: 28867205
Summary:
Theoretical studies suggest that many of the emergent properties associated with multicellular systems arise already in small networks. However, the number of experimental models that can be used to explore collective dynamics in well-defined cell networks is still very limited. This study focused on collective cell behavior in the female germline cyst in Drosophila melanogaster, a stereotypically wired network of 16 cells that grows by approximately 4 orders of magnitude with unequal distribution of volume among its constituents. Multicellular growth was quantified with single-cell resolution, and it was shown that proximity to the oocyte, as defined on the network, is the principal factor that determines cell size; consequently, cells grow in groups. To rationalize this emergent pattern of cell sizes, a tractable mathematical model is proposed that depends on intercellular transport on a cell lineage tree. In addition to correctly predicting the divergent pattern of cell sizes, this model reveals allometric growth of cells within the network, an emergent property of this system and a feature commonly associated with differential growth on an organismal scale.
Fairchild, M. J., Islam, F. and Tanentzapf, G. (2017). Identification of genetic networks that act in the somatic cells of the testis to mediate the developmental program of spermatogenesis. PLoS Genet 13(9): e1007026. PubMed ID: 28957323
Summary:
Spermatogenesis is a dynamic developmental process requiring precisely timed transitions between discrete stages. Specifically, the germline undergoes three transitions: from mitotic spermatogonia to spermatocytes, from meiotic spermatocytes to spermatids, and from morphogenetic spermatids to spermatozoa. The somatic cells of the testis provide essential support to the germline throughout spermatogenesis, but their precise role during these developmental transitions has not been comprehensively explored. This study describes the identification and characterization of genes that are required in the somatic cells of the Drosophila melanogaster testis for progress through spermatogenesis. Phenotypic analysis of candidate genes pinpointed the stage of germline development disrupted. Bioinformatic analysis revealed that particular gene classes were associated with specific developmental transitions. Requirement for genes associated with endocytosis, cell polarity, and microtubule-based transport corresponded with the development of spermatogonia, spermatocytes, and spermatids, respectively. Overall, this study identified mechanisms that act specifically in the somatic cells of the testis to regulate spermatogenesis.
Pae, J., Cinalli, R. M., Marzio, A., Pagano, M. and Lehmann, R. (2017). GCL and CUL3 control the switch between cell lineages by mediating localized degradation of an RTK. Dev Cell 42(2): 130-142.e137. PubMed ID: 28743001
Summary:
The separation of germline from somatic lineages is fundamental to reproduction and species preservation. This study shows that Drosophila Germ cell-less (GCL) is a critical component in this process by acting as a switch that turns off a somatic lineage pathway. GCL, a conserved BTB (Broad-complex, Tramtrack, and Bric-a-brac) protein, is a substrate-specific adaptor for Cullin3-RING ubiquitin ligase complex (CRL3GCL). CRL3GCL promotes PGC fate by mediating degradation of Torso, a receptor tyrosine kinase (RTK) and major determinant of somatic cell fate. This mode of RTK degradation does not depend upon receptor activation but is prompted by release of GCL from the nuclear envelope during mitosis. The cell-cycle-dependent change in GCL localization provides spatiotemporal specificity for RTK degradation and sequesters CRL3GCL to prevent it from participating in excessive activities. This precisely orchestrated mechanism of CRL3GCL function and regulation defines cell fate at the single-cell level.
Lu, K. L. and Yamashita, Y. M. (2017). Germ cell connectivity enhances cell death in response to DNA damage in the Drosophila testis. Elife 6 [Epub ahead of print]. PubMed ID: 28809158
Summary:
Two broadly known characteristics of germ cells in many organisms are their development as a 'cyst' of interconnected cells and their high sensitivity to DNA damage. This study provides evidence that in the Drosophila testis, connectivity serves as a mechanism that confers to spermatogonia a high sensitivity to DNA damage. All spermatogonia within a cyst die synchronously even when only a subset of them exhibit detectable DNA damage. Mutants of the fusome, an organelle that is known to facilitate intracyst communication, compromise synchronous spermatogonial death and reduces overall germ cell death. These data indicate that a death-promoting signal is shared within the cyst, leading to death of the entire cyst. Taken together, it is proposed that intercellular connectivity supported by the fusome uniquely increases the sensitivity of the germline to DNA damage, thereby protecting the integrity of gamete genomes that are passed on to the next generation.

Wednedsay October 18th

Chen, Y. and Amrein, H. (2017). Ionotropic receptors mediate Drosophila oviposition preference through sour gustatory receptor neurons. Curr Biol 27(18): 2741-2750.e2744. PubMed ID: 28889974
Summary:
Carboxylic acids are present in many foods, being especially abundant in fruits. Yet, relatively little is known about how acids are detected by gustatory systems and whether they have a potential role in nutrition or provide other health benefits. This study identified sour gustatory receptor neurons (GRNs) in tarsal taste sensilla of Drosophila melanogaster. Most tarsal sensilla were found to harbor a sour GRN that is specifically activated by carboxylic and mineral acids but does not respond to sweet- and bitter-tasting chemicals or salt. One pair of taste sensilla features two GRNs that respond only to a subset of carboxylic acids and high concentrations of salt. All sour GRNs prominently express two Ionotropic Receptor (IR) genes, IR76b and IR25a, and this study shows that both these genes are necessary for the detection of acids. Furthermore, IR25a and IR76b were shown to be essential in sour GRNs of females for oviposition preference on acid-containing food. These investigations reveal that acids activate a unique set of taste cells largely dedicated to sour taste, and they indicate that both pH/proton concentration and the structure of carboxylic acids contribute to sour GRN activation. Together, these studies provide new insights into the cellular and molecular basis of sour taste.
Dombrovski, M., Poussard, L., Moalem, K., Kmecova, L., Hogan, N., Schott, E., Vaccari, A., Acton, S. and Condron, B. (2017). Cooperative behavior emerges among Drosophila larvae. Curr Biol 27(18): 2821-2826.e2822. PubMed ID: 28918946
Summary:
This paper describes a model experimental system of cooperative behavior involving Drosophila larvae. While foraging in liquid food, larvae are observed to align themselves and coordinate their movements in order to drag a common air cavity and dig deeper. Large-scale cooperation is required to maintain contiguous air contact across the posterior breathing spiracles. On the basis of a directed genetic screen, it was found that vision plays a key role in cluster dynamics. The experiments show that blind larvae form fewer clusters and dig less efficiently than wild-type and that socially isolated larvae behave as if they were blind. Furthermore, it was observed that blind and socially isolated larvae do not integrate effectively into wild-type clusters. Behavioral data indicate that vision and social experience are required to coordinate precise movements between pairs of larvae, therefore increasing the degree of cooperativity within a cluster. Hence, it is hypothesized that vision and social experience allow Drosophila larvae to assemble cooperative digging groups leading to more effective feeding and potential evasion of predators. Most importantly, these results indicate that control over membership of such a cooperative group can be regulated.
Hampel, S., McKellar, C. E., Simpson, J. H. and Seeds, A. M. (2017). Simultaneous activation of parallel sensory pathways promotes a grooming sequence in Drosophila. Elife 6. PubMed ID: 28887878
Summary:
A central model that describes how behavioral sequences are produced features a neural architecture that readies different movements simultaneously, and a mechanism where prioritized suppression between the movements determines their sequential performance. A previous paper described a model whereby suppression drives a Drosophila grooming sequence that is induced by simultaneous activation of different sensory pathways that each elicit a distinct movement. The current study has confirm this model using transgenic expression to identify and optogenetically activate sensory neurons that elicit specific grooming movements. Simultaneous activation of different sensory pathways elicits a grooming sequence that resembles the naturally induced sequence. Moreover, the sequence proceeds after the sensory excitation is terminated, indicating that a persistent trace of this excitation induces the next grooming movement once the previous one is performed. This reveals a mechanism whereby parallel sensory inputs can be integrated and stored to elicit a delayed and sequential grooming response.
Beckwith, E. J., Geissmann, Q., French, A. S. and Gilestro, G. F. (2017). Regulation of sleep homeostasis by sexual arousal. Elife 6. PubMed ID: 28893376
Summary:
In all animals, sleep pressure is under continuous tight regulation. It is universally accepted that this regulation arises from a two-process model, integrating both a circadian and a homeostatic controller. This study has explored the role of environmental social signals as a third, parallel controller of sleep homeostasis and sleep pressure. It was shown that, in Drosophila melanogaster males, sleep pressure after sleep deprivation can be counteracted by raising their sexual arousal, either by engaging the flies with prolonged courtship activity or merely by exposing them to female pheromones.

Tuesday, October 17th

Zhu, M., Zhang, S., Tian, X. and Wu, C. (2017). Mask mitigates MAPT- and FUS-induced degeneration by enhancing autophagy through lysosomal acidification. Autophagy 14:1-15. PubMed ID: 28806139
Summary:
This study shows that Mask, an Ankyrin-repeat and KH-domain containing protein, plays a key role in promoting autophagy flux and mitigating degeneration caused by protein aggregation or impaired ubiquitin-proteasome system (UPS) function. In Drosophila eye models of human tauopathy or amyotrophic lateral sclerosis diseases, loss of Mask function enhanced, while gain of Mask function mitigated, eye degenerations induced by eye-specific expression of human pathogenic MAPT/TAU or FUS proteins. The fly larval muscle, a more accessible tissue, was then used to study the underlying molecular mechanisms in vivo. Mask was found to modulate the global abundance of K48- and K63-ubiquitinated proteins by regulating macroautophagy/autophagy-lysosomal-mediated degradation, but not UPS function. Indeed, upregulation of Mask compensated the partial loss of UPS function. It was further demonstrated that Mask promotes autophagic flux by enhancing lysosomal function, and that Mask is necessary and sufficient for promoting the expression levels of the proton-pumping vacuolar (V)-type ATPases in a TFEB-independent manner. Moreover, the beneficial effects conferred by Mask expression on the UPS dysfunction and neurodegenerative models depend on intact autophagy-lysosomal pathway. These findings highlight the importance of lysosome acidification in cellular surveillance mechanisms and establish a model for exploring strategies to mitigate neurodegeneration by boosting lysosomal function.
Drager, N. M., Nachman, E., Winterhoff, M., Bruhmann, S., Shah, P., Katsinelos, T., Boulant, S., Teleman, A. A., Faix, J. and Jahn, T. R. (2017). Bin1 directly remodels actin dynamics through its BAR domain. EMBO Rep. PubMed ID: 28893863
Summary:
Endocytic processes are facilitated by both curvature-generating BAR-domain proteins and the coordinated polymerization of actin filaments. Under physiological conditions, the N-BAR protein Bin1 has been shown to sense and curve membranes in a variety of cellular processes. Recent studies have identified Bin1 as a risk factor for Alzheimer's disease, although its possible pathological function in neurodegeneration is currently unknown. This study reports that Bin1 not only shapes membranes, but is also directly involved in actin binding through its BAR domain. A moderate actin bundling activity by human Bin1 was observed, and its ability to stabilize actin filaments against depolymerization is described. Moreover, Bin1 is also involved in stabilizing tau-induced actin bundles, which are neuropathological hallmarks of Alzheimer's disease. Evidence for this effect in vivo, where downregulation of Bin1 in a Drosophila model of tauopathy was observed to significantly reduce the appearance of tau-induced actin inclusions. Together, these findings reveal the ability of Bin1 to modify actin dynamics and provide a possible mechanistic connection between Bin1 and tau-induced pathobiological changes of the actin cytoskeleton.
Das, T. K. and Cagan, R. L. (2017). KIF5B-RET oncoprotein signals through a multi-kinase signaling hub. Cell Rep 20(10): 2368-2383. PubMed ID: 28877471
Summary:
Gene fusions are increasingly recognized as important cancer drivers. The KIF5B-RET fusion gene has been identified as a primary driver in a subset of lung adenocarcinomas. Targeting human KIF5B-RET to epithelia in Drosophila directed multiple aspects of transformation, including hyperproliferation, epithelial-to-mesenchymal transition, invasion, and extension of striking invadopodia-like processes. The KIF5B-RET-transformed human bronchial cell line showed similar aspects of transformation, including invadopodia-like processes. Through a combination of genetic and biochemical studies, it was demonstrated that the kinesin and kinase domains of KIF5B-RET act together to establish an emergent microtubule and RAB-vesicle-dependent RET-SRC-EGFR-FGFR signaling hub. Drugs designed to inhibit RET alone were determined to work poorly in KIF5B-RET-transformed cells. However, combining the RET inhibitor sorafenib with drugs that target EGFR, microtubules, or FGFR led to strong efficacy in both Drosophila and human cell line KIF5B-RET models. This work demonstrates the utility of exploring the full biology of fusions to identify rational therapeutic strategies.
Hope, K. A., LeDoux, M. S. and Reiter, L. T. (2017). Glial overexpression of Dube3a causes seizures and synaptic impairments in Drosophila concomitant with down regulation of the Na+/K+ pump ATPalpha. Neurobiol Dis 108: 238-248. PubMed ID: 28888970
Summary:
Duplication 15q syndrome (Dup15q) is an autism-associated disorder co-incident with high rates of pediatric epilepsy. Additional copies of the E3 ubiquitin ligase UBE3A are thought to cause Dup15q phenotypes, yet models overexpressing UBE3A in neurons have not recapitulated the epilepsy phenotype. This study shows that Drosophila endogenously expresses Dube3a (fly UBE3A homolog) in glial cells and neurons, prompting an investigation into the consequences of glial Dube3a overexpression. This study expands on previous work showing that the Na+/K+ pump ATPalpha is a direct ubiquitin ligase substrate of Dube3a. A robust seizure-like phenotype was observed in flies overexpressing Dube3a in glial cells, but not neurons. Glial-specific knockdown of ATPalpha also produced seizure-like behavior, and this phenotype was rescued by simultaneously overexpressing ATPalpha and Dube3a in glia. These data provides the basis of a paradigm shift in Dup15q research given that clinical phenotypes have long been assumed to be due to neuronal UBE3A overexpression.

Monday, October 16th

Ertl, H. A., Russo, D. P., Srivastava, N., Brooks, J. T., Dao, T. N. and LaRocque, J. R. (2017). The Role of Blm Helicase in homologous recombination, gene conversion tract length, and recombination between diverged sequences in Drosophila. Genetics [Epub ahead of print]. PubMed ID: 28912341
Summary:
DNA double-strand breaks (DSBs) are a particularly deleterious class of DNA damage that threatens genome integrity. DSBs are repaired by three pathways: non-homologous end joining (NHEJ), homologous recombination (HR), and single-strand annealing (SSA). Drosophila melanogaster Blm (DmBlm) is the ortholog of Saccharomyces cerevisiae SGS1 and human BLM, and has been shown to suppress crossovers in mitotic cells and repair mitotic DNA gaps via HR. To further elucidate the role of DmBlm in repair of a simple DSB, and in particular recombination mechanisms, the DR-white and DR-white.mu repair assays were used in multiple mutant allele backgrounds. DmBlm null and helicase-dead mutants both demonstrated a decrease in repair by noncrossover HR, and a concurrent increase in non-HR events, possibly including SSA, crossovers, deletions, and NHEJ, although detectable processing of the ends was not significantly impacted. Interestingly, gene conversion tract lengths of HR repair events were substantially shorter in DmBlm null but not helicase-dead mutants, compared to heterozygote controls. Using DR-white.mu, this study found that, in contrast to Sgs1, DmBlm is not required for suppression of recombination between diverged sequences. Taken together, these data suggest that DmBlm helicase function plays a role in HR, and the steps that contribute to determining gene conversion tract length are helicase-independent.
Brustel, J., Kirstein, N., Izard, F., Grimaud, C., Prorok, P., Cayrou, C., Schotta, G., Abdelsamie, A. F., Dejardin, J., Mechali, M., Baldacci, G., Sardet, C., Cadoret, J. C., Schepers, A. and Julien, E. (2017). Histone H4K20 tri-methylation at late-firing origins ensures timely heterochromatin replication. EMBO J 36(18): 2726-2741. PubMed ID: 28778956
Summary:
Evolutionary Homolog Study
Among other targets, the protein lysine methyltransferase PR-Set7 (see Drosophila SET domain containing 7) induces histone H4 lysine 20 monomethylation (H4K20me1), which is the substrate for further methylation by the Suv4-20h methyltransferase. Although these enzymes have been implicated in control of replication origins, the specific contribution of H4K20 methylation to DNA replication remains unclear. This study shows that H4K20 mutation in mammalian cells, unlike in Drosophila, partially impairs S-phase progression and protects from DNA re-replication induced by stabilization of PR-Set7. Using Epstein-Barr virus-derived episomes, it was further demonstrated that conversion of H4K20me1 to higher H4K20me2/3 states by Suv4-20h is not sufficient to define an efficient origin per se, but rather serves as an enhancer for MCM2-7 helicase (see Drosophila MCM5) loading and replication activation at defined origins. Consistent with this, it was found that Suv4-20h-mediated H4K20 tri-methylation (H4K20me3) is required to sustain the licensing and activity of a subset of ORCA/LRWD1-associated origins, which ensure proper replication timing of late-replicating heterochromatin domains. Altogether, these results reveal Suv4-20h-mediated H4K20 tri-methylation as a critical determinant in the selection of active replication initiation sites in heterochromatin regions of mammalian genomes.
Hannon, C. E., Blythe, S. A. and Wieschaus, E. F. (2017). Concentration dependent chromatin states induced by the Bicoid morphogen gradient. Elife 6. PubMed ID: 28891464
Summary:
In Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. This study has measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, it was found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context. Bcd drives an open chromatin state at a subset of its targets. These data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations. This may be a common property of developmental transcription factors that must gain early access to their target enhancers while the chromatin state of the genome is being remodeled during large-scale transitions in the gene regulatory landscape.
Harmston, N., Ing-Simmons, E., Tan, G., Perry, M., Merkenschlager, M. and Lenhard, B. (2017). Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nat Commun 8(1): 441. PubMed ID: 28874668
Summary:
Developmental genes in metazoan genomes are surrounded by dense clusters of conserved noncoding elements (CNEs). CNEs exhibit unexplained extreme levels of sequence conservation, with many acting as developmental long-range enhancers. Clusters of CNEs define the span of regulatory inputs for many important developmental regulators and have been described previously as genomic regulatory blocks (GRBs). Their function and distribution around important regulatory genes raises the question of how they relate to 3D conformation of these loci. This study shows that clusters of CNEs strongly coincide with topological organisation, predicting the boundaries of hundreds of topologically associating domains (TADs) in human and Drosophila. The set of TADs that are associated with high levels of noncoding conservation exhibit distinct properties compared to TADs devoid of extreme noncoding conservation. The close correspondence between extreme noncoding conservation and TADs suggests that these TADs are ancient, revealing a regulatory architecture conserved over hundreds of millions of years. Metazoan genomes contain many clusters of conserved noncoding elements. This study provides evidence that these clusters coincide with distinct topologically associating domains in humans and Drosophila, revealing a conserved regulatory genomic architecture.

Saturday, October 14th

Gerdoe-Kristensen, S., Lund, V. K., Wandall, H. H. and Kjaerulff, O. (2017). Mactosylceramide prevents glial cell overgrowth by inhibiting insulin and fibroblast growth factor receptor signaling. J Cell Physiol 232(11): 3112-3127. PubMed ID: 28019653
Summary:
Receptor tyrosine kinase (RTK) signaling controls key aspects of cellular differentiation, proliferation, survival, metabolism, and migration. Deregulated RTK signaling also underlies many cancers. Glycosphingolipids (GSL) are essential elements of the plasma membrane. By affecting clustering and activity of membrane receptors, GSL modulate signal transduction, including that mediated by the RTK. GSL are abundant in the nervous system, and glial development in Drosophila is emerging as a useful model for studying how GSL modulate RTK signaling. Drosophila has a simple GSL biosynthetic pathway, in which the mannosyltransferase Egghead controls conversion of glucosylceramide (GlcCer) to mactosylceramide (MacCer). Lack of elongated GSL in egghead (egh) mutants causes overgrowth of subperineurial glia (SPG), largely due to aberrant activation of phosphatidylinositol 3-kinase (PI3K). However, to what extent this effect involves changes in upstream signaling events is unresolved. This study shows that glial overgrowth in egh is strongly linked to increased activation of Insulin and fibroblast growth factor receptors (FGFR). Glial hypertrophy is phenocopied when overexpressing gain-of-function mutants of the Drosophila insulin receptor (InR) and the FGFR homolog Heartless (Htl) in wild type SPG, and is suppressed by inhibiting Htl and InR activity in egh. Knockdown of GlcCer synthase in the SPG fails to suppress glial overgrowth in egh nerves, and slightly promotes overgrowth in wild type, suggesting that RTK hyperactivation is caused by absence of MacCer and not by GlcCer accumulation. It is concluded that an early product in GSL biosynthesis, MacCer, prevents inappropriate activation of insulin and fibroblast growth factor receptors in Drosophila glia.
Banerjee, S., Mino, R. E., Fisher, E. S. and Bhat, M. A. (2017). A versatile genetic tool to study midline glia function in the Drosophila CNS. Dev Biol [Epub ahead of print]. PubMed ID: 28602954
Summary:
In the Drosophila CNS midline, neuron-glial interactions underlie ensheathment of commissural axons by midline glial (MG) cells in a manner similar to mammalian oligodendrocytes. Although there has been some advance in the study of neuron-glial interactions and ensheathment of axons in the CNS midline, key aspects of axonal ensheathment are still not fully understood. Previous studies have identified two key molecular players from the neuronal and glial cell types in the CNS midline. These are the neuronal transmembrane protein Neurexin IV (Nrx IV) and the membrane-anchored MG protein Wrapper, both of which interact in trans to mediate neuron-glial interactions and ensheathment of commissural axons. This study attempted to further understanding of MG biology and try to overcome some of the technical difficulties posed by the lack of a robust MG driver that will specifically allow expression or knockdown of genes in MG. BAC transgenic flies were generated of wrapper-GAL4. The GAL4/UAS system was used to drive GFP-reporter lines (membrane-bound mCD8-GFP; microtubule-associated tau-GFP) and nuclear lacZ using wrapper-GAL4 to highlight the MG cells and/or their processes that surround and perform axonal ensheathment functions in the embryonic midline. The utility was demonstrated of the wrapper-GAL4 driver line to down-regulate known MG genes specifically in Wrapper-positive cells. Finally, the functionality of the wrapper-GAL4 driver was validated by rescue of wrapper mutant phenotypes and lethality. Together, these studies provide a versatile genetic tool to investigate MG functions and aid in future investigations where genetic screens using wrapper-GAL4 could be designed to identify novel molecular players at the Drosophila midline and unravel key aspects of MG biology.
Skeath, J. B., Wilson, B. A., Romero, S. E., Snee, M. J., Zhu, Y. and Lacin, H. (2017). The extracellular metalloprotease AdamTS-A anchors neural lineages in place within and preserves the architecture of the central nervous system. Development 144(17):3102-3113. PubMed ID: 28760813
Summary:
The extracellular matrix (ECM) regulates cell migration and sculpts organ shape. AdamTS proteins are extracellular metalloproteases known to modify ECM proteins and promote cell migration, but demonstrated roles for AdamTS proteins in regulating CNS structure and ensuring cell lineages remain fixed in place have not been uncovered. Using forward genetic approaches in Drosophila, this study found that reduction of AdamTS-A function induces both the mass exodus of neural lineages out of the CNS and drastic perturbations to CNS structure. Expressed and active in surface glia, AdamTS-A acts in parallel to perlecan and in opposition to viking/collagen IV and betaPS-integrin to keep CNS lineages rooted in place and to preserve the structural integrity of the CNS. viking/collagen IV and betaPS-integrin are known to promote tissue stiffness and oppose the function of perlecan, which reduces tissue stiffness. This work supports a model in which AdamTS-A anchors cells in place and preserves CNS architecture by reducing tissue stiffness.
Li, Y., Zhao, D., Horie, T., Chen, G., Bao, H., Chen, S., Liu, W., Horie, R., Liang, T., Dong, B., Feng, Q., Tao, Q. and Liu, X. (2017). Conserved gene regulatory module specifies lateral neural borders across bilaterians. Proc Natl Acad Sci U S A 114(31): E6352-e6360. PubMed ID: 28716930
Summary:
The lateral neural plate border (NPB), the neural part of the vertebrate neural border, is composed of central nervous system (CNS) progenitors and peripheral nervous system (PNS) progenitors. In invertebrates, PNS progenitors are also juxtaposed to the lateral boundary of the CNS. Whether there are conserved molecular mechanisms determining vertebrate and invertebrate lateral neural borders remains unclear. This study presents evidence that orthologs of the NPB specification module specify the invertebrate lateral neural border, which is composed of CNS and PNS progenitors. First, like in vertebrates, the conserved neuroectoderm lateral border specifier Msx/vab-15 (see Drosophila Drop/Msh) specifies lateral neuroblasts in Caenorhabditis elegans. Second, orthologs of the vertebrate NPB specification module [Msx/vab-15, Pax3/7/pax-3 (see Drosophila Paired), and Zic/ref-2 (see Drosophila Odd-paired)] are significantly enriched in worm lateral neuroblasts. Third, Msx/vab-15 was shown to regulate the development of mechanosensory neurons derived from lateral neural progenitors in multiple invertebrate species, including C. elegans, Drosophila, and Ciona. These data suggest a common origin of the molecular mechanism specifying lateral neural borders across bilaterians.

Friday, October 13th

Brown, H. E., Desai, T., Murphy, A. J., Pancholi, H., Schmidt, Z. W., Swahn, H. and Liebl, E. C. (2017). The function of Drosophila larval class IV dendritic arborization sensory neurons in the larval-pupal transition is separable from their function in mechanical nociception responses. PLoS One 12(9): e0184950. PubMed ID: 28910410
Summary:
The sensory and physiological inputs which govern the larval-pupal transition in Drosophila, and the neuronal circuity that integrates them, are complex. Previous work identified a dosage-sensitive genetic interaction between the genes encoding the Rho-GEF Trio and the zinc-finger transcription factor Sequoia that interfered with the larval-pupal transition. Specifically, it is reported that heterozygous mutations in sequoia (seq) dominantly exacerbated the trio mutant phenotype, and this seq-enhanced trio mutant genotype blocked the transition of third instar larvae from foragers to wanderers, a requisite behavioral transition prior to pupation. In this work, the GAL4-UAS system was used to rescue this phenotype by tissue-specific trio expression. Expressing trio in the class IV dendritic arborization (da) sensory neurons rescues the larval-pupal transition, demonstrating the reliance of the larval-pupal transition on the integrity of these sensory neurons. As nociceptive responses also rely on the functionality of the class IV da neurons, mechanical nociceptive responses were tested in the mutant and rescued larvae, and it was found that mechanical nociception is separable from the ability to undergo the larval-pupal transition. This demonstrates for the first time that the roles of the class IV da neurons in governing two critical larval behaviors, the larval-pupal transition and mechanical nociception, are functionally separable from each other.
Gu, T., Zhao, T., Kohli, U. and Hewes, R. S. (2017). The large and small SPEN family proteins stimulate axon outgrowth during neurosecretory cell remodeling in Drosophila. Dev Biol. PubMed ID: 28916169
Summary:
Split ends (SPEN) is the founding member of a well conserved family of nuclear proteins with critical functions in transcriptional regulation and the post-transcriptional processing and nuclear export of transcripts. In animals, the SPEN proteins fall into two size classes that perform either complementary or antagonistic functions in different cellular contexts. This study shows that the two Drosophila representatives of this family, SPEN and Spenito (NITO), regulate metamorphic remodeling of the CCAP/bursicon neurosecretory cells. CCAP/bursicon cell-targeted overexpression of SPEN had no effect on the larval morphology or the pruning back of the CCAP/bursicon cell axons at the onset of metamorphosis. During the subsequent outgrowth phase of metamorphic remodeling, overexpression of either SPEN or NITO strongly inhibited axon extension, axon branching, peripheral neuropeptide accumulation, and soma growth. Cell-targeted loss-of-function alleles for both spen and nito caused similar reductions in axon outgrowth, indicating that the absolute levels of SPEN and NITO activity are critical to support the developmental plasticity of these neurons. Although nito RNAi did not affect SPEN protein levels, the phenotypes produced by SPEN overexpression were suppressed by nito RNAi. It is proposed that SPEN and NITO function additively or synergistically in the CCAP/bursicon neurons to regulate multiple aspects of neurite outgrowth during metamorphic remodeling.
Guo, H., Kunwar, K. and Smith, D. (2017). Odorant receptor sensitivity modulation in Drosophila. J Neurosci 37(39): 9465-9473. PubMed ID: 28871035
Summary:
The ability to modulate sensitivity in sensory systems is essential for useful information to be extracted from fluctuating stimuli in a wide range of background conditions. This study reveals that dephosphorylation of OrcoS289 that occurs upon prolonged odor exposure is a mechanism underlying reduction in odorant sensitivity in Drosophila primary olfactory neurons in both sexes. OrcoS289A mutants, unable to phosphorylate this position, have low intrinsic odorant sensitivity that is independent of altered expression or localization. A phosphomimetic allele, OrcoS289D, has enhanced odorant sensitivity compared with wild-type controls. To explore the functional ramifications of this phosphorylation in vivo, phospho-specific antiserum to OrcoS289 were generated, and it was shown that phosphorylation at this residue is dynamically regulated by odorant exposure with concomitant modulation of odorant sensitivity. OrcoS289 is phosphorylated in the sensitized state, and odorant exposure triggers dephosphorylation and desensitization without altering receptor localization. It was furthern show that dephosphorylation of OrcoS289 is triggered by neuronal activity, and not conformational changes in the receptor occurring upon ligand binding. Mutant flies unable to regulate Orco function through phosphorylation at S289 are defective for odor-guided behavior. These findings provide insight into the mechanisms underlying regulation of insect odorant receptors in vivo.
Azevedo, A. W. and Wilson, R. I. (2017). Active mechanisms of vibration encoding and frequency filtering in central mechanosensory neurons. Neuron [Epub ahead of print]. PubMed ID: 28943231
Summary:
To better understand biophysical mechanisms of mechanosensory processing, this study investigated two cell types in the Drosophila brain (A2 and B1 cells) that are postsynaptic to antennal vibration receptors. A2 cells receive excitatory synaptic currents in response to both directions of movement: thus, twice per vibration cycle. The membrane acts as a low-pass filter, so that voltage and spiking mainly track the vibration envelope rather than individual cycles. By contrast, B1 cells are excited by only forward or backward movement, meaning they are sensitive to vibration phase. They receive oscillatory synaptic currents at the stimulus frequency, and they bandpass filter these inputs to favor specific frequencies. Different cells prefer different frequencies, due to differences in their voltage-gated conductances. Both Na+ and K+ conductances suppress low-frequency synaptic inputs, so cells with larger voltage-gated conductances prefer higher frequencies. These results illustrate how membrane properties and voltage-gated conductances can extract distinct stimulus features into parallel channels.

Thursday, October 12th

Abramczuk, M. K., Burkard, T. R., Rolland, V., Steinmann, V., Duchek, P., Jiang, Y., Wissel, S., Reichert, H. and Knoblich, J. A. (2017). The splicing co-factor Barricade/Tat-SF1, is required for cell cycle and lineage progression in Drosophila neural stem cells. Development [Epub ahead of print]. PubMed ID: 28935704
Summary:
Stem cells need to balance self-renewal and differentiation for correct tissue development and homeostasis. Defects in this balance can lead to developmental defects or tumor formation. In recent years, mRNA splicing has emerged as one important mechanism regulating cell fate decisions. This study addresses the role of the evolutionary conserved splicing co-factor Barricade (Barc)/Tat-SF1/CUS2 in Drosophila neural stem cell (neuroblast) lineage formation. Barc is required for the generation of neurons during Drosophila brain development by ensuring correct neural progenitor proliferation and differentiation. Barc associates with components of the U2 small nuclear ribonucleic proteins (snRNP), and its depletion causes alternative splicing in form of intron retention in a subset of genes. Using bioinformatics analysis and a cell culture based splicing assay, Barc-dependent introns were found to share three major traits: they are short, GC rich and have weak 3' splice sites. These results show that Barc, together with the U2snRNP, plays an important role in regulating neural stem cell lineage progression during brain development and facilitates correct splicing of a subset of introns.
Clark, J. P., Rahman, R., Yang, N., Yang, L. H. and Lau, N. C. (2017). Drosophila PAF1 modulates PIWI/piRNA silencing capacity. Curr Biol 27(17): 2718-2726.e2714. PubMed ID: 28844648
Summary:
To test the directness of factors in initiating PIWI-directed gene silencing, this study employed a Piwi-interacting RNA (piRNA)-targeted reporter assay in Drosophila ovary somatic sheet (OSS) cells. This assay confirmed direct silencing roles for piRNA biogenesis factors and PIWI-associated factors but suggested that chromatin-modifying proteins may act downstream of the initial silencing event. These data also revealed that RNA-polymerase-II-associated proteins like PAF1 and RTF1 antagonize PIWI-directed silencing. PAF1 knockdown enhances PIWI silencing of reporters when piRNAs target the transcript region proximal to the promoter. Loss of PAF1 suppresses endogenous transposable element (TE) transcript maturation, whereas a subset of gene transcripts and long-non-coding RNAs adjacent to TE insertions are affected by PAF1 knockdown in a similar fashion to piRNA-targeted reporters. Additionally, transcription activation at specific TEs and TE-adjacent loci during PIWI knockdown is suppressed when PIWI and PAF1 levels are both reduced. This study suggests a mechanistic conservation between fission yeast PAF1 repressing AGO1/small interfering RNA (siRNA)-directed silencing and Drosophila PAF1 opposing PIWI/piRNA-directed silencing.
Ryu, Y. H., Kenny, A., Gim, Y., Snee, M. and Macdonald, P. M. (2017). Multiple cis-acting signals, some weak by necessity, collectively direct robust transport of Oskar mRNA to the oocyte. J Cell Sci. PubMed ID: 28760927
Summary:
Localization of mRNAs can involve multiple steps, each with its own cis-acting localization signals and transport factors. How is the transition between different steps orchestrated? This study shows that the initial step in localization of Drosophila oskar mRNA - transport from nurse cells to the oocyte - relies on multiple cis-acting signals. Some of these are binding sites for the translational control factor Bruno, suggesting that Bruno plays an additional role in mRNA transport. Although transport of oskar mRNA is essential and robust, the localization activity of individual transport signals is weak. Notably, increasing the strength of individual transport signals, or adding a strong transport signal, disrupts the later stages of oskar mRNA localization. It is proposed that the oskar transport signals are weak by necessity; their weakness facilitates transfer of the oskar mRNA from the oocyte transport machinery to the machinery for posterior localization.
Church, V. A., Pressman, S., Isaji, M., Truscott, M., Cizmecioglu, N. T., Buratowski, S., Frolov, M. V. and Carthew, R. W. (2017). Microprocessor recruitment to elongating RNA polymerase II is required for differential expression of microRNAs. Cell Rep 20(13): 3123-3134. PubMed ID: 28954229
Summary:
The cellular abundance of mature microRNAs (miRNAs) is dictated by the efficiency of nuclear processing of primary miRNA transcripts (pri-miRNAs) into pre-miRNA intermediates. The Microprocessor complex of Drosha and DGCR8 carries this out, but it has been unclear what controls Microprocessor's differential processing of various pri-miRNAs. This study shows that Drosophila DGCR8 (Pasha) directly associates with the C-terminal domain of the RNA polymerase II elongation complex when it is phosphorylated by the Cdk9 kinase (pTEFb). When association is blocked by loss of Cdk9 activity, a global change in pri-miRNA processing is detected. Processing of pri-miRNAs with a UGU sequence motif in their apical junction domain increases, while processing of pri-miRNAs lacking this motif decreases. Therefore, phosphorylation of RNA polymerase II recruits Microprocessor for co-transcriptional processing of non-UGU pri-miRNAs that would otherwise be poorly processed. In contrast, UGU-positive pri-miRNAs are robustly processed by Microprocessor independent of RNA polymerase association.

Wednesday, October 11th

Bergman, C. M., Han, S., Nelson, M. G., Bondarenko, V. and Kozeretska, I. (2017). Genomic analysis of P elements in natural populations of Drosophila melanogaster. PeerJ 5: e3824. PubMed ID: 28929030
Summary:
The Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their P element composition mate and produce offspring. This study compared estimates of genomic P element content with gonadal dysgenesis phenotypes for isofemale strains obtained from three worldwide populations of D. melanogaster to illuminate the molecular basis of natural variation in cytotype status. P element abundance estimated from genome sequences of isofemale strains is shown to be highly correlated across different bioinformatics approaches, but abundance estimates are sensitive to method and filtering strategies as well as incomplete inbreeding of isofemale strains. P element content was found to vary significantly across populations, with strains from a North American population having fewer P elements but a higher proportion of full-length elements than strains from populations sampled in Europe or Africa. Despite these geographic differences in P element abundance and structure, neither the number of P elements nor the ratio of full-length to internally-truncated copies is strongly correlated with the degree of gonadal dysgenesis exhibited by an isofemale strain. Thus, variation in P element abundance and structure across different populations does not necessarily lead to corresponding geographic differences in gonadal dysgenesis phenotypes. Finally, it was confirmed that population differences in the abundance and structure of P elements that are observed from isofemale lines can also be observed in pool-seq samples from the same populations. This work supports the view that genomic P element content alone is not sufficient to explain variation in gonadal dysgenesis across strains of D. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences in P element induced phenotypes.
Baudouin-Gonzalez, L., Santos, M. A., Tempesta, C., Sucena, E., Roch, F. and Tanaka, K. (2017). Diverse cis-regulatory mechanisms contribute to expression evolution of tandem gene duplicates. Mol Biol Evol [Epub ahead of print]. PubMed ID: 28961967
Summary:
Pairs of duplicated genes generally display a combination of conserved expression patterns inherited from their unduplicated ancestor and newly acquired domains. However, how the cis-regulatory architecture of duplicated loci evolves to produce these expression patterns is poorly understood. This study directly examined the gene-regulatory evolution of two tandem duplicates, the Drosophila Ly6 genes CG9336 and CG9338, which arose at the base of the drosophilids between 40 and 60 million years ago. Comparing the expression patterns of the two paralogs in four Drosophila species with that of the unduplicated ortholog in the tephritid Ceratitis capitata, they were shown to diverge from each other as well as from the unduplicated ortholog. Moreover, the expression divergence appears to have occurred close to the duplication event and also more recently in a lineage-specific manner. The comparison of the tissue-specific cis-regulatory modules (CRMs) controlling the paralog expression in the four Drosophila species indicates that diverse cis-regulatory mechanisms, including the novel tissue-specific enhancers, differential inactivation, and enhancer sharing, contributed to the expression evolution. This analysis also reveals a surprisingly variable cis-regulatory architecture, in which the CRMs driving conserved expression domains change in number, location, and specificity. Altogether, this study provides a detailed historical account that uncovers a highly dynamic picture of how the paralog expression patterns and their underlying cis-regulatory landscape evolve. It is argued that these findings will encourage studying cis-regulatory evolution at the whole-locus level in order to understand how interactions between enhancers and other regulatory levels shape the evolution of gene expression.
Calvo-Martin, J. M., Papaceit, M. and Segarra, C. (2017). Molecular population genetics of the Polycomb genes in Drosophila subobscura. PLoS One 12(9): e0185005. PubMed ID: 28910411
Summary:
Polycomb group (PcG) proteins are important regulatory factors that modulate the chromatin state. They form protein complexes that repress gene expression by the introduction of posttranslational histone modifications. The study of PcG proteins divergence in Drosophila revealed signals of coevolution among them and an acceleration of the nonsynonymous evolutionary rate in the lineage ancestral to the obscura group species, mainly in subunits of the Pcl-PRC2 complex. This study examined the nucleotide polymorphism of PcG genes in a natural population of D. subobscura to detect whether natural selection has also modulated the evolution of these important regulatory genes in a more recent time scale. Results show that most genes are under the action of purifying selection and present a level and pattern of polymorphism consistent with predictions of the neutral model, the exceptions being Su(z)12 and Pho. MK tests indicate an accumulation of adaptive changes in the SU(Z)12 protein during the divergence of D. subobscura and D. guanche. In contrast, the HKA test shows a deficit of polymorphism at Pho. The most likely explanation for this reduced variation is the location of this gene in the dot-like chromosome and would indicate that this chromosome also has null or very low recombination in D. subobscura, as reported in D. melanogaster.
Clark, E. (2017). Dynamic patterning by the Drosophila pair-rule network reconciles long-germ and short-germ segmentation. PLoS Biol 15(9): e2002439. PubMed ID: 28953896
Summary:
Drosophila segmentation is a well-established paradigm for developmental pattern formation. However, the later stages of segment patterning, regulated by the "pair-rule" genes, are still not well understood at the system level. Building on established genetic interactions, a logical model of the Drosophila pair-rule system was constructed that takes into account the demonstrated stage-specific architecture of the pair-rule gene network. Simulation of this model can accurately recapitulate the observed spatiotemporal expression of the pair-rule genes, but only when the system is provided with dynamic "gap" inputs. This result suggests that dynamic shifts of pair-rule stripes are essential for segment patterning in the trunk and provides a functional role for observed posterior-to-anterior gap domain shifts that occur during cellularisation. The model also suggests revised patterning mechanisms for the parasegment boundaries and explains the aetiology of the even-skipped null mutant phenotype. Strikingly, a slightly modified version of the model is able to pattern segments in either simultaneous or sequential modes, depending only on initial conditions. This suggests that fundamentally similar mechanisms may underlie segmentation in short-germ and long-germ arthropods.

Tuesday, October 10th

Anderson, E. N. and Wharton, K. A. (2017). Alternative cleavage of the bone morphogenetic protein (BMP), Gbb, produces ligands with distinct developmental functions and receptor preference. J Biol Chem [Epub ahead of print]. PubMed ID: 28924042
Summary:
The family of TGF-beta and BMP signaling proteins are made as proprotein dimers, then cleaved by proprotein convertases to release the C-terminal domain as an active ligand dimer. Multiple proteolytic processing sites in Glass bottom boat (Gbb), the Drosophila BMP7 ortholog, can produce distinct ligand forms. Cleavage at the S1 or atypical S0 site in Gbb produces Gbb15, the conventional small BMP ligand, while NS site cleavage produces a larger Gbb38 ligand. It was hypothesized that the Gbb prodomain is involved not only in regulating the production of specific ligands but also their signaling output. Blocking NS cleavage increased association of the full-length prodomain with Gbb15, resulting in a concomitant decrease in signaling activity. Moreover, NS cleavage was required in vivo for Gbb-Decapentaplegic (Dpp) heterodimer-mediated wing vein patterning but not for Gbb15-Dpp heterodimer activity in cell culture. Gbb NS cleavage was also required for viability through its regulation of pupal ecdysis in a type II receptor Wishful thinking (Wit)-dependent manner. In fact, Gbb38-mediated signaling exhibits a preference for Wit over the other type II receptor Punt. Finally, Gbb38 was found to be produced when processing at the S1/S0 site is blocked by O-linked glycosylation in third instar larvae. These findings demonstrate that BMP prodomain cleavage ensures that the mature ligand is not inhibited by the prodomain. Furthermore, alternative processing of BMP proproteins produces ligands that signal through different receptors and exhibit specific developmental functions.
Bhattacharya, A., Li, K., Quiquand, M., Rimesso, G. and Baker, N. E. (2017). The Notch pathway regulates the Second Mitotic Wave cell cycle independently of bHLH proteins. Dev Biol [Epub ahead of print]. PubMed ID: 28919436
Summary:
Notch regulates both neurogenesis and cell cycle activity to coordinate precursor cell generation in the differentiating Drosophila eye. Mosaic analysis with mitotic clones mutant for Notch components was used to identify the pathway of Notch signaling that regulates the cell cycle in the Second Mitotic Wave. Although S phase entry depends on Notch signaling and on the transcription factor Su(H), the transcriptional co-activator Mam and the bHLH repressor genes of the E(spl)-Complex were not essential, although these are Su(H) coactivators and targets during the regulation of neurogenesis. The Second Mitotic Wave showed little dependence on ubiquitin ligases neuralized or mindbomb, and although the ligand Delta is required non-autonomously, partial cell cycle activity occurred in the absence of known Notch ligands. This study found that myc was not essential for the Second Mitotic Wave. The Second Mitotic Wave did not require the HLH protein Extra macrochaetae, and the bHLH protein Daughterless was required only cell-nonautonomously. Similar cell cycle phenotypes for Daughterless and Atonal were consistent with requirement for neuronal differentiation to stimulate Delta expression, affecting Notch activity in the Second Mitotic Wave indirectly. Therefore Notch signaling acts to regulate the Second Mitotic Wave without activating bHLH gene targets.
Augustin, H., McGourty, K., Allen, M. J., Madem, S. K., Adcott, J., Kerr, F., Wong, C. T., Vincent, A., Godenschwege, T., Boucrot, E. and Partridge, L. (2017). Reduced insulin signaling maintains electrical transmission in a neural circuit in aging flies. PLoS Biol 15(9): e2001655. PubMed ID: 28902870
Summary:
Lowered insulin/insulin-like growth factor (IGF) signaling (IIS) can extend healthy lifespan in worms, flies, and mice, but it can also have adverse effects (the "insulin paradox"). Chronic, moderately lowered IIS rescues age-related decline in neurotransmission through the Drosophila giant fiber system (GFS), a simple escape response neuronal circuit, by increasing targeting of the gap junctional protein innexin shaking-B to gap junctions (GJs). Endosomal recycling of GJs was also stimulated in cultured human cells when IIS was reduced. Furthermore, increasing the activity of the recycling small guanosine triphosphatases (GTPases) Rab4 or Rab11 was sufficient to maintain GJs upon elevated IIS in cultured human cells and in flies, and to rescue age-related loss of GJs and of GFS function. Lowered IIS thus elevates endosomal recycling of GJs in neurons and other cell types, pointing to a cellular mechanism for therapeutic intervention into aging-related neuronal disorders.
Borch Jensen, M., Qi, Y., Riley, R., Rabkina, L. and Jasper, H. (2017). PGAM5 promotes lasting FoxO activation after developmental mitochondrial stress and extends lifespan in Drosophila. Elife 6. PubMed ID: 28891792
Summary:
The mitochondrial unfolded protein response (UPRmt) has been associated with long lifespan across metazoans. In Caenorhabditis elegans, mild developmental mitochondrial stress activates UPRmt reporters and extends lifespan. This study shows that similar developmental stress is necessary and sufficient to extend Drosophila lifespan, and identify Phosphoglycerate Mutase 5 (PGAM5) as a mediator of this response. Developmental mitochondrial stress leads to activation of FoxO, via Apoptosis Signal-regulating Kinase 1 (ASK1) and Jun-N-terminal Kinase (JNK). This activation persists into adulthood and induces a select set of chaperones, many of which have been implicated in lifespan extension in flies. Persistent FoxO activation can be reversed by a high-protein diet in adulthood, through mTORC1 and GCN-2 activity. Accordingly, the observed lifespan extension is prevented on a high-protein diet and in FoxO-null flies. The diet-sensitivity of this pathway has important implications for interventions that seek to engage the UPRmt to improve metabolic health and longevity.
Carvalho, G. B., Drago, I., Hoxha, S., Yamada, R., Mahneva, O., Bruce, K. D., Soto Obando, A., Conti, B. and Ja, W. W. (2017). The 4E-BP growth pathway regulates the effect of ambient temperature on Drosophila metabolism and lifespan. Proc Natl Acad Sci U S A 114(36): 9737-9742. PubMed ID: 28827349
Summary:
Changes in body temperature can profoundly affect survival. The dramatic longevity-enhancing effect of cold has long been known in organisms ranging from invertebrates to mammals, yet the underlying mechanisms have only recently begun to be uncovered. In the nematode Caenorhabditis elegans, this process is regulated by a thermosensitive membrane TRP channel and the DAF-16/FOXO transcription factor, but in more complex organisms the underpinnings of cold-induced longevity remain largely mysterious. This study reports that, in Drosophila melanogaster, variation in ambient temperature triggers metabolic changes in protein translation, mitochondrial protein synthesis, and posttranslational regulation of the translation repressor, 4E-BP (eukaryotic translation initiation factor 4E-binding protein).4E-BP determines Drosophila lifespan in the context of temperature changes, revealing a genetic mechanism for cold-induced longevity in this model organism. These results suggest that the 4E-BP pathway, chiefly thought of as a nutrient sensor, may represent a master metabolic switch responding to diverse environmental factors.
Dai, J., Ma, M., Feng, Z. and Pastor-Pareja, J. C. (2017). Inter-adipocyte adhesion and signaling by Collagen IV intercellular concentrations in Drosophila. Curr Biol 27(18): 2729-2740.e2724. PubMed ID: 28867208
Summary:
Sheet-forming Collagen IV is the main component of basement membranes, which are planar polymers of extracellular matrix underlying epithelia and surrounding organs in all animals. Adipocytes in both insects and mammals are mesodermal in origin and often classified as mesenchymal. However, they form true tissues where cells remain compactly associated. Neither the mechanisms providing this tissue-level organization nor its functional significance are known. This study shows that discrete Collagen IV intercellular concentrations (CIVICs), distinct from basement membranes and thicker in section, mediate inter-adipocyte adhesion in Drosophila. Loss of these Collagen-IV-containing structures in the larval fat body caused intercellular gaps and disrupted continuity of the adipose tissue layer. Integrin and Syndecan matrix receptors attach adipocytes to CIVICs and direct their formation. Finally, Integrin-mediated adhesion to CIVICs was shown to promote normal adipocyte growth and prevents autophagy through Src-Pi3K-Akt signaling. These results evidence a surprising non-basement membrane role of Collagen IV in non-epithelial tissue morphogenesis while demonstrating adhesion and signaling functions for these structures.

Monday, October 9th

Narciso, C. E., Contento, N. M., Storey, T. J., Hoelzle, D. J. and Zartman, J. J. (2017). Release of applied mechanical loading stimulates intercellular calcium waves in Drosophila wing discs. Biophys J 113(2): 491-501. PubMed ID: 28746859
Summary:
Mechanical forces are critical inputs for organogenesis and wound healing. Calcium ions (Ca2+) are critical second messengers in cells for integrating environmental and mechanical cues. This paper reports a chip-based regulated environment for microorgans that enables systematic investigations of the crosstalk between an organ's mechanical stress environment and biochemical signaling under genetic and chemical perturbations. This method enabled defining the essential conditions for generating organ-scale intercellular Ca2+ waves in Drosophila wing discs that are also observed in vivo during organ development. Mechanically induced intercellular Ca2+ waves were found to require fly extract growth serum as a chemical stimulus. Using the chip-based regulated environment for microorgans, it was demonstrated that not the initial application but instead the release of mechanical loading is sufficient, but not necessary, to initiate intercellular Ca2+ waves. The Ca2+ response depends on the prestress intercellular Ca2+ activity and not on the magnitude or duration of the mechanical stimulation applied. Mechanically induced intercellular Ca2+ waves rely on IP3R-mediated Ca2+-induced Ca2+ release and propagation through gap junctions. Thus, intercellular Ca2+ waves in developing epithelia may be a consequence of stress dissipation during organ growth.
Neto, M., Naval-Sanchez, M., Potier, D., Pereira, P. S., Geerts, D., Aerts, S. and Casares, F. (2017). Nuclear receptors connect progenitor transcription factors to cell cycle control. Sci Rep 7(1): 4845. PubMed ID: 28687780
Summary:
The specification and growth of organs is controlled simultaneously by networks of transcription factors. While the connection between these transcription factors with fate determinants is increasingly clear, how they establish the link with the cell cycle is far less understood. This study investigated this link in the developing Drosophila eye, where two transcription factors, the MEIS1 homologue hth and the Zn-finger tsh, synergize to stimulate the proliferation of naive eye progenitors. Experiments combining transcriptomics, open-chromatin profiling, motif analysis and functional assays indicate that these progenitor transcription factors exert a global regulation of the proliferation program. Rather than directly regulating cell cycle genes, they control proliferation through an intermediary layer of nuclear receptors of the ecdysone/estrogen-signaling pathway including EcR, Ftz-f1 and Hr46/DHR3. This regulatory subnetwork between hth, tsh and nuclear receptors might be conserved from Drosophila to mammals, as a significant co-overexpression of their human homologues was found in specific cancer types.
Arata, M., Sugimura, K. and Uemura, T. (2017). Difference in Dachsous levels between migrating cells coordinates the direction of collective cell migration. Dev Cell 42(5): 479-497.e410. PubMed ID: 28898677
Summary:
In contrast to extracellular chemotactic gradients, how cell-adhesion molecules contribute to directing cell migration remains more elusive. This study examined the collective migration of Drosophila larval epidermal cells (LECs) along the anterior-posterior axis and proposes a migrating cell group-autonomous mechanism in which an atypical cadherin Dachsous (Ds) plays a pivotal role. In each abdominal segment, the amount of Ds in each LEC varied along the axis of migration (Ds imbalance), which polarized Ds localization at cell boundaries. This Ds polarity was necessary for coordinating the migratory direction. Another atypical cadherin, Fat (Ft), and an unconventional myosin Dachs, both of which bind to Ds, also showed biased cell-boundary localizations, and both were required for the migration. Altogether, it is proposed that the Ds imbalance within the migrating tissue provides the directional cue and that this is decoded by Ds-Ft-mediated cell-cell contacts, which restricts lamellipodia formation to the posterior end of the cell.
Ochoa-Espinosa, A., Harmansa, S., Caussinus, E. and Affolter, M. (2017). Myosin II is not required for Drosophila tracheal branch elongation and cell intercalation. Development 144(16): 2961-2968. PubMed ID: 28811312
Summary:
The Drosophila tracheal system consists of an interconnected network of monolayered epithelial tubes that ensures oxygen transport in the larval and adult body. During tracheal dorsal branch (DB) development, individual DBs elongate as a cluster of cells, led by tip cells at the front and trailing cells in the rear. Branch elongation is accompanied by extensive cell intercalation and cell lengthening of the trailing stalk cells. Although cell intercalation is governed by Myosin II (MyoII)-dependent forces during tissue elongation in the Drosophila embryo that lead to germ-band extension, it remained unclear whether MyoII plays a similar active role during tracheal branch elongation and intercalation. This study used a nanobody-based approach to selectively knock down MyoII in tracheal cells. The data show that, despite the depletion of MyoII function, tip cell migration and stalk cell intercalation (SCI) proceed at a normal rate. This confirms a model in which DB elongation and SCI in the trachea occur as a consequence of tip cell migration, which produces the necessary forces for the branching process.

Friday, October 6th

Palu, R. A. S., Praggastis, S. A. and Thummel, C. S. (2017). Parental obesity leads to metabolic changes in the F2 generation in Drosophila. Mol Metab 6(7): 631-639. PubMed ID: 28702320
Summary:
A significant portion of the heritable risk for complex metabolic disorders cannot be attributed to classic Mendelian genetic factors. At least some of this missing heritability is thought to be due to the epigenetic influence of parental and grandparental metabolic state on offspring health. Previous work suggests that this transgenerational phenomenon is evolutionarily conserved in Drosophila. These studies, however, have all depended on dietary paradigms to alter parental metabolic state, which can have inconsistent heritable effects on the metabolism of offspring. This study use AKHR null alleles to induce obesity in the parental generation and then score both metabolic parameters and genome-wide transcriptional responses in AKHR heterozygote F1 progeny and genetically wild-type F2 progeny. Unexpectedly, elevated glycogen levels and changes in gene expression were observed in AKHR heterozygotes due to haploinsufficiency at this locus. It was also shown that genetic manipulation of parental metabolism using AKHR mutations results in significant physiological changes in F2 wild-type offspring of the grandpaternal/maternal lineage. These results demonstrate that genetic manipulation of parental metabolism in Drosophila can have an effect on the health of F2 progeny, providing a non-dietary paradigm to better understand the mechanisms behind the transgenerational inheritance of metabolic state.
Richards, C. D., Warr, C. G. and Burke, R. (2017). A role for the Drosophila zinc transporter Zip88E in protecting against dietary zinc toxicity. PLoS One 12(7): e0181237. PubMed ID: 28704512
Summary:
Zinc absorption in animals is thought to be regulated in a local, cell autonomous manner with intestinal cells responding to dietary zinc content. The Drosophila zinc transporter Zip88E shows strong sequence similarity to Zips 42C.1, 42C.2 and 89B as well as mammalian Zips 1, 2 and 3, suggesting that it may act in concert with the apically-localised Drosophila zinc uptake transporters to facilitate dietary zinc absorption by importing ions into the midgut enterocytes. However, the functional characterisation of Zip88E presented in this study indicates that Zip88E may instead play a role in detecting and responding to zinc toxicity. Larvae homozygous for a null Zip88E allele are viable yet display heightened sensitivity to elevated levels of dietary zinc. This decreased zinc tolerance is accompanied by an overall decrease in Metallothionein B transcription throughout the larval midgut. A Zip88E reporter gene is expressed only in the salivary glands, a handful of enteroendocrine cells at the boundary between the anterior and middle midgut regions, and in two parallel strips of sensory cell projections connecting to the larval ventral ganglion. Zip88E expression solely in this restricted subset of cells is sufficient to rescue the Zip88E mutant phenotype. Together, these data suggest that Zip88E may be functioning in a small subset of cells to detect excessive zinc levels and induce a systemic response to reduce dietary zinc absorption and hence protect against toxicity.
Thul, P. J., Tschapalda, K., Kolkhof, P., Thiam, A. R., Oberer, M. and Beller, M. (2017). Lipid droplet subset targeting of the Drosophila protein CG2254/dmLdsdh1. J Cell Sci 130(18):3141-3157. PubMed ID: 28775149
Summary:
Lipid droplets (LDs) are the principal organelles of lipid storage. They consist of a hydrophobic core of storage lipids, surrounded by a phospholipid monolayer with proteins attached. While some of these proteins are essential to regulate cellular and organismic lipid metabolism, key questions concerning LD protein function, such as their targeting to LDs, are still unanswered. Intriguingly, some proteins are restricted to LD subsets by an as yet unknown mechanism. This finding makes LD targeting even more complex. This study characterized the Drosophila protein CG2254 which targets LD subsets in cultured cells and different larval Drosophila tissues, where the prevalence of LD subsets appears highly dynamic. An amphipathic amino acid stretch was shown to mediate CG2254 LD localization. Additionally, a juxtaposed sequence stretch was identified limiting CG2254 localization to LD subsets. This sequence is sufficient to restrict a chimeric protein - consisting of the subset targeting sequence introduced to an otherwise pan LD localized protein sequence - to LD subsets. Based on its subcellular localization and annotated function, it is suggested to rename CG2254 to Lipid droplet subset dehydrogenase 1 (Ldsdh1).
Andersen, M. K., MacMillan, H. A., Donini, A. and Overgaard, J. (2017). Cold tolerance of Drosophila species is tightly linked to epithelial K+ transport capacity of the Malpighian tubules and rectal pads. J Exp Biol [Epub ahead of print]. PubMed ID: 28947500
Summary:
Insect chill tolerance is strongly associated with the ability to maintain ion and water homeostasis during cold exposure. Maintenance of K+ balance is particularly important due to its role in setting the cell membrane potential that is involved in many aspects of cellular function and viability. In most insects, K+ balance is maintained through secretion at the Malpighian tubules balancing reabsorption from the hindgut and passive leak arising from the gut lumen. This study examined K+ flux across the Malpighian tubules and the rectal pads in the hindgut in five Drosophila species that differ in cold tolerance. Chill tolerant species were found to be better at maintaining K+ secretion and supressing reabsorption during cold exposure. In contrast, chill susceptible species exhibited large reductions in secretion with no change, or a paradoxical increase, in K+ reabsorption. Using an assay to measure paracellular leak, chill susceptible species were found to experience a large increase in leak during cold exposure, which could explain the increased K+ reabsorption found in these species. The data therefore strongly support the hypothesis that cold tolerant Drosophila species are better at maintaining K+ homeostasis through an increased ability to maintain K+ secretion rates and through reduced leakage of K+ towards the hemolymph. These adaptations are manifested both at the Malpighian tubule and at the rectal pads in the hindgut and ensure that cold tolerant species experience less perturbation of K+ homeostasis during cold stress.

Thursday, October 5th

Yoshino, J., Morikawa, R. K., Hasegawa, E. and Emoto, K. (2017). Neural circuitry that evokes escape behavior upon activation of nociceptive sensory neurons in Drosophila larvae. Curr Biol 27(16):2499-2504. PubMed ID: 28803873
Summary:
Noxious stimuli trigger a stereotyped escape response in animals. In Drosophila larvae, class IV dendrite arborization (C4 da) sensory neurons in the peripheral nervous system are responsible for perception of multiple nociceptive modalities, including noxious heat and harsh mechanical stimulation, through distinct receptors. Silencing or ablation of C4 da neurons largely eliminates larval responses to noxious stimuli, whereas optogenetic activation of C4 da neurons is sufficient to provoke corkscrew-like rolling behavior similar to what is observed when larvae receive noxious stimuli, such as high temperature or harsh mechanical stimulation. How C4 da activation triggers the escape behavior in the circuit level is still incompletely understood. This study identified segmentally arrayed local interneurons (medial clusters of C4 da second-order interneurons [mCSIs]) in the ventral nerve cord that are necessary and sufficient to trigger rolling behavior. GFP reconstitution across synaptic partners (GRASP) analysis indicates that C4 da axons form synapses with mCSI dendrites. Optogenetic activation of mCSIs induces the rolling behavior, whereas silencing mCSIs reduces the probability of rolling behavior upon C4 da activation. Further anatomical and functional studies suggest that the C4 da-mCSI nociceptive circuit evokes rolling behavior at least in part through segmental nerve a (SNa) motor neurons. These findings thus uncover a local circuit that promotes escape behavior upon noxious stimuli in Drosophila larvae and provide mechanistic insights into how noxious stimuli are transduced into the stereotyped escape behavior in the circuit level.
Wong, A. C., Wang, Q. P., Morimoto, J., Senior, A. M., Lihoreau, M., Neely, G. G., Simpson, S. J. and Ponton, F. (2017). Gut microbiota modifies olfactory-guided microbial preferences and foraging decisions in Drosophila. Curr Biol 27(15): 2397-2404.e2394. PubMed ID: 28756953
Summary:
The gut microbiota affects a wide spectrum of host physiological traits, including development, germline, immunity, nutrition, and longevity. Association with microbes also influences fitness-related behaviors such as mating and social interactions. Although the gut microbiota is evidently important for host wellbeing, how hosts become associated with particular assemblages of microbes from the environment remains unclear. This study presents evidence that the gut microbiota can modify microbial and nutritional preferences of Drosophila melanogaster. By experimentally manipulating the gut microbiota of flies subjected to behavioral and chemosensory assays, fly-microbe attractions were found to be shaped by the identity of the host microbiota. Conventional flies exhibit preference for their associated Lactobacillus, a behavior also present in axenic flies as adults and marginally as larvae. By contrast, fly preference for Acetobacter is primed by early-life exposure and can override the innate preference. These microbial preferences are largely olfactory guided and have profound impact on host foraging, as flies continuously trade off between acquiring beneficial microbes and balancing nutrients from food. This study shows a role of animal microbiota in shaping host fitness-related behavior through their chemosensory responses, opening a research theme on the interrelationships between the microbiota, host sensory perception, and behavior.
Robie, A. A., Hirokawa, J., Edwards, A. W., Umayam, L. A., Lee, A., Phillips, M. L., Card, G. M., Korff, W., Rubin, G. M., Simpson, J. H., Reiser, M. B. and Branson, K. (2017). Mapping the neural substrates of behavior. Cell 170(2): 393-406.e328. PubMed ID: 28709004
Summary:
Assigning behavioral functions to neural structures has long been a central goal in neuroscience and is a necessary first step toward a circuit-level understanding of how the brain generates behavior. This study mapped the neural substrates of locomotion and social behaviors for Drosophila melanogaster using automated machine-vision and machine-learning techniques. From videos of 400,000 flies, the behavioral effects were quantified of activating 2,204 genetically targeted populations of neurons. A novel quantification of anatomy was combined with behavioral analysis to create brain-behavior correlation maps, which are shared as browsable web pages and interactive software. Based on these maps, hypotheses were generated of regions of the brain causally related to sensory processing, locomotor control, courtship, aggression, and sleep. The maps directly specify genetic tools to target these regions, which were used to identify a small population of neurons with a role in the control of walking.
Xiao, C., Qiu, S. and Robertson, R. M. (2017). The white gene controls copulation success in Drosophila melanogaster. Sci Rep 7(1): 7712. PubMed ID: 28794482
Summary:
Characteristics of male courtship behavior in Drosophila melanogaster have been well-described, but the genetic basis of male-female copulation is largely unknown. This study shows that the white (w) gene, a classical gene for eye color, is associated with copulation success. 82.5% of wild-type Canton-S flies copulated within 60 minutes in circular arenas, whereas few white-eyed mutants mated successfully. The w + allele exchanged to the X chromosome or duplicated to the Y chromosome in the white-eyed genetic background rescued the defect of copulation success. The w +-associated copulation success was independent of eye color phenotype. Addition of the mini-white (mw +) gene to the white-eyed mutant rescued the defect of copulation success in a manner that was mw + copy number-dependent. Lastly, male-female sexual experience mimicked the effects of w +/mw + in improving successful copulation. These data suggest that the w + gene controls copulation success in Drosophila melanogaster.
Zhao, W., Gong, C., Ouyang, Z., Wang, P., Wang, J., Zhou, P., Zheng, N. and Gong, Z. (2017). Turns with multiple and single head cast mediate Drosophila larval light avoidance. PLoS One 12(7): e0181193. PubMed ID: 28700684
Summary:
Drosophila larvae exhibit klinotaxis (directional orientation involving turning toward a stimulus) when placed in a gradient of temperature, chemicals, or light. The larva samples environmental stimuli by casting its head from side to side. By comparing the results of two consecutive samples, it decides the direction of movement, appearing as a turn proceeded by one or more head casts. By analyzing larval behavior in a light-spot-based phototaxis assay, this study showed that, in addition to turns with a single cast (1-cast), turns with multiple head casts (n-cast) helped to improve the success of light avoidance. Upon entering the light spot, the probability of escape from light after the first head cast was only ~30%. As the number of head casts increased, the chance of successful light avoidance increased and the overall chance of escaping from light increased to >70%. The amplitudes of first head casts that failed in light avoidance were significantly smaller in n-cast turns than those in 1-cast events, indicating that n-cast turns might be planned before completion of the first head cast. In n-casts, the amplitude of the second head cast was generally larger than that of the first head cast, suggesting that larvae tried harder in later attempts to improve the efficacy of light avoidance. It is proposed that both 1-cast turns and n-cast turns contribute to successful larval light avoidance, and both can be initiated at the first head cast.
Cao, W., Song, L., Cheng, J., Yi, N., Cai, L., Huang, F. D. and Ho, M. (2017). An automated rapid iterative negative geotaxis assay for analyzing adult climbing behavior in a Drosophila model of neurodegeneration. J Vis Exp(127). PubMed ID: 28931001
Summary:
Neurodegenerative diseases are frequently associated with a progressive loss of movement ability, reduced life span, and age-dependent neurodegeneration. To understand the mechanism of these cellular events, and their causal relationships with each other, Drosophila melanogaster, with its sophisticated genetic tools and diverse behavioral features, are used as disease models for assessing neurodegenerative phenotypes. This study describes a high-throughput method to analyze Drosophila adult negative geotaxis behavior, as an indication for possible motor defects associated with neurodegeneration. An automated machine is designed and developed to drive fly synchronization using an initial electric impulse, later allowing the recording of negative geotaxis behavior over a course of seconds to minutes. Images from the digitally recorded video are then processed with the self-designed RflyDetection software for statistical data manipulation. Different from the manually controlled negative geotaxis assay based on single flies, this precise, fast, and high-throughput protocol allows data acquisition from more than hundreds of flies simultaneously, providing an efficient approach to advance understanding in the underlying mechanism of locomotor deficits associated with neurodegeneration.

Wednesday, October 4th

Zhang, X., Xu, K., Wei, D., Wu, W., Yang, K. and Yuan, M. (2017). Baculovirus infection induces disruption of the nuclear lamina. Sci Rep 7(1): 7823. PubMed ID: 28798307
Summary:
Baculovirus nucleocapsids egress from the nucleus primarily via budding at the nuclear membrane. The nuclear lamina underlying the nuclear membrane represents a substantial barrier to nuclear egress. Whether the nuclear lamina undergoes disruption during baculovirus infection remains unknown. This study generated clonal cell line, Sf9-L, that stably expresses GFP-tagged Drosophila lamin B. GFP autofluorescence colocalized with immunofluorescent anti-lamin B at the nuclear rim of Sf9-L cells, indicating GFP-lamin B was incorporated into the nuclear lamina. Meanwhile, virus was able to replicate normally in Sf9-L cells. Next, alterations to the nuclear lamina were investigated during baculovirus infection in Sf9-L cells. A portion of GFP-lamin B localized diffusely at the nuclear rim, and some GFP-lamin B was redistributed within the nucleus during the late phase of infection, suggesting the nuclear lamina was partially disrupted. Immunoelectron microscopy revealed associations between GFP-lamin B and the edges of the electron-dense stromal mattes of the virogenic stroma, intranuclear microvesicles, and ODV envelopes and nucleocapsids within the nucleus, indicating the release of some GFP-lamin B from the nuclear lamina. Additionally, GFP-lamin B phosphorylation increased upon infection. Based on these data, baculovirus infection induced lamin B phosphorylation and disruption of the nuclear lamina.
Sharma, V., Kohli, S. and Brahmachari, V. (2017). Correlation between desiccation stress response and epigenetic modifications of genes in Drosophila melanogaster: An example of environment-epigenome interaction. Biochim Biophys Acta 1860(10):1058-1068. PubMed ID: 28801151
Summary:
Tolerance to water stress is accompanied by biochemical changes which in turn are due to transcriptional alteration. This study investigated the correlation between stress response and epigenetic modification underlying gene expression modulation during desiccation stress in Canton-S. Altered resistance of flies in desiccation stress is reported for heterozygote mutants of PcG and TrxG members. Pc/+ mutant shows lower survival, while ash1/+ mutants show higher survival under desiccation stress as compared to Canton-S. Expression alteration in stress related genes as well the genes of the Polycomb and trithorax complex was detected in Canton-S subjected to desiccation stress. Concomitant with this, there is an altered enrichment of H3K27me3 and H3K4me3 at the upstream regions of the stress responsive genes. The enrichment of activating mark, H3K4me3, is higher in non-stress condition while H3K27me3, the repressive mark, is more pronounced under stress condition, which in turn, can be correlated with the binding of Pc and Ash1. These results show that desiccation stress induces dynamic switching in expression and enrichment of PcG and TrxG in the upstream region of genes, which correlates with histone modifications. This this study provides evidence that epigenetic modulation could be one of the mechanisms to adapt to the desiccation stress in Drosophila. Thus, this study proposes the interaction of epigenome and environmental factors.
Zenk, F., Loeser, E., Schiavo, R., Kilpert, F., Bogdanovic, O. and Iovino, N. (2017). Germ line-inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition. Science 357(6347): 212-216. PubMed ID: 28706074
Summary:
Gametes carry parental genetic material to the next generation. Stress-induced epigenetic changes in the germ line can be inherited and can have a profound impact on offspring development. However, the molecular mechanisms and consequences of transgenerational epigenetic inheritance are poorly understood. This study found that Drosophila oocytes transmit the repressive histone mark H3K27me3 to their offspring. Maternal contribution of the histone methyltransferase Enhancer of zeste, the enzymatic component of Polycomb repressive complex 2, is required for active propagation of H3K27me3 during early embryogenesis. H3K27me3 in the early embryo prevents aberrant accumulation of the active histone mark H3K27ac at regulatory regions and precocious activation of lineage-specific genes at zygotic genome activation. Disruption of the germ line-inherited Polycomb epigenetic memory causes embryonic lethality that cannot be rescued by late zygotic reestablishment of H3K27me3. Thus, maternally inherited H3K27me3, propagated in the early embryo, regulates the activation of enhancers and lineage-specific genes during development.
Li, T., Hodgson, J. W., Petruk, S., Mazo, A. and Brock, H. W. (2017). Additional sex combs interacts with enhancer of zeste and trithorax and modulates levels of trimethylation on histone H3K4 and H3K27 during transcription of hsp70. Epigenetics Chromatin 10(1): 43. PubMed ID: 28927461
Summary:
Maintenance of cell fate determination requires the Polycomb group for repression; the trithorax group for gene activation; and the enhancer of trithorax and Polycomb (ETP) group for both repression and activation. Additional sex combs (Asx) is a genetically identified ETP for the Hox loci, but the molecular basis of its dual function is unclear. This study shows that in vitro, Asx binds directly to the SET domains of the histone methyltransferases (HMT) Enhancer of zeste [E(z)] (H3K27me3) and Trx (H3K4me3) through a bipartite interaction site separated by 846 amino acid residues. In Drosophila S2 cell nuclei, Asx interacts with E(z) and Trx in vivo. Drosophila Asx is required for repression of heat-shock gene hsp70 and is recruited downstream of the hsp70 promoter. Changes in the levels of H3K4me3 and H3K27me3 downstream of the hsp70 promoter in Asx mutants relative to wild type show that Asx regulates H3K4 and H3K27 trimethylation. It is proposed that during transcription Asx modulates the ratio of H3K4me3 to H3K27me3 by selectively recruiting the antagonistic HMTs, E(z) and Trx or other nucleosome-modifying enzymes to hsp70.
Song, S., Herranz, H. and Cohen, S. M. (2017). The chromatin remodeling BAP complex limits tumor promoting activity of the Hippo pathway effector Yki to prevent neoplastic transformation in Drosophila epithelia. Dis Model Mech [Epub ahead of print]. PubMed ID: 28754838
Summary:
SWI/SNF chromatin remodeling complexes are mutated in many human cancers. This report makes use of a Drosophila genetic model for epithelial tumor formation to explore the tumor suppressive role of SWI/SNF complex proteins. Members of the BAP complex (a core complex containing Brahma, Snr1, Bap111, Moira (Mor) core associated with Osa) exhibit tumor suppressor activity in tissue overexpressing the Yorkie (Yki) proto-oncogene, but not in tissue overexpressing EGFR. The BAP complex has been reported to serve as a Yki-binding cofactor to support Yki target expression. However, this study observed that depletion of BAP leads to ectopic expression of Yki targets both autonomously and non-autonomously, suggesting additional indirect effects. Evidence is provided that BAP complex depletion causes upregulation of the Wingless and Dpp morphogens to promote tumor formation in cooperation with Yki.
Zhang, S., Pan, C., Lv, X., Wu, W., Chen, H., Wu, W., Wu, H., Zhang, L. and Zhao, Y. (2017). Repression of Abd-B by Polycomb is critical for cell identity maintenance in adult Drosophila testis. Sci Rep 7(1): 5101. PubMed ID: 28698559
Summary:
Hox genes play a fundamental role in regulating animal development. However, less is known about their functions on homeostasis maintenance in adult stem cells. This study reports that the repression of an important axial Hox gene, Abdominal-B (Abd-B), in cyst stem cells (CySCs) is essential for the homeostasis and cell identity maintenance in the adult Drosophila testis. Derepression of Abd-B in CySCs disrupts the proper self-renewal of both germline stem cells (GSCs) and CySCs, and leads to an excessive expansion of early stage somatic cells, which originate from both lineages. It was further demonstrated that canonical Polycomb (Pc) and functional pathway of Polycomb group (PcG) proteins are responsible for maintaining the germline cell identity non-autonomously via repressing Abd-B in CySCs in the adult Drosophila testis.

Tuesday, October 3rd

Molina-Mateo, D., Fuenzalida-Uribe, N., Hidalgo, S., Molina-Fernandez, C., Abarca, J., Zarate, R. V., Escandon, M., Figueroa, R., Tevy, M. F. and Campusano, J. M. (2017). Characterization of a presymptomatic stage in a Drosophila Parkinson's disease model: Unveiling dopaminergic compensatory mechanisms. Biochim Biophys Acta [Epub ahead of print]. PubMed ID: 28716706
Summary:
Parkinson disease (PD) is a degenerative disorder characterized by several motor symptoms including shaking, rigidity, slow movement and difficult walking, which has been associated to the death of nigro-striatal dopaminergic neurons. Although the molecular mechanisms responsible for this disease are not clear, hereditary PD is linked to mutations in specific genes, including the PTEN-induced putative kinase 1 (PINK1). This work provides a thorough temporal description of the behavioral effects induced by a mutation in the PINK1 gene in adult Drosophila. The data suggests that the motor deficits associated to PD are fully revealed only by the third week of age. However, olfactory dysfunction is detected as early as the first week of age. Immunofluorescence and neurochemical data is provided that leads to the idea that compensatory changes occur in this Drosophila model for PD. These compensatory changes are associated to specific components of the dopaminergic system: the biosynthetic enzymes, Tyrosine hydroxylase and Dopa decarboxylase, and the Dopamine transporter, a plasma membrane protein involved in maintaining dopamine extracellular levels at physiologically relevant levels. Thus, behavioral, immunofluorescence and neurochemical data help define for the first time presymptomatic and symptomatic phases in this PD animal model, and that compensatory changes occur in the dopaminergic neurons in the presymptomatic stage.
Lee, B. I., Suh, Y. S., Chung, Y. J., Yu, K. and Park, C. B. (2017). Shedding light on Alzheimer's beta-amyloidosis: Photosensitized methylene blue inhibits self-assembly of beta-amyloid peptides and disintegrates their aggregates. Sci Rep 7(1): 7523. PubMed ID: 28790398
Summary:
Abnormal aggregation of β-amyloid (Aβ) peptides is a major hallmark of Alzheimer's disease (AD). In spite of numerous attempts to prevent the β-amyloidosis, no effective drugs for treating AD have been developed to date. Among many candidate chemicals, methylene blue (MB) has proved its therapeutic potential for AD in a number of in vitro and in vivo studies; but the result of recent clinical trials performed with MB and its derivative was negative. With the aid of multiple photochemical analyses, this study first reports that photoexcited MB molecules can block Aβ42 aggregation in vitro. Furthermore, an in vivo study using Drosophila AD model demonstrates that photoexcited MB is highly effective in suppressing synaptic toxicity, resulting in a reduced damage to the neuromuscular junction (NMJ), an enhanced locomotion, and decreased vacuole in the brain. The hindrance effect is attributed to Aβ42 oxidation by singlet oxygen generated from photoexcited MB. Finally, this study shows that photoexcited MB possess a capability to disaggregate the pre-existing Aβ42 aggregates and reduce Aβ-induced cytotoxicity. This work suggests that light illumination can provide an opportunity to boost the efficacies of MB toward photodynamic therapy of AD in future.
Yalcin, B., Zhao, L., Stofanko, M., O'Sullivan, N. C., Kang, Z. H., Roost, A., Thomas, M. R., Zaessinger, S., Blard, O., Patto, A. L., Sohail, A., Baena, V., Terasaki, M. and O'Kane, C. J. (2017). Modeling of axonal endoplasmic reticulum network by spastic paraplegia proteins. Elife 6. PubMed ID: 28742022
Summary:
Axons contain a smooth tubular endoplasmic reticulum (ER) network that is thought to be continuous with ER throughout the neuron; the mechanisms that form this axonal network are unknown. Mutations affecting reticulon or REEP (Drosophila Reep1) proteins, with intramembrane hairpin domains that model ER membranes, cause an axon degenerative disease, hereditary spastic paraplegia (HSP). This study shows that Drosophila axons have a dynamic axonal ER network, which these proteins help to model. Loss of HSP hairpin proteins causes ER sheet expansion, partial loss of ER from distal motor axons, and occasional discontinuities in axonal ER. Ultrastructural analysis reveals an extensive ER network in axons, which shows larger and fewer tubules in larvae that lack reticulon and REEP proteins, consistent with loss of membrane curvature. Therefore HSP hairpin-containing proteins are required for shaping and continuity of axonal ER, thus suggesting roles for ER modeling in axon maintenance and function.
De Nobrega, A. K., Mellers, A. P. and Lyons, L. C. (2017). Aging and circadian dysfunction increase alcohol sensitivity and exacerbate mortality in Drosophila melanogaster. Exp Gerontol 97: 49-59. PubMed ID: 28750752
Summary:
Alcohol abuse is a rising problem in middle-aged and older individuals resulting in serious health, family and economic consequences. Effective treatment necessitates the identification of factors influencing alcohol toxicity with aging. This study investigated the interaction between aging, alcohol toxicity and circadian function using Drosophila as a model system. As wild type flies age, sensitivity to alcohol increases and circadian regulation of alcohol-induced behaviors weakens. Decreased circadian modulation is correlated with significantly greater alcohol sensitivity during the subjective day. The circadian clock modulates alcohol-induced mortality in younger flies with increased mortality following alcohol exposure at night. Older flies exhibit significantly longer recovery times following alcohol-induced sedation and increased mortality following binge-like or chronic alcohol exposure. Flies rendered arrhythmic either genetically or environmentally exhibit significantly increased alcohol sensitivity, longer recovery times and increased mortality. It is hypothesized that the circadian clock phase specifically buffers behavioral and cellular alcohol sensitivity with this protection diminishing as the circadian clock weakens with age.

Monday, October 2nd

Trylinski, M., Mazouni, K. and Schweisguth, F. (2017). Intra-lineage fate decisions involve activation of Notch receptors basal to the midbody in Drosophila sensory organ precursor cells. Curr Biol 27(15): 2239-2247. PubMed ID: 28736165
Summary:
Notch receptors regulate cell fate decisions during embryogenesis and throughout adult life. In many cell lineages, binary fate decisions are mediated by directional Notch signaling between the two sister cells produced by cell division. How Notch signaling is restricted to sister cells after division to regulate intra-lineage decision is poorly understood. More generally, where ligand-dependent activation of Notch occurs at the cell surface is not known, as methods to detect receptor activation in vivo are lacking. In Drosophila pupae, Notch signals during cytokinesis to regulate the intra-lineage pIIa/pIIb decision in the sensory organ lineage. This study identified two pools of Notch along the pIIa-pIIb interface, apical and basal to the midbody. Analysis of the dynamics of Notch, Delta, and Neuralized distribution in living pupae suggests that ligand endocytosis and receptor activation occur basal to the midbody. Using selective photo-bleaching of GFP-tagged Notch and photo-tracking of photo-convertible Notch, this study showed that nuclear Notch is indeed produced by receptors located basal to the midbody. Thus, only a specific subset of receptors, located basal to the midbody, contributes to signaling in pIIa. This is the first in vivo characterization of the pool of Notch contributing to signaling. A simple mechanism of cell fate decision based on intra-lineage signaling is proposed: ligands and receptors localize during cytokinesis to the new cell-cell interface, thereby ensuring signaling between sister cells, hence intra-lineage fate decision.
Tripathi, B. K., Das, R., Mukherjee, A. and Mutsuddi, M. (2017). Interaction of Spoonbill with Prospero in Drosophila: Implications in neuroblast development. Genesis 55(9). PubMed ID: 28722203
Summary:
Identification of Spoon as a suppressor of SCA8 associated neurodegeneration provides a hint about its role in neuronal development and maintenance. However, a detailed molecular characterization of spoon has not yet been reported. This study describes spatial expression pattern of Spoon during Drosophila development. Quantitative real time-PCR and fluorescent RNA-RNA in situ hybridization indicate that Spoon is expressed at relatively high levels in larval brain and photoreceptors of eye-antennal discs. Immunostaining reveals that Spoon is subcellularly localized in the cytoplasm and is also membrane bound. Strong expression is also seen in adult ovary and testes. Spoon immunostaining exhibits unique pattern of expression in larval brain. Spoon in the neuroblasts colocalizes with Prospero, a transcription factor regulating genes involved in neuroblast self-renewal or cell-cycle control. Co-immunoprecipitation suggests that Spoon and Prospero reside in the same protein complex. Using Drosophila model of SCA8 RNA neuropathy this study has also shown that loss of Prospero hinders the suppression of SCA8 associated neurodegeneration by Spoonbill, suggesting Prospero and Spoon might genetically interact and function together. This study presents Spoon as a novel interacting partner of Prospero and this might be critical in determining the polarized localization of cell fate determinants.
Tsankova, A., Pham, T. T., Garcia, D. S., Otte, F. and Cabernard, C. (2017). Cell polarity regulates biased myosin activity and dynamics during asymmetric cell division via Drosophila Rho kinase and Protein kinase N. Dev Cell 42(2): 143-155.e145. PubMed ID: 28712722
Summary:
Cell and tissue morphogenesis depends on the correct regulation of non-muscle Myosin II, but how this motor protein is spatiotemporally controlled is incompletely understood. This study shows that in asymmetrically dividing Drosophila neural stem cells, cell intrinsic polarity cues provide spatial and temporal information to regulate biased Myosin activity. Using live cell imaging and a genetically encoded Myosin activity sensor, Drosophila Rho kinase (Rok) was found to enrich for activated Myosin on the neuroblast cortex prior to nuclear envelope breakdown (NEB). After NEB, the conserved polarity protein Partner of Inscuteable (Pins) sequentially enriches Rok and Protein Kinase N (Pkn) on the apical neuroblast cortex. These data suggest that apical Rok first increases phospho-Myosin, followed by Pkn-mediated Myosin downregulation, possibly through Rok inhibition. It is proposed that polarity-induced spatiotemporal control of Rok and Pkn is important for unequal cortical expansion, ensuring correct cleavage furrow positioning and the establishment of physical asymmetry.
Trible, W., Olivos-Cisneros, L., McKenzie, S. K., Saragosti, J., Chang, N. C., Matthews, B. J., Oxley, P. R. and Kronauer, D. J. C. (2017). orco mutagenesis causes loss of antennal lobe glomeruli and impaired social behavior in ants. Cell 170(4): 727-735.e710. PubMed ID: 28802042
Summary:
Life inside ant colonies is orchestrated with diverse pheromones, but it is not clear how ants perceive these social signals. It has been proposed that pheromone perception in ants evolved via expansions in the numbers of odorant receptors (ORs) and antennal lobe glomeruli. This study generated the first mutant lines in the clonal raider ant, Ooceraea biroi, by disrupting orco, a gene required for the function of all ORs. orco mutants were found to exhibit severe deficiencies in social behavior and fitness, suggesting they are unable to perceive pheromones. Surprisingly, unlike in Drosophila melanogaster, orco mutant ants also lack most of the approximately 500 antennal lobe glomeruli found in wild-type ants. These results illustrate that ORs are essential for ant social organization and raise the possibility that, similar to mammals, receptor function is required for the development and/or maintenance of the highly complex olfactory processing areas in the ant brain.
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