x What's hot today: Current papers in developmental biology and gene function

What's hot today:
Current papers in developmental biology and gene function





ARCHIVE

Thursday, November 30th

What's hot today
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Rui, M., Qian, J., Liu, L., Cai, Y., Lv, H., Han, J., Jia, Z. and Xie, W. (2017). The neuronal protein Neurexin directly interacts with the Scribble-Pix complex to stimulate F-actin assembly for synaptic vesicle clustering. J Biol Chem [Epub ahead of print]. PubMed ID: 28710284
Summary:
Synaptic vesicles (SVs) form distinct pools at synaptic terminals, and this well-regulated separation is necessary for normal neuro-transmission. However, how SV cluster in particular synaptic compartments to maintain normal neurotransmitter release remains a mystery. The presynaptic protein Neurexin (NRX) plays a significant role in synaptic architecture and function, and some evidences suggest that NRX is associated with neurological disorders, including autism spectrum disorders. However, the role of NRX in SV clustering is unclear. Using the neuromuscular junction at the 2-3 instar stages of Drosophila larvae as a model and biochemical, imaging, and electrophysiology techniques, this study demonstrate that Drosophila NRX (DNRX) plays critical roles in regulating synaptic terminal clustering and release of SVs. DNRX controls the terminal clustering and release of SVs by stimulating presynaptic F-actin. Furthermore, the results indicate that DNRX functions through the scaffold protein Scribble and the GEF protein Pixie to activate the small GTPase Rac1. A direct interaction was observed between the C-terminal PDZ-binding motif of DNRX and the PDZ domains of Scribble and that Scribble bridges DNRX to DPix, forming a DNRX/Scribble/DPix complex that activates Rac1 and subsequently stimulates presynaptic F-actin assembly and SV clustering. Taken together, this work provides important insights into the function of DNRX in regulating SV clustering, which could help inform further research into pathological neurexin-mediated mechanisms in neurological disorders such as autism.
Zhang, X., Rui, M., Gan, G., Huang, C., Yi, J., Lv, H. and Xie, W. (2017). Neuroligin 4 regulates synaptic growth via the Bone morphogenetic protein (BMP) signaling pathway at the Drosophila neuromuscular junction. J Biol Chem [Epub ahead of print]. PubMed ID: 28912273
Summary:
The neuroligin (Nlg) family of neural cell adhesion molecules is thought to be required for synapse formation and development, and has been linked to the development of autism spectrum disorders in humans. In Drosophila melanogaster, mutations in the neuroligin 1-3 genes have been reported to induce synapse developmental defects at neuromuscular junctions (NMJs), but the role of neuroligin 4 (dnlg4) in synapse development has not been determined. This study reports that the Drosophila Neuroligin 4 (DNlg4) is different from DNlg1-3 in that it presynaptically regulates NMJ synapse development. Loss of dnlg4 results in reduced growth of NMJs with fewer synaptic boutons. The morphological defects caused by dnlg4 mutant are associated with a corresponding decrease in synaptic transmission efficacy. All of these defects could only be rescued when DNlg4 was expressed in the presynapse of NMJs. To understand the basis of DNlg4 function, genetic interactions were sought; connections with the components of the bone morphogenetic protein (BMP) signaling pathway. Immunostaining and western blot analyses demonstrated that the regulation of NMJ growth by DNlg4 was due to the positive modulation of BMP signaling by DNlg4. Specifically, BMP type I receptor Tkv abundance was reduced in dnlg4 mutants, and immunoprecipitation assays showed that DNlg4 and Tkv physically interacted in vivo. This study demonstrates that DNlg4 presynaptically regulates neuromuscular synaptic growth via the BMP signaling pathway by modulating Tkv.
Reddy-Alla, S., et al. (2017). Stable positioning of Unc13 restricts synaptic vesicle fusion to defined release sites to promote synchronous neurotransmission. Neuron 95(6): 1350-1364.e1312. PubMed ID: 28867551
Summary:
Neural information processing depends on precisely timed, Ca2+-activated synaptic vesicle exocytosis from release sites within active zones (AZs), but molecular details are unknown. This study found that the (M)Unc13-family member Unc13A generates release sites and showed the physiological relevance of their restrictive AZ targeting. Super-resolution and intravital imaging of Drosophila neuromuscular junctions revealed that (unlike the other release factors Unc18 and Syntaxin-1A) Unc13A was stably and precisely positioned at AZs. Local Unc13A levels predicted single AZ activity. Different Unc13A portions selectively affected release site number, position, and functionality. An N-terminal fragment stably localized to AZs, displaced endogenous Unc13A, and reduced the number of release sites, while a C-terminal fragment generated excessive sites at atypical locations, resulting in reduced and delayed evoked transmission that displayed excessive facilitation. Thus, release site generation by the Unc13A C terminus and their specific AZ localization via the N terminus ensure efficient transmission and prevent ectopic, temporally imprecise release.
Bodzeta, A., Kahms, M. and Klingauf, J. (2017). The presynaptic v-ATPase reversibly disassembles and thereby modulates exocytosis but is not part of the fusion machinery. Cell Rep 20(6): 1348-1359. PubMed ID: 28793259
Evolutionary Homolog Study
Vacuolar H+-ATPase (v-ATPase) is a multi-subunit complex comprising two domains: the cytosolic V1 domain catalyzing ATP hydrolysis and the membranous V0 sector translocating protons across membranes. In addition to proton pumping, a direct function of the V0 proteolipid ring in membrane fusion has been proposed for yeast vacuolar fusion and synaptic vesicle exocytosis in Drosophila. This study shows in cultured hippocampal neurons that in recycling synaptic vesicles, v-ATPases are only transiently assembled in a pH-dependent fashion during the tightly coupled cycle of exo-endocytosis. Upon locking v-ATPase in an assembled state by saliphenylhalamide, use- and time-dependent release depression was observed for stimuli exceeding release of primed vesicles but no abrogation of exocytosis. Thus, the membranous V0 sector is not part of the exocytotic fusion machinery. Instead, v-ATPase modulates release upstream of docking to favor fusion of fully filled synaptic vesicles.

Wednesday, November 29th

Lovick, J. K., Omoto, J. J., Ngo, K. T. and Hartenstein, V. (2017). Development of the anterior visual input pathway to the Drosophila central complex. J Comp Neurol. PubMed ID: 28675433
Summary:
The anterior visual pathway (AVP) conducts visual information from the medulla of the optic lobe via the anterior optic tubercle (AOTU) and bulb (BU) to the ellipsoid body (EB) of the central complex. The anatomically defined neuron classes connecting the AOTU, BU, and EB represent discrete lineages, genetically and developmentally specified sets of cells derived from common progenitors (Omoto, 2017). This paper analyzed the formation of the AVP from early larval to adult stages. The immature fiber tracts of the AVP, formed by secondary neurons of lineages DALcl1/2 and DALv2, assemble into structurally distinct primordia of the AOTU, BU, and EB within the late larval brain. During the early pupal period (P6-P48) these primordia grow in size and differentiate into the definitive subcompartments of the AOTU, BU, and EB. The primordium of the EB has a complex composition. DALv2 neurons form the anterior EB primordium, which starts out as a bilateral structure, then crosses the midline between P6 and P12, and subsequently bends to adopt the ring shape of the mature EB. Columnar neurons of the central complex, generated by the type II lineages DM1-4, form the posterior EB primordium. Starting out as an integral part of the fan-shaped body (FB) primordium, the posterior EB primordium moves forward and merges with the anterior EB primordium. This study documents the extension of neuropil glia around the nascent EB and BU, and analyzes the relationship of primary and secondary neurons of the AVP lineages.
Boyan, G., Liu, Y., Khalsa, S. K. and Hartenstein, V. (2017). A conserved plan for wiring up the fan-shaped body in the grasshopper and Drosophila. Dev Genes Evol 227(4): 253-269. PubMed ID: 28752327
Summary:
The central complex comprises an elaborate system of modular neuropils which mediate spatial orientation and sensory-motor integration in insects such as the grasshopper and Drosophila. The neuroarchitecture of the largest of these modules, the fan-shaped body, is characterized by its stereotypic set of decussating fiber bundles. These are generated during development by axons from four homologous protocerebral lineages which enter the commissural system and subsequently decussate at stereotypic locations across the brain midline. Since the commissural organization prior to fan-shaped body formation has not been previously analyzed in either species, it was not clear how the decussating bundles relate to individual lineages, or if the projection pattern is conserved across species. This study traced the axonal projections from the homologous central complex lineages into the commissural system of the embryonic and larval brains of both the grasshopper and Drosophila. Projections into the primordial commissures of both species are found to be lineage-specific and allow putatively equivalent fascicles to be identified. Comparison of the projection pattern before and after the commencement of axon decussation in both species reveals that equivalent commissural fascicles are involved in generating the columnar neuroarchitecture of the fan-shaped body. Further, the tract-specific columns in both the grasshopper and Drosophila can be shown to contain axons from identical combinations of central complex lineages, suggesting that this columnar neuroarchitecture is also conserved.
Dylla, K. V., Raiser, G., Galizia, C. G. and Szyszka, P. (2017). Trace Conditioning in Drosophila Induces Associative Plasticity in Mushroom Body Kenyon Cells and Dopaminergic Neurons. Front Neural Circuits 11: 42. PubMed ID: 28676744
Summary:
Dopaminergic neurons (DANs) signal punishment and reward during associative learning. In mammals, DANs show associative plasticity that correlates with the discrepancy between predicted and actual reinforcement (prediction error) during classical conditioning. Also in insects, such as Drosophila, DANs show associative plasticity that is, however, less understood. This study examined associative plasticity in DANs and their synaptic partners, the Kenyon cells (KCs) in the mushroom bodies (MBs), while training Drosophila to associate an odorant with a temporally separated electric shock (trace conditioning). In most MB compartments DANs strengthened their responses to the conditioned odorant relative to untrained animals. This response plasticity preserved the initial degree of similarity between the odorant- and the shock-induced spatial response patterns, which decreased in untrained animals. Contrary to DANs, KCs (alpha'/beta'-type) decreased their responses to the conditioned odorant relative to untrained animals. No evidence was found for prediction error coding by DANs during conditioning. Rather, the data supports the hypothesis that DAN plasticity encodes conditioning-induced changes in the odorant's predictive power.
Foley, B. R., Marjoram, P. and Nuzhdin, S. V. (2017). Basic reversal-learning capacity in flies suggests rudiments of complex cognition. PLoS One 12(8): e0181749. PubMed ID: 28813432
Summary:
The most basic models of learning are reinforcement learning models (for instance, classical and operant conditioning) that posit a constant learning rate; however many animals change their learning rates with experience. This process is sometimes studied by reversing an existing association between cues and rewards, and measuring the rate of relearning. Augmented reversal-learning, where learning rates increase with practice, can be an important component of behavioral flexibility; and may provide insight into higher cognition. Previous studies of reversal-learning in Drosophila have not measured learning rates, but have tended to focus on measuring gross deficits in reversal-learning, as the ratio of two timepoints. These studies have uncovered a diversity of mechanisms underlying reversal-learning, but natural genetic variation in this trait has yet to be assessed. A reversal-learning regime was conducted on a diverse panel of Drosophila melanogaster genotypes. Highly significant genetic variation was found in their baseline ability to learn. They were also found to have a consistent, and strong (1.3x), increase in their learning speed with reversal. No evidence, however, was found that there was genetic variation in their ability to increase their learning rates with experience. This may suggest that Drosophila have a hitherto unrecognized ability to integrate acquired information, and improve their decision making; but that their mechanisms for doing so are under strong constraints.

Tuesday, November 28th

Moshe, A. and Kaplan, T. (2017). Genome-wide search for Zelda-like chromatin signatures identifies GAF as a pioneer factor in early fly development. Epigenetics Chromatin 10(1): 33. PubMed ID: 28676122
Summary:
The protein Zelda was shown to play a key role in early Drosophila development, binding thousands of promoters and enhancers prior to maternal-to-zygotic transition (MZT), and marking them for transcriptional activation. Recent studies have shown that Zelda acts through specific chromatin patterns of histone modifications to mark developmental enhancers and active promoters. Intriguingly, some Zelda sites still maintain these chromatin patterns in Drosophila embryos lacking maternal Zelda protein. A computational method was developed to analyze and refine the chromatin landscape surrounding early Zelda peaks, using a multichannel spectral clustering. This allowed characterization of their chromatin patterns through MZT (mitotic cycles 8-14). Specifically, this study focused on H3K4me1, H3K4me3, H3K18ac, H3K27ac, and H3K27me3 and identified three different classes of chromatin signatures, matching "promoters," "enhancers" and "transiently bound" Zelda peaks. The genome was then further scanned using these chromatin patterns, and additional loci - with no Zelda binding - were identified that show similar chromatin patterns, resulting with hundreds of Zelda-independent putative enhancers. These regions were found to be enriched with GAGA factor (GAF, Trl) and are typically located near early developmental zygotic genes. Overall this analysis suggests that GAF, together with Zelda, plays an important role in activating the zygotic genome. This computational approach offers an efficient algorithm for characterizing chromatin signatures around some loci of interest and allows a genome-wide identification of additional loci with similar chromatin patterns.
Chowdhary, S., Tomer, D., Dubal, D., Sambre, D. and Rikhy, R. (2017). Analysis of mitochondrial organization and function in the Drosophila blastoderm embryo. Sci Rep 7(1): 5502. PubMed ID: 28710464
Summary:
Mitochondria are inherited maternally as globular and immature organelles in metazoan embryos. This study used the Drosophila blastoderm embryo to characterize their morphology, distribution and functions in embryogenesis. Mitochondria were found to be relatively small, dispersed and distinctly distributed along the apico-basal axis in proximity to microtubules by motor protein transport. Live imaging, photobleaching and photoactivation analyses of mitochondrially targeted GFP show that they are mobile in the apico-basal axis along microtubules and are immobile in the lateral plane thereby associating with one syncytial cell. Photoactivated mitochondria distribute equally to daughter cells across the division cycles. ATP depletion by pharmacological and genetic inhibition of the mitochondrial electron transport chain (ETC) activates AMPK and decreases syncytial metaphase furrow extension. In summary, this study shows that small and dispersed mitochondria of the Drosophila blastoderm embryo localize by microtubule transport and provide ATP locally for the fast syncytial division cycles. This study opens the possibility of use of Drosophila embryogenesis as a model system to study the impact of maternal mutations in mitochondrial morphology and metabolism on embryo patterning and differentiation.
Huang, A., Amourda, C., Zhang, S., Tolwinski, N. S. and Saunders, T. E. (2017). Decoding temporal interpretation of the morphogen Bicoid in the early Drosophila embryo. Elife 6. PubMed ID: 28691901
Summary:
Morphogen gradients provide essential spatial information during development. Not only the local concentration but also duration of morphogen exposure is critical for correct cell fate decisions. Yet, how and when cells temporally integrate signals from a morphogen remains unclear. This study used optogenetic manipulation to switch off Bicoid-dependent transcription in the early Drosophila embryo with high temporal resolution, allowing time-specific and reversible manipulation of morphogen signalling. Bicoid transcriptional activity was found to be dispensable for embryonic viability in the first hour after fertilization, but persistently required throughout the rest of the blastoderm stage. Short interruptions of Bicoid activity alter the most anterior cell fate decisions, while prolonged inactivation expands patterning defects from anterior to posterior. Such anterior susceptibility correlates with high reliance of anterior gap gene expression on Bicoid. Therefore, cell fates exposed to higher Bicoid concentration require input for longer duration, demonstrating a previously unknown aspect of Bicoid decoding.
Lin, S. Z., Li, B., Lan, G. and Feng, X. Q. (2017). Activation and synchronization of the oscillatory morphodynamics in multicellular monolayer. Proc Natl Acad Sci U S A 114(31): 8157-8162. PubMed ID: 28716911
Summary:
Oscillatory morphodynamics provides necessary mechanical cues for many multicellular processes. Owing to their collective nature, these processes require robustly coordinated dynamics of individual cells, which are often separated too distantly to communicate with each other through biomaterial transportation. Although it is known that the mechanical balance generally plays a significant role in the systems' morphologies, it remains elusive whether and how the mechanical components may contribute to the systems' collective morphodynamics. This study examined the collective oscillations in the Drosophila amnioserosa tissue to elucidate the regulatory roles of the mechanical components. The tensile stress was identified is the key activator that switches the collective oscillations on and off. This regulatory role is shown analytically using the Hopf bifurcation theory. The physical properties of the tissue boundary were found to be directly responsible for synchronizing the oscillatory intensity and polarity of all inner cells and for orchestrating the spatial oscillation patterns in the tissue.

Monday, November 27th

Lei, Y., Liu, K., Hou, L., Ding, L., Li, Y. and Liu, L. (2017). Small chaperons and autophagy protected neurons from necrotic cell death. Sci Rep 7(1): 5650. PubMed ID: 28720827
Summary:
Neuronal necrosis occurs during early phase of ischemic insult. However, knowledge of neuronal necrosis is still inadequate. To study the mechanism of neuronal necrosis, a Drosophila genetic model of neuronal necrosis was established by calcium overloading through expression of a constitutively opened cation channel mutant. This study performed further genetic screens and identified a suppressor of neuronal necrosis, CG17259, which encodes a seryl-tRNA synthetase. Loss-of-function (LOF) CG17259 activated eIF2alpha phosphorylation and subsequent up-regulation of chaperons (Hsp26 and Hsp27) and autophagy. Genetically, down-regulation of eIF2alpha phosphorylation, Hsp26/Hsp27 or autophagy reduced the protective effect of LOF CG17259, indicating they function downstream of CG17259. The protective effect of these protein degradation pathways indicated activation of a toxic protein during neuronal necrosis. The data indicated that p53 was likely one such protein, because p53 was accumulated in the necrotic neurons and down-regulation of p53 rescued necrosis. In the SH-SY5Y human cells, tunicamycin (TM), a PERK activator, promoted transcription of hsp27; and necrosis induced by glutamate could be rescued by TM, associated with reduced p53 accumulation. In an ischemic stroke model in rats, p53 protein was also increased, and TM treatment could reduce the p53 accumulation and brain damage.
Zhu, M., Zhang, S., Tian, X. and Wu, C. (2017). Mask mitigates MAPT- and FUS-induced degeneration by enhancing autophagy through lysosomal acidification. Autophagy [Epub ahead of print]. PubMed ID: 28806139
Summary:
Accumulation of intracellular misfolded or damaged proteins is associated with both normal aging and late-onset degenerative diseases. Two cellular clearance mechanisms, the ubiquitin-proteasome system (UPS) and the macroautophagy/autophagy-lysosomal pathway, work in concert to degrade harmful protein aggregates and maintain protein homeostasis. 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 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. Mask was found to modulates the global abundance of K48- and K63-ubiquitinated proteins by regulating autophagy-lysosome-mediated degradation, but not UPS function. Indeed, upregulation of Mask compensated the partial loss of UPS function. Mask promotes autophagic flux by enhancing lysosomal function, and Mask is necessary and sufficient for promoting the expression levels of the proton-pumping vacuolar (V)-type ATPases in a TFEB-independent manner.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.
Foo, L. C. (2017). Cyclin-dependent kinase 9 is required for the survival of adult Drosophila melanogaster glia. Sci Rep 7(1): 6796. PubMed ID: 28754981
Summary:
Neuronal and glial progenitor cells exist in the adult Drosophila brain. The primarily glial progenitor cells rely on a microRNA, mir-31a, to inhibit the expression of a predicted E3 ubiquitin ligase, CG16947. Erroneous inheritance of CG16947 by the progeny when the neural progenitor cell divides leads to death of the progeny, however how CG16947 achieves glial cell death is unknown. This study has identified the interacting partner of CG16947 to be cdk9. Reduction of cdk9 expression in glia causes glial loss; highlighting the importance of cdk9 in mediating the survival of glia. Further, glial loss observed in mir-31a mutants was prevented with adult-specific expression of cdk9 in glia. Biochemical evidence is provided that the binding of CG16947 to Cdk9 causes its degradation. Taken together, this data shows that cdk9 plays a role in the survival of adult glia in the Drosophila brain. Thus, a fine balance exists between mir-31a and CG16947 expression in the progenitor cells that in turn regulates the levels of cdk9 in the progeny. This serves to allow the progenitor cells to regulate the number of glia in the adult brain.
Melani, M., Valko, A., Romero, N. M., Aguilera, M. O., Acevedo, J. M., Bhujabal, Z., Perez-Perri, J., de la Riva-Carrasco, R. V., Katz, M. J., Sorianello, E., D'Alessio, C., Juhasz, G., Johansen, T., Colombo, M. I. and Wappner, P. (2017). Zonda is a novel early component of the autophagy pathway in Drosophila. Mol Biol Cell [Epub ahead of print]. PubMed ID: 28904211
Summary:
Autophagy is an evolutionary conserved process by which eukaryotic cells undergo self-digestion of cytoplasmic components. This study reports that a novel Drosophila immunophilin, named Zonda (CG5482), is critically required for starvation-induced autophagy. Zonda operates at early stages of the process, specifically for Vps34-mediated phosphatidylinositol 3-phosphate (PI3P) deposition. Zonda displays an even distribution under basal conditions, and soon after starvation nucleates in endoplasmic reticulum-associated foci that colocalize with omegasome markers. Zonda nucleation depends on Atg1, Atg13 and Atg17 but does not require Vps34, Vps15, Atg6 or Atg14. Zonda interacts physically with ATG1 through its kinase domain, as well as with ATG6 and Vps34. It is proposed that Zonda is an early component of the autophagy cascade necessary for Vps34-dependent PI3P deposition and omegasome formation.

Friday, November 24th

Kreko-Pierce, T. and Eaton, B. A. (2017). The Drosophila LC8 homologue Cut-up specifies the axonal transport of proteasomes. J Cell Sci. PubMed ID: 28808087
Summary:
Because of their functional polarity and elongated morphologies, microtubule-based transport of proteins and organelles is critical for normal neuronal function. The proteasome is required throughout the neuron for the highly regulated degradation of a broad set of protein targets whose functions underlie key physiological responses including synaptic plasticity and axonal degeneration. Molecularly, the relationship between proteasome transport and the transport of the targets of proteasomes is unclear. The dynein motor complex is required for the microtubule-based motility of numerous proteins and organelles in neurons. This study demonstrates that microtubule-based transport of proteasomes within the neuron utilizes a distinct dynein light chain compared to synaptic proteins. Live imaging of proteasomes and synaptic vesicle proteins in axons and synapses finds that these cargoes traffic independently and that proteasomes exhibit significantly reduced retrograde transport velocities compared to synaptic vesicle proteins. Genetic and biochemical analyses reveals that the Drosophila homologue of the LC8 dynein light chain Cut-up binds proteasomes and functions specifically during their transport. These data support the model that Cut-up functions to specify the dynein-mediated transport of neuronal proteasomes.
Dewey, E. B. and Johnston, C. A. (2017). Diverse mitotic functions of the cytoskeletal crosslinking protein Shortstop suggest a role in Dynein/Dynactin activity. Mol Biol Cell. PubMed ID: 28747439
Summary:
Proper assembly and orientation of the bipolar mitotic spindle is critical to the fidelity of cell division. Mitotic precision fundamentally contributes to cell fate specification, tissue development and homeostasis, and chromosome distribution within daughter cells. Defects in these events is thought to contribute to several human diseases. The underlying mechanisms that function in spindle morphogenesis and positioning remain incompletely defined, however. This study describes diverse roles for the actin-microtubule crosslinker, Shortstop (Shot), in mitotic spindle function in Drosophila Shot localizes to mitotic spindle poles and its knockdown results in an unfocused spindle pole morphology and a disruption of proper spindle orientation. Loss of Shot also leads to chromosome congression defects, cell cycle progression delay, and defective chromosome segregation during anaphase. These mitotic errors trigger apoptosis in Drosophila epithelial tissue, and blocking this apoptotic response results in a marked induction of the EMT marker MMP-1. The Actin-binding domain of Shot directly interacts with Actin-related protein-1 (Arp-1), a key component of the Dynein/Dynactin complex. Knockdown of Arp-1 phenocopies Shot loss universally, whereas chemical disruption of F-actin does so selectively. This work highlights novel roles for Shot in mitosis and suggests a mechanism involving Dynein/Dynactin activation.
Viswanathan, M. C., Schmidt, W., Rynkiewicz, M. J., Agarwal, K., Gao, J., Katz, J., Lehman, W. and Cammarato, A. (2017). Distortion of the Actin A-triad results in contractile disinhibition and cardiomyopathy. Cell Rep 20(11): 2612-2625. PubMed ID: 28903042
Summary:
Striated muscle contraction is regulated by the movement of tropomyosin over the thin filament surface, which blocks or exposes myosin binding sites on actin. Findings suggest that electrostatic contacts, particularly those between K326, K328, and R147 on actin and tropomyosin, establish an energetically favorable F-actin-tropomyosin configuration, with tropomyosin positioned in a location that impedes actomyosin associations and promotes relaxation. This study provides data that directly support a vital role for these actin residues, termed the A-triad, in tropomyosin positioning in intact functioning muscle. By examining the effects of an A295S alpha-cardiac actin hypertrophic cardiomyopathy-causing mutation, over a range of increasingly complex in silico, in vitro, and in vivo Drosophila muscle models, it is proposed that subtle A-triad-tropomyosin perturbation can destabilize thin filament regulation, which leads to hypercontractility and triggers disease. These efforts increase understanding of basic thin filament biology and help unravel the mechanistic basis of a complex cardiac disorder.
Wave Propagation of Junctional Remodeling in Collective Cell Movement of Epithelial Tissue: Numerical Simulation Study. Hiraiwa, T., Kuranaga, E. and Shibata, T. (2017). Front Cell Dev Biol 5: 66. PubMed ID: 28770197
Summary:
During animal development, epithelial cells forming a monolayer sheet move collectively to achieve the morphogenesis of epithelial tissues. One driving mechanism of such collective cell movement is junctional remodeling, which is found in the process of clockwise rotation of Drosophila male terminalia during metamorphosis. However, it still remains unknown how the motions of cells are spatiotemporally organized for collective movement by this mechanism. Since these moving cells undergo elastic deformations, the influence of junctional remodeling may mechanically propagate among them, leading to spatiotemporal pattern formations. This study, using a numerical cellular vertex model, found that the junctional remodeling in collective cell movement exhibits spatiotemporal self-organization without requiring spatial patterns of molecular signaling activity. The junctional remodeling propagates as a wave in a specific direction with a much faster speed than that of cell movement. Such propagation occurs in both the absence and presence of fluctuations in the contraction of cell boundaries.

Thursday, November 23

Gleason, R. J., Vora, M., Li, Y., Kane, N. S., Liao, K. and Padgett, R. W. (2017). C. elegans SMA-10 regulates BMP receptor trafficking. PLoS One 12(7): e0180681. PubMed ID: 28704415
Summary:
Signal transduction of the conserved transforming growth factor-beta (TGFbeta) family signaling pathway functions through two distinct serine/threonine transmembrane receptors, the type I and type II receptors. Endocytosis orchestrates the assembly of signaling complexes by coordinating the entry of receptors with their downstream signaling mediators. Recently, it was shown that the C. elegans type I bone morphogenetic protein (BMP) receptor SMA-6 (see Drosophila Thickveins), part of the TGFbeta family, is recycled through the retromer complex while the type II receptor, DAF-4 (see Drosophila Punt) is recycled in a retromer-independent, ARF-6 dependent manner. From genetic screens in C. elegans aimed at identifying new modifiers of BMP signaling, this study reports on SMA-10, a conserved LRIG (leucine-rich and immunoglobulin-like domains) transmembrane protein. It is a positive regulator of BMP signaling that binds to the SMA-6 receptor. This study shows that the loss of sma-10 leads to aberrant endocytic trafficking of SMA-6, resulting in its accumulation in distinct intracellular endosomes including the early endosome, multivesicular bodies (MVB), and the late endosome with a reduction in signaling strength. These studies show that trafficking defects caused by the loss of sma-10 are not universal, but affect only a limited set of receptors. Likewise, in Drosophila, it was found that the fly homolog of sma-10, lambik (lbk), reduces signaling strength of the BMP pathway, consistent with its function in C. elegans and suggesting evolutionary conservation of function. Loss of sma-10 results in reduced ubiquitination of the type I receptor SMA-6, suggesting a possible mechanism for its regulation of BMP signaling.
Tsurumi, A., Zhao, C. and Li, W. X. (2017). Canonical and non-canonical JAK/STAT transcriptional targets may be involved in distinct and overlapping cellular processes. BMC Genomics 18(1): 718. PubMed ID: 28893190
Summary:
In addition to a canonical pathway that uses the phosphorylated form of the STAT transcription factor, a non-canonical JAK/STAT pathway involving heterochromatin formation by unphosphorylated STAT was recently uncovered. This study has used the simple Drosophila system in which the non-canonical pathway was initially characterized, to compare putative canonical versus non-canonical transcriptional targets across the genome. Microarray expression patterns were analyzed of wildtype, Jak gain- and loss-of-function mutants, as well as the Stat loss-of-function mutant during embryogenesis, since the contribution of the canonical signal transduction pathway has been well-characterized in these contexts. Previous studies have also demonstrated that Jak gain-of-function and Stat mutants counter heterochromatin silencing to de-repress target genes by the non-canonical pathway. Compared to canonical target genomic loci, non-canonical targets were significantly more associated with sites enriched with heterochromatin-related factors (p = 0.004). Furthermore, putative canonical and non-canonical transcriptional targets identified displayed some differences in biological pathways they regulate, as determined by Gene Ontology (GO) enrichment analyses. Canonical targets were enriched mainly with genes relevant to development and immunity, as expected, whereas the non-canonical target gene set mainly showed enrichment of genes for various metabolic responses and stress response, highlighting the possibility that some differences may exist between the two loci. Canonical and non-canonical JAK/STAT genes may regulate distinct and overlapping sets of genes and may perform specific overall functions in physiology. Further studies at different developmental stages, or using distinct tissues may identify additional targets and provide insight into which gene targets are unique to the canonical or non-canonic pathway.
Damulewicz, M., Loboda, A., Jozkowicz, A., Dulak, J. and Pyza, E. (2017). Haeme oxygenase protects against UV light DNA damages in the retina in clock-dependent manner. Sci Rep 7(1): 5197. PubMed ID: 28701782
Summary:
This study has shown that in the retina of Drosophila, the expression of the ho gene, encoding haeme oxygenase (HO), is regulated by light but only at the beginning of the day. This timing must be set by the circadian clock as light pulses applied at other time points during the day do not increase the ho mRNA level. Moreover, light-induced activation of HO does not depend on the canonical phototransduction pathway but instead involves cryptochrome and is enhanced by ultraviolet (UV) light. Interestingly, the level of DNA damage in the retina after UV exposure was inversely related to the circadian oscillation of the ho mRNA level during the night, being the highest when the HO level was low and reversed during the day. Accordingly, induction of HO by hemin was associated with low DNA damage, while inhibition of HO activity by SnPPIX aggravated the damage. These data suggest that HO acts in the retina to decrease oxidative DNA damage in photoreceptors caused by UV-rich light in the morning.
Cardoso, M. A., Fontenele, M., Lim, B., Bisch, P. M., Shvartsman, S. Y. and Araujo, H. M. (2017). A novel function for the IkappaB inhibitor Cactus in promoting Dorsal nuclear localization and activity in the Drosophila embryo. Development 144(16): 2907-2913. PubMed ID: 28705899
Summary:
The evolutionarily conserved Toll signaling pathway controls innate immunity across phyla and embryonic patterning in insects. In the Drosophila embryo, Toll is required to establish gene expression domains along the dorsal-ventral axis. Pathway activation induces degradation of the IkappaB inhibitor Cactus, resulting in a ventral-to-dorsal nuclear gradient of the NFkappaB effector Dorsal. This study investigated how cactus modulates Toll signals through its effects on the Dorsal gradient and on Dorsal target genes. Quantitative analysis using a series of loss- and gain-of-function conditions shows that the ventral and lateral aspects of the Dorsal gradient can behave differently with respect to Cactus fluctuations. In lateral and dorsal embryo domains, loss of Cactus allows more Dorsal to translocate to the nucleus. Unexpectedly, cactus loss-of-function alleles decrease Dorsal nuclear localization ventrally, where Toll signals are high. Overexpression analysis suggests that this ability of Cactus to enhance Toll stems from the mobilization of a free Cactus pool induced by the Calpain A protease. These results indicate that Cactus acts to bolster Dorsal activation, in addition to its role as a NFkappaB inhibitor, ensuring a correct response to Toll signals.

Wednesday, November 22nd

Galasso, A., Cameron, C. S., Frenguelli, B. G. and Moffat, K. G. (2017). An AMPK-dependent regulatory pathway in tau-mediated toxicity. Biol Open [Epub ahead of print]. PubMed ID: 28808138
Summary:
Neurodegenerative tauopathies are characterized by accumulation of hyperphosphorylated tau aggregates primarily degraded by autophagy. The 5'AMP-activated protein kinase (AMPK) is expressed in most cells, including neurons. Alongside its metabolic functions, it is also known to be activated in Alzheimer's brains, phosphorylate tau and be a critical autophagy activator. Whether it plays a neurotoxic or neuroprotective role remains unclear. Complexly in tauopathies, while stress conditions can result in AMPK activation enhancing tau-mediated toxicity, AMPK activation is not always concomitant with autophagic induction. Using a Drosophila in vivo quantitative approach, this study has analysed the impact of AMPK and autophagy on tau-mediated toxicity, recapitulating the AMPK-mediated tauopathy condition: increased tau phosphorylation, without corresponding autophagy activation. It was demonstrated that AMPK, binding to and phosphorylating tau at Ser-262, a site reported to facilitate soluble tau accumulation, affects its degradation. This phosphorylation results in exacerbation of tau toxicity and is ameliorated via rapamycin-induced autophagy stimulation. These findings support the development of combinatorial therapies effective at reducing tau toxicity targeting tau phosphorylation and AMPK-independent autophagic induction. The proposed in vivo tool represents an ideal readout to perform preliminary screening for drugs promoting this process.
Chung, C. G., Kwon, M. J., Jeon, K. H., Hyeon, D. Y., Han, M. H., Park, J. H., Cha, I. J., Cho, J. H., Kim, K., Rho, S., Kim, G. R., Jeong, H., Lee, J. W., Kim, T., Kim, K., Kim, K. P., Ehlers, M. D., Hwang, D. and Lee, S. B. (2017). Golgi Outpost Synthesis Impaired by Toxic Polyglutamine Proteins Contributes to Dendritic Pathology in Neurons. Cell Rep 20(2): 356-369. PubMed ID: 28700938
Summary:
Dendrite aberration is a common feature of neurodegenerative diseases caused by protein toxicity, but the underlying mechanisms remain largely elusive. This study shows that nuclear polyglutamine (polyQ) toxicity resulted in defective terminal dendrite elongation accompanied by a loss of Golgi outposts (GOPs) and a decreased supply of plasma membrane (PM) in Drosophila class IV dendritic arborization (da) (C4 da) neurons. mRNA sequencing revealed that genes downregulated by polyQ proteins included many secretory pathway-related genes, including COPII genes regulating GOP synthesis. Transcription factor enrichment analysis identified CREB3L1/CrebA, which regulates COPII gene expression. CrebA overexpression in C4 da neurons restores the dysregulation of COPII genes, GOP synthesis, and PM supply. Chromatin immunoprecipitation (ChIP)-PCR revealed that CrebA expression is regulated by CREB-binding protein (CBP), which is sequestered by polyQ proteins. Furthermore, co-overexpression of CrebA and Rac1 synergistically restores the polyQ-induced dendrite pathology. Collectively, these results suggest that GOPs impaired by polyQ proteins contribute to dendrite pathology through the CBP-CrebA-COPII pathway.
Brandt, T., Mourier, A., Tain, L. S., Partridge, L., Larsson, N. G. and Kuhlbrandt, W. (2017). Changes of mitochondrial ultrastructure and function during ageing in mice and Drosophila. Elife 6. PubMed ID: 28699890
Summary:
Ageing is a progressive decline of intrinsic physiological functions. This study examined the impact of ageing on the ultrastructure and function of mitochondria in mouse and fruit flies (Drosophila melanogaster) by electron cryo-tomography and respirometry and discovered distinct age-related changes in both model organisms. Mitochondrial function and ultrastructure are maintained in mouse heart, whereas subpopulations of mitochondria from mouse liver show age-related changes in membrane morphology. Subpopulations of mitochondria from young and old mouse kidney resemble those described for apoptosis. In aged flies, respiratory activity is compromised and the production of peroxide radicals is increased. In about 50% of mitochondria from old flies, the inner membrane organization breaks down. This establishes a clear link between inner membrane architecture and functional decline. Mitochondria were affected by ageing to very different extents, depending on the organism and possibly on the degree to which tissues within the same organism are protected against mitochondrial damage.
Chen, J., Xue, J., Ruan, J., Zhao, J., Tang, B. and Duan, R. (2017). Drosophila CHIP protects against mitochondrial dysfunction by acting downstream of Pink1 in parallel with Parkin. Faseb j. PubMed ID: 28778978
Summary:
Mitochondrial kinase PTEN-induced putative kinase 1 (PINK1) and E3 ubiquitin ligase Parkin function in a common pathway to regulate mitochondrial homeostasis contributing to the pathogenesis of Parkinson disease. The carboxyl terminus of Hsc70-interacting protein (CHIP) acts as a heat shock protein 70/heat shock protein 90 cochaperone to mediate protein folding or as an E3 ubiquitin ligase to target proteins for degradation. In this study, overexpression of Drosophila CHIP suppressed a range of Pink1 mutant phenotypes in flies, including abnormal wing posture, thoracic indentation, locomotion defects, muscle degeneration, and loss of dopaminergic neurons. Mitochondrial defects of Pink1 mutant, such as excessive fusion, reduced ATP content, and crista disorganization, were rescued by CHIP but not its ligase-dead mutants. Similar phenotypes and mitochondrial impairment were ameliorated in Parkin mutant flies by wild-type CHIP. Inactivation of CHIP with null fly mutants resulted in mitochondrial defects, such as reduced thoracic ATP content at 3 d old, decreased thoracic mitochondrial DNA content, and defective mitochondrial morphology at 60 d old. CHIP mutants did not exacerbate the phenotypes of Pink1 mutant flies but markedly shortened the life span of Parkin mutant flies. These results indicate that CHIP is involved in mitochondrial integrity and may act downstream of Pink1 in parallel with Parkin.

Tuesday, November 21st

Stern, D. L., Clemens, J., Coen, P., Calhoun, A. J., Hogenesch, J. B., Arthur, B. J. and Murthy, M. (2017). Experimental and statistical reevaluation provides no evidence for Drosophila courtship song rhythms. Proc Natl Acad Sci U S A 114(37): 9978-9983. PubMed ID: 28851830
Summary:
From 1980 to 1992, a series of influential papers reported on the discovery, genetics, and evolution of a periodic cycling of the interval between Drosophila male courtship song pulses. The molecular mechanisms underlying this periodicity were never described. To reinitiate investigation of this phenomenon, automated segmentation of songs has been performed, but that study failed to detect the proposed rhythm. Various studies have reported that the previous study failed to detect song rhythms because (i) the flies did not sing enough and (ii) the segmenter did not identify many of the song pulses. Another study manually annotated a subset of the previous recordings and reported that two strains displayed rhythms with genotype-specific periodicity, in agreement with the original reports. Attempts to replicate this finding have failed and show that the manually annotated data, the original automatically segmented data, and a new dataset provide no evidence for either the existence of song rhythms or song periodicity differences between genotypes. Furthermore, the methods and analysis were reexamined and it was found that the automated segmentation method was not biased to prevent detection of putative song periodicity. It is concluded that there is no evidence for the existence of Drosophila courtship song rhythms.
Xue, A., Wang, H. and Zhu, J. (2017). Dissecting genetic architecture of startle response in Drosophila melanogaster using multi-omics information. Sci Rep 7(1): 12367. PubMed ID: 28959013
Summary:
Startle behavior is important for survival, and abnormal startle responses are related to several neurological diseases. Drosophila melanogaster provides a powerful system to investigate the genetic underpinnings of variation in startle behavior. Since mechanically induced, startle responses and environmental conditions can be readily quantified and precisely controlled. The 156 wild-derived fully sequenced lines of the Drosophila Genetic Reference Panel (DGRP) were used to identify SNPs and transcripts associated with variation in startle behavior. The results validated highly significant effects of 33 quantitative trait SNPs (QTSs) and 81 quantitative trait transcripts (QTTs) directly associated with phenotypic variation of startle response. QTT variation was found to be controlled by 20 QTSs (tQTSs) and 73 transcripts (tQTTs). Association mapping based on genomic and transcriptomic data enabled construction of a complex genetic network that underlies variation in startle behavior. Based on principles of evolutionary conservation, human orthologous genes could be superimposed on this network. This study provided both genetic and biological insights into the variation of startle response behavior of Drosophila melanogaster, and highlighted the importance of genetic network to understand the genetic architecture of complex traits.
Fernandez, R. W., Akinleye, A. A., Nurilov, M., Feliciano, O., Lollar, M., Aijuri, R. R., O'Donnell, J. M. and Simon, A. F. (2017). Modulation of social space by dopamine in Drosophila melanogaster, but no effect on the avoidance of the Drosophila stress odorant. Biol Lett 13(8). PubMed ID: 28794277
Summary:
Appropriate response to others is necessary for social interactions. Yet little is known about how neurotransmitters regulate attractive and repulsive social cues. Using genetic and pharmacological manipulations in Drosophila melanogaster, this study shows that dopamine is contributing the response to others in a social group, specifically, social spacing, but not the avoidance of odours released by stressed flies (dSO). Interestingly, this dopamine-mediated behaviour is prominent only in the day-time, and its effect varies depending on tissue, sex and type of manipulation. Furthermore, alteration of dopamine levels has no effect on dSO avoidance regardless of sex, which suggests that a different neurotransmitter regulates this response.
Kim, D., Alvarez, M., Lechuga, L. M. and Louis, M. (2017). Species-specific modulation of food-search behavior by respiration and chemosensation in Drosophila larvae. Elife 6. PubMed ID: 28871963
Summary:
Animals explore their environment to encounter suitable food resources. Despite its vital importance, this behavior puts individuals at risk by consuming limited internal energy during locomotion. A novel assay has been developed to investigate how food-search behavior is organized in Drosophila melanogaster larvae dwelling in hydrogels mimicking their natural habitat. Three main behavioral modes are defined: resting at the gel's surface, digging while feeding near the surface, and apneic dives. In unstimulated conditions, larvae spend most of their time digging. By contrast, deep and long exploratory dives are promoted by olfactory stimulations. Hypoxia and chemical repellents impair diving. Remarkable differences are reported in the dig-and-dive behavior of D. melanogaster and the fruit-pest D. suzukii. The present paradigm offers an opportunity to study how sensory and physiological cues are integrated to balance the limitations of dwelling in imperfect environmental conditions and the risks associated with searching for potentially more favorable conditions.

Monday, November 20th

LeBlanc, M. G. and Lehmann, R. (2017). Domain-specific control of germ cell polarity and migration by multifunction Tre1 GPCR. J Cell Biol 216(9): 2945-2958. PubMed ID: 28687666
Summary:
The migration of primordial germ cells (PGCs) from their place of origin to the embryonic gonad is an essential reproductive feature in many animal species. In Drosophila melanogaster, a single G protein-coupled receptor, Trapped in endoderm 1 (Tre1), mediates germ cell polarization at the onset of active migration and directs subsequent migration of PGCs through the midgut primordium. How these different aspects of cell behavior are coordinated through a single receptor is not known. This study demonstrates that two highly conserved domains, the E/N/DRY and NPxxY motifs, have overlapping and unique functions in Tre1. The Tre1-NRY domain via G protein signaling is required for reading and responding to guidance and survival cues controlled by the lipid phosphate phosphatases Wunen and Wunen2. In contrast, the Tre1-NPIIY domain has a separate role in Rho1- and E-cadherin-mediated polarization at the initiation stage independent of G protein signaling. It is proposed that this bifurcation of the Tre1 G protein-coupled receptor signaling response via G protein-dependent and independent branches enables distinct spatiotemporal regulation of germ cell migration.
Cooper, J. C. and Phadnis, N. (2017). Parallel evolution of sperm hyper-activation Ca2+ channels. Genome Biol Evol 9(7): 1938-1949. PubMed ID: 28810709
Summary:
Sperm hyper-activation is a dramatic change in sperm behavior where mature sperm burst into a final sprint in the race to the egg. The mechanism of sperm hyper-activation in many metazoans, including humans, consists of a jolt of Ca2+ into the sperm flagellum via CatSper ion channels. Surprisingly, all nine CatSper genes have been independently lost in several animal lineages. In Drosophila, sperm hyper-activation is performed through the cooption of the polycystic kidney disease 2 (pkd2) Ca2+ channel. The parallels between CatSpers in primates and pkd2 in Drosophila provide a unique opportunity to examine the molecular evolution of the sperm hyper-activation machinery in two independent, nonhomologous calcium channels separated by > 500 million years of divergence. This study used a comprehensive phylogenomic approach to investigate the selective pressures on these sperm hyper-activation channels. First, it was found that the entire CatSper complex evolves rapidly under recurrent positive selection in primates. Second, it was found that pkd2 has parallel patterns of adaptive evolution in Drosophila. Third, this adaptive evolution of pkd2 is driven by its role in sperm hyper-activation. These patterns of selection suggest that the evolution of the sperm hyper-activation machinery is driven by sexual conflict with antagonistic ligands that modulate channel activity.
Chen, D., Zhu, X., Zhou, L., Wang, J., Tao, X., Wang, S., Sun, F., Kan, X., Han, Z. and Gu, Y. (2017). Gilgamesh is required for the maintenance of germline stem cells in Drosophila testis. Sci Rep 7(1): 5737. PubMed ID: 28720768
Summary:
Emerging evidence supports that stem cells are regulated by both intrinsic and extrinsic mechanisms. However, factors that determine the fate of stem cells remain incompletely understood. The Drosophila testis provides an exclusive powerful model in searching for potential important regulatory factors and their underlying mechanisms for controlling the fate of germline stem cells (GSCs). This study found that Drosophila gilgamesh (gish), which encodes a homologue of human CK1-gamma (casein kinase 1-gamma), is required intrinsically for GSC maintenance. These genetic analyses indicate gish is not required for Dpp/Gbb signaling silencing of bam and is dispensable for Dpp/Gbb signaling-dependent Dad expression. Finally, this study shows that overexpressers of gish fail to dramatically increase the number of GSCs. These findings demonstrate that gish controls the fate of GSCs in Drosophila testis by a novel Dpp/Gbb signaling-independent pathway.
Luo, L., Siah, C. K. and Cai, Y. (2017). Engrailed acts with Nejire to control decapentaplegic expression in the Drosophila ovarian stem cell niche. Development 144(18): 3224-3231. PubMed ID: 28928281
Summary:
Homeostasis of adult tissues is maintained by a small number of stem cells, which are sustained by their niches. In the Drosophila female germline stem cell (GSC) niche, Decapentaplegic (Dpp) is the primary factor that promotes GSC self-renewal. However, the mechanism regulating dpp expression in the niche is largely unknown. This study identified a 2.0 kb fragment located in a 5' cis-regulatory region of the dpp locus containing enhancer activity that drives its expression in the niche. This region is distinct from a previously characterized 3' cis-regulatory enhancer responsible for dpp expression in imaginal discs. These data demonstrate that Engrailed, a homeodomain-containing transcription factor that serves as a cap cell marker, binds to this region and regulates dpp expression in cap cells. Further data suggest that En forms a complex with Nejire (Nej), the Drosophila ortholog of histone acetyltransferase CBP/p300, and directs Nej to this cis-regulatory region where Nej functions as the co-activator for dpp expression. Therefore, this study defines the molecular pathway controlling dpp expression in the Drosophila ovarian stem cell niche.

Friday, November 17th

Rowley, M. J., Nichols, M. H., Lyu, X., Ando-Kuri, M., Rivera, I. S. M., Hermetz, K., Wang, P., Ruan, Y. and Corces, V. G. (2017). Evolutionarily conserved principles predict 3D chromatin organization. Mol Cell 67(5): 837-852.e837. PubMed ID: 28826674
Summary:
Topologically associating domains (TADs), CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP, this study shows that Drosophila chromatin is organized into domains that are termed compartmental domains that correspond precisely with A/B compartments at high resolution. Transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C. elegans and A. thaliana. Architectural proteins insulate compartmental domains by reducing interaction frequencies between neighboring regions in Drosophila, but CTCF loops do not play a distinct role in this organism. In mammals, compartmental domains exist alongside CTCF loop domains to form topological domains. The results suggest that compartmental domains are responsible for domain structure in all eukaryotes, with CTCF playing an important role in domain formation in mammals.
Chavez, J., Murillo-Maldonado, J. M., Bahena, V., Cruz, A. K., Castaneda-Sortibran, A., Rodriguez-Arnaiz, R., Zurita, M. and Valadez-Graham, V. (2017). dAdd1 and dXNP prevent genome instability by maintaining HP1a localization at Drosophila telomeres. Chromosoma [Epub ahead of print]. PubMed ID: 28688038
Summary:
An important component of the telomeres is the heterochromatin protein 1a (HP1a). Mutations in Su(var)205, the gene encoding HP1a in Drosophila, result in telomeric fusions, retrotransposon regulation loss and larger telomeres, leading to chromosome instability. Previously, it was found that several proteins physically interact with HP1a, including dXNP and dAdd1 (orthologues to the mammalian ATRX gene). This study found that mutations in the genes encoding the dXNP and dAdd1 proteins affect chromosome stability, causing chromosomal aberrations, including telomeric defects, similar to those observed in Su(var)205 mutants. In somatic cells, dXNP and dAdd1 participate were shown to participate in the silencing of the telomeric HTT array of retrotransposons, preventing anomalous retrotransposon transcription and integration. Furthermore, the lack of dAdd1 results in the loss of HP1a from the telomeric regions without affecting other chromosomal HP1a binding sites; mutations in dxnp also affected HP1a localization but not at all telomeres, suggesting a specialized role for dAdd1 and dXNP proteins in locating HP1a at the tips of the chromosomes. These results place dAdd1 as an essential regulator of HP1a localization and function in the telomere heterochromatic domain.
Eagen, K. P., Aiden, E. L. and Kornberg, R. D. (2017). Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map. Proc Natl Acad Sci U S A 114(33): 8764-8769. PubMed ID: 28765367
Summary:
The locations of chromatin loops in Drosophila were determined by Hi-C (chemical cross-linking, restriction digestion, ligation, and high-throughput DNA sequencing). Whereas most loop boundaries or "anchors" are associated with CTCF protein in mammals, loop anchors in Drosophila were found most often in association with the polycomb group (PcG) proteinPolycomb (Pc), a subunit of polycomb repressive complex 1 (PRC1). Loops were frequently located within domains of PcG-repressed chromatin. Promoters located at PRC1 loop anchors regulate some of the most important developmental genes and are less likely to be expressed than those not at PRC1 loop anchors. Although DNA looping has most commonly been associated with enhancer-promoter communication, the results indicate that loops are also associated with gene repression.
Colmenares, S. U., Swenson, J. M., Langley, S. A., Kennedy, C., Costes, S. V. and Karpen, G. H. (2017). Drosophila histone demethylase KDM4A has enzymatic and non-enzymatic roles in controlling heterochromatin integrity. Dev Cell 42(2): 156-169.e155. PubMed ID: 28743002
Summary:
Eukaryotic genomes are broadly divided between gene-rich euchromatin and the highly repetitive heterochromatin domain, which is enriched for proteins critical for genome stability and transcriptional silencing. This study shows that Drosophila KDM4A (dKDM4A), previously characterized as a euchromatic histone H3 K36 demethylase and transcriptional regulator, predominantly localizes to heterochromatin and regulates heterochromatin position-effect variegation (PEV), organization of repetitive DNAs, and DNA repair. dKDM4A demethylase activity is dispensable for PEV. In contrast, dKDM4A enzymatic activity is required to relocate heterochromatic double-strand breaks outside the domain, as well as for organismal survival when DNA repair is compromised. Finally, DNA damage triggers dKDM4A-dependent changes in the levels of H3K56me3, suggesting that dKDM4A demethylates this heterochromatic mark to facilitate repair. It is concluded that dKDM4A, in addition to its previously characterized role in euchromatin, utilizes both enzymatic and structural mechanisms to regulate heterochromatin organization and functions.

Thursday, November 16th

Parhad, S. S., Tu, S., Weng, Z. and Theurkauf, W. E. (2017). Adaptive evolution leads to cross-species incompatibility in the piRNA transposon silencing machinery. Dev Cell [Epub ahead of print]. PubMed ID: 28919205
Summary:
Reproductive isolation defines species divergence and is linked to adaptive evolution of hybrid incompatibility genes. Hybrids between Drosophila melanogaster and Drosophila simulans are sterile, and phenocopy mutations in the PIWI interacting RNA (piRNA) pathway, which silences transposons and shows pervasive adaptive evolution, and Drosophila rhino and deadlock encode rapidly evolving components of a complex that binds to piRNA clusters. This study shows that Rhino and Deadlock interact and co-localize in simulans and melanogaster, but simulans Rhino does not bind melanogaster Deadlock, due to substitutions in the rapidly evolving Shadow domain. Significantly, a chimera expressing the simulans Shadow domain in a melanogaster Rhino backbone fails to support piRNA production, disrupts binding to piRNA clusters, and leads to ectopic localization to bulk heterochromatin. Fusing melanogaster Deadlock to simulans Rhino, by contrast, restores localization to clusters. Deadlock binding thus directs Rhino to piRNA clusters, and Rhino-Deadlock co-evolution has produced cross-species incompatibilities, which may contribute to reproductive isolation.
Beckwith, E. J., Hernando, C. E., Polcownuk, S., Bertolin, A. P., Mancini, E., Ceriani, M. F. and Yanovsky, M. J. (2017). Rhythmic behavior is controlled by the SRm160 splicing factor in Drosophila melanogaster. Genetics [Epub ahead of print]. PubMed ID: 28801530
Summary:
While many transcription factors underlying circadian oscillations are known, the splicing factors that modulate these rhythms remain largely unexplored. A genome-wide assessment of the alterations of gene expression in a null mutant of the alternative splicing regulator SR-related matrix protein of 160 kD (SRm160) revealed the extent to which alternative splicing impacts on behavior-related genes. SRm160 affects gene expression in pacemaker neurons of the Drosophila brain to ensure proper oscillations of the molecular clock. A reduced level of SRm160 in adult pacemaker neurons impairs circadian rhythms in locomotor behavior, and this phenotype is caused, at least in part, by a marked reduction in period (per) levels. Moreover, rhythmic accumulation of the neuropeptide Pigment-dispersing factor (PDF) in the dorsal projections of these neurons is abolished after SRm160 depletion. The lack of rhythmicity in SRm160 downregulated flies is reversed by a fully spliced per construct, but not by an extra copy of the endogenous locus, showing that SRm160 positively regulates per levels in a splicing-dependent manner. These findings highlight the significant effect of alternative splicing on the nervous system and particularly on brain function in an in vivo model.
Trettin, K. D., Sinha, N. K., Eckert, D. M., Apple, S. E. and Bass, B. L. (2017). Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA. Proc Natl Acad Sci U S A 114(38): E7939-e7948. PubMed ID: 28874570
Summary:
Loquacious-PD (Loqs-PD) is required for biogenesis of many endogenous siRNAs in Drosophila. In vitro, Loqs-PD enhances the rate of dsRNA cleavage by Dicer-2 and also enables processing of substrates normally refractory to cleavage. Using purified components, and Loqs-PD truncations, this study provides a mechanistic basis for Loqs-PD functions. These studies indicate that the 22 amino acids at the C terminus of Loqs-PD, including an FDF-like motif, directly interact with the Hel2 subdomain of Dicer-2's helicase domain. This interaction is RNA-independent, but modulation of Dicer-2 cleavage also was found to requires dsRNA binding by Loqs-PD. Furthermore, while the first dsRNA-binding motif of Loqs-PD is dispensable for enhancing cleavage of optimal substrates, it is essential for enhancing cleavage of suboptimal substrates. Finally, these studies define a previously unrecognized Dicer interaction interface and suggest that Loqs-PD is well positioned to recruit substrates into the helicase domain of Dicer-2.
Wang, M., Ly, M., Lugowski, A., Laver, J. D., Lipshitz, H. D., Smibert, C. A. and Rissland, O. S. (2017). ME31B globally represses maternal mRNAs by two distinct mechanisms during the Drosophila maternal-to-zygotic transition. Elife 6. PubMed ID: 28875934
Summary:
In animal embryos, control of development is passed from exclusively maternal gene products to those encoded by the embryonic genome in a process referred to as the maternal-to-zygotic transition (MZT). An RNA-binding protein, ME31B, binds to and represses the expression of thousands of maternal mRNAs during the Drosophila MZT. However, ME31B carries out repression in different ways during different phases of the MZT. Early, it represses translation while, later, its binding leads to mRNA destruction, most likely as a consequence of translational repression in the context of robust mRNA decay. In a process dependent on the PNG kinase, levels of ME31B and its partners, Cup and Trailer Hitch (TRAL), decrease by over 10-fold during the MZT, leading to a change in the composition of mRNA-protein complexes. It is proposed that ME31B is a global repressor whose regulatory impact changes based on its biological context.

Wednesday, November 15th

Agrawal, P., Houl, J. H., Gunawardhana, K. L., Liu, T., Zhou, J., Zoran, M. J. and Hardin, P. E. (2017). Drosophila CRY entrains clocks in body tissues to light and maintains passive membrane properties in a non-clock body tissue independent of light. Curr Biol [Epub ahead of print]. PubMed ID: 28781048
Summary:
Circadian clocks regulate daily rhythms in physiology, metabolism, and behavior via cell-autonomous transcriptional feedback loops. In Drosophila, the blue-light photoreceptor Cryptochrome (Cry) synchronizes these feedback loops to light:dark cycles by binding to and degrading Timeless (Tim) protein. CRY also acts independently of TIM in Drosophila to alter potassium channel conductance in arousal neurons after light exposure, and in many animals CRY acts independently of light to repress rhythmic transcription. CRY expression has been characterized in the Drosophila brain and eyes, but not in peripheral clock and non-clock tissues in the body. To investigate CRY expression and function in body tissues, a GFP-tagged-cry transgene was generated that rescues light-induced behavioral phase resetting in cry03 mutant flies and sensitively reports GFP-CRY expression. In bodies, CRY is detected in clock-containing tissues including Malpighian tubules, where it mediates both light-dependent TIM degradation and clock function. In larval salivary glands, which lack clock function but are amenable to electrophysiological recording, CRY prevents membrane input resistance from falling to low levels in a light-independent manner. The ability of CRY to maintain high input resistance in these non-excitable cells also requires the K+ channel subunits Hyperkinetic, Shaker, and Ether-a-go-go. These findings for the first time define CRY expression in Drosophila peripheral tissues and reveal that CRY acts together with K+ channels to maintain passive membrane properties in a non-clock-containing peripheral tissue independent of light.
Warrington, S. J., Strutt, H., Fisher, K. H. and Strutt, D. (2017). A dual function for Prickle in regulating frizzled stability during feedback-dependent amplification of planar polarity. Curr Biol 27(18): 2784-2797.e2783. PubMed ID: 28918952
Summary:
The core planar polarity pathway coordinates epithelial cell polarity during animal development, and loss of its activity gives rise to a range of defects, from aberrant morphogenetic cell movements to failure to correctly orient structures, such as hairs and cilia. The core pathway functions via a mechanism involving segregation of its protein components to opposite cells ends, where they form asymmetric intracellular complexes that couple cell-cell polarity. This segregation is a self-organizing process driven by feedback interactions between the core proteins themselves. Despite intense efforts, the molecular pathways underlying feedback have proven difficult to elucidate using conventional genetic approaches. This study investigated core protein function during planar polarization of the Drosophila wing by combining quantitative measurements of protein dynamics with loss-of-function genetics, mosaic analysis, and temporal control of gene expression. Focusing on the key core protein Frizzled, its stable junctional localization is promoted by the core proteins Strabismus, Dishevelled, Prickle, and Diego. In particular, this study shows that the stabilizing function of Prickle on Frizzled requires Prickle activity in neighboring cells. Conversely, Prickle in the same cell has a destabilizing effect on Frizzled. This destabilizing activity is dependent on the presence of Dishevelled and blocked in the absence of Dynamin and Rab5 activity, suggesting an endocytic mechanism. Overall, this approach reveals for the first time essential in vivo stabilizing and destabilizing interactions of the core proteins required for self-organization of planar polarity.
Zhang, T., Hsu, F. N., Xie, X. J., Li, X., Liu, M., Gao, X., Pei, X., Liao, Y., Du, W. and Ji, J. Y. (2017). Reversal of hyperactive Wnt signaling-dependent adipocyte defects by peptide boronic acids. Proc Natl Acad Sci U S A 114(36): E7469-e7478. PubMed ID: 28827348
Summary:
Deregulated Wnt signaling and altered lipid metabolism have been linked to obesity, diabetes, and various cancers, highlighting the importance of identifying inhibitors that can modulate Wnt signaling and aberrant lipid metabolism. This study has established a Drosophila model with hyperactivated Wnt signaling caused by partial loss of axin, a key component of the Wnt cascade. The Axin mutant larvae are transparent and have severe adipocyte defects caused by up-regulation of beta-catenin transcriptional activities. This study demonstrates pharmacologic mitigation of these phenotypes in Axin mutants by identifying bortezomib and additional peptide boronic acids. The suppressive effect of peptide boronic acids on hyperactive Wnt signaling is dependent on alpha-catenin; the rescue effect is completely abolished with the depletion of alpha-catenin in adipocytes. These results indicate that rather than targeting the canonical Wnt signaling pathway directly, pharmacologic modulation of beta-catenin activity through alpha-catenin is a potentially attractive approach to attenuating Wnt signaling in vivo.
Tain, L. S., Sehlke, R., Jain, C., Chokkalingam, M., Nagaraj, N., Essers, P., Rassner, M., Gronke, S., Froelich, J., Dieterich, C., Mann, M., Alic, N., Beyer, A. and Partridge, L. (2017). A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance. Mol Syst Biol 13(9): 939. PubMed ID: 28916541
Summary:
Lowered activity of the insulin/IGF signalling (IIS) network can ameliorate the effects of ageing in laboratory animals and, possibly, humans. Although transcriptome remodelling in long-lived IIS mutants has been extensively documented, the causal mechanisms contributing to extended lifespan, particularly in specific tissues, remain unclear. This study has characterized the proteomes of four key insulin-sensitive tissues in a long-lived Drosophila IIS mutant and control, and detected 44% of the predicted proteome (6,085 proteins). Expression of ribosome-associated proteins in the fat body was reduced in the mutant, with a corresponding, tissue-specific reduction in translation. Expression of mitochondrial electron transport chain proteins in fat body was increased, leading to increased respiration, which was necessary for IIS-mediated lifespan extension, and alone sufficient to mediate it. Proteasomal subunits showed altered expression in IIS mutant gut, and gut-specific over-expression of the RPN6 proteasomal subunit, was sufficient to increase proteasomal activity and extend lifespan, whilst inhibition of proteasome activity abolished IIS-mediated longevity. This study thus uncovered strikingly tissue-specific responses of cellular processes to lowered IIS acting in concert to ameliorate ageing.

Tuesday, November 14th

Zouaz, A., Auradkar, A., Delfini, M. C., Macchi, M., Barthez, M., Ela Akoa, S., Bastianelli, L., Xie, G., Deng, W. M., Levine, S. S., Graba, Y. and Saurin, A. J. (2017). The Hox proteins Ubx and AbdA collaborate with the transcription pausing factor M1BP to regulate gene transcription. EMBO J. PubMed ID: 28871058
Summary:
In metazoans, the pausing of RNA polymerase II at the promoter (paused Pol II) has emerged as a widespread and conserved mechanism in the regulation of gene transcription. While critical in recruiting Pol II to the promoter, the role transcription factors play in transitioning paused Pol II into productive Pol II is, however, little known. By studying how Drosophila Hox transcription factors control transcription, this study uncovered a molecular mechanism that increases productive transcription. The Hox proteins AbdA and Ubx target gene promoters previously bound by the transcription pausing factor M1BP, containing paused Pol II and enriched with promoter-proximal Polycomb Group (PcG) proteins, yet lacking the classical H3K27me3 PcG signature. AbdA binding to M1BP-regulated genes results in reduction in PcG binding, the release of paused Pol II, increases in promoter H3K4me3 histone marks and increased gene transcription. Linking transcription factors, PcG proteins and paused Pol II states, these data identify a two-step mechanism of Hox-driven transcription, with M1BP binding leading to Pol II recruitment followed by AbdA targeting, which results in a change in the chromatin landscape and enhanced transcription.
Gursky, V. V., Kozlov, K. N., Kulakovskiy, I. V., Zubair, A., Marjoram, P., Lawrie, D. S., Nuzhdin, S. V. and Samsonova, M. G. (2017). Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network. PLoS One 12(9): e0184657. PubMed ID: 28898266
Summary:
This study applied a sequence-level model of gap gene expression in the early development of Drosophila to analyze single nucleotide polymorphisms (SNPs) in a panel of natural sequenced D. melanogaster lines. Using a thermodynamic modeling framework, both analytical and computational descriptions are provided of how single-nucleotide variants affect gene expression. The analysis reveals that the sequence variants increase (decrease) gene expression if located within binding sites of repressors (activators). The sign of SNP influence (activation or repression) may change in time and space. The thermodynamic modeling approach predicts non-local and non-linear effects arising from SNPs, and combinations of SNPs, in individual fly genotypes. Simulation of individual fly genotypes using this model reveals that this non-linearity reduces to almost additive inputs from multiple SNPs. Further, signatures are seen of the action of purifying selection in the gap gene regulatory regions. To infer the specific targets of purifying selection, the patterns of polymorphism in the data were analyzed at two phenotypic levels: the strengths of binding and expression. Combinations of SNPs show evidence of being under selective pressure, while individual SNPs do not. The model predicts that SNPs appear to accumulate in the genotypes of the natural population in a way biased towards small increases in activating action on the expression pattern.
Yao, L., Wang, S., Orzechowski-Westholm, J., Dai, Q., Matsuda, R., Hosono, C., Bray, S., Lai, E. C. and Samakovlis, C. (2017). Genome-wide identification of Grainy head targets in Drosophila reveals regulatory interactions with the POU-domain transcription factor, Vvl. Development [Epub ahead of print]. PubMed ID: 28760809
Summary:
Grainy head (Grh) is a conserved transcription factor (TF) controlling epithelial differentiation and regeneration. To elucidate Grh functions, embryonic Grh targets were identified by ChIP-seq and gene expression analysis. Grh was shown to control hundreds of target genes. Repression or activation correlates with the distance of Grh binding sites to the transcription start sites of its targets. Analysis of 54 Grh-responsive enhancers during development and upon wounding suggests cooperation with distinct TFs in different contexts. In the airways, Grh repressed genes encode key TFs involved in branching and cell differentiation. Reduction of the POU-domain TF, Vvl, (ventral veins lacking) largely ameliorates the airway morphogenesis defects of grh mutants. Vvl and Grh proteins additionally interact with each other and regulate a set of common enhancers during epithelial morphogenesis. It is concluded that Grh and Vvl participate in a regulatory network controlling epithelial maturation.
Krebs, A. R., Imanci, D., Hoerner, L., Gaidatzis, D., Burger, L. and Schubeler, D. (2017). Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused promoters. Mol Cell 67(3): 411-422.e414. PubMed ID: 28735898
Summary:
Transcription initiation entails chromatin opening followed by pre-initiation complex formation and RNA polymerase II recruitment. Subsequent polymerase elongation requires additional signals, resulting in increased residence time downstream of the start site, a phenomenon referred to as pausing. This study has harnessed single-molecule footprinting to quantify distinct steps of initiation in vivo throughout the Drosophila genome. This identifies the impact of promoter structure on initiation dynamics in relation to nucleosomal occupancy. Additionally, perturbation of transcriptional initiation reveals an unexpectedly high turnover of polymerases at paused promoters-an observation confirmed at the level of nascent RNAs. These observations argue that absence of elongation is largely caused by premature termination rather than by stable polymerase stalling. In support of this non-processive model, it was observed that induction of the paused heat shock promoter depends on continuous initiation. This study provides a framework to quantify protein binding at single-molecule resolution and refines concepts of transcriptional pausing.

Monday, November 13th

Zhang, H. and Blumenthal, E. M. (2017). Identification of multiple functional receptors for tyramine on an insect secretory epithelium. Sci Rep 7(1): 168. PubMed ID: 28279025
Summary:
The biogenic amine tyramine (TA) regulates many aspects of invertebrate physiology and development. Although three TA receptor subtypes have been identified (TAR1-3), specific receptors have not been linked to physiological responses in native tissue. In the Malpighian (renal) tubule of Drosophila melanogaster, TA activates a transepithelial chloride conductance, resulting in diuresis and depolarization of the transepithelial potential. In the current work, mutation or RNAi-mediated knockdown in the stellate cells of the tubule of TAR2 (tyrR, CG7431) resulted in a dramatic reduction, but not elimination, of the TA-mediated depolarization. Mutation or knockdown of TAR3 (tyrRII, CG16766) had no effect. However, deletion of both genes, or knockdown of TAR3 on a TAR2 mutant background, eliminated the TA responses. Thus while TAR2 is responsible for the majority of the TA sensitivity of the tubule, TAR3 also contributes to the response. Knockdown or mutation of TAR2 also eliminated the response of tubules to the related amine octopamine (OA), indicating that OA can activate TAR2. This finding contrasts to reports that heterologously expressed TAR2 is highly selective for TA over OA. This is the first report of TA receptor function in a native tissue and indicates unexpected complexity in the physiology of the Malpighian tubule.
Warren, J. L., Jr., Hoxha, E., Jumbo-Lucioni, P. and De Luca, M. (2017). Reduction of Syndecan transcript levels in the insulin-producing cells affects glucose homeostasis in adult Drosophila melanogaster. DNA Cell Biol [Epub ahead of print]. PubMed ID: 28945109
Summary:
Signaling by direct cell-matrix interactions has been shown to impact the transcription, secretion, and storage of insulin in mammalian beta cells. However, more research is still needed in this area. Syndecans are transmembrane heparan sulfate proteoglycans that function independently and in synergy with integrin-mediated signaling to mediate cell adhesion to the extracellular matrix. This study used the model organism Drosophila melanogaster to determine whether knockdown of the Syndecan (Sdc) gene expression specifically in the insulin-producing cells (IPCs) might affect insulin-like peptide (ILP) production and secretion. IPCs of adult flies produce three ILPs (ILP2, ILP3, and ILP5), which have significant homology to mammalian insulin. Flies with reduced Sdc expression in the IPCs did not show any difference in the expression of ilp genes compared to controls. However, they had significantly reduced levels of the circulating ILP2 protein, higher circulating carbohydrates, and were less glucose tolerant than control flies. Finally, IPCs-specific Sdc knockdown led to reduced levels of head Glucose transporter1 gene expression, extracellular signal-regulated kinase phosphorylation, and reactive oxygen species. Taken together, these findings suggest a cell autonomous role for Sdc in insulin release in D. melanogaster.
Tsai, P. I., Papakyrikos, A. M., Hsieh, C. H. and Wang, X. (2017). Drosophila MIC60/Mitofilin conducts dual roles in mitochondrial motility and crista structure. Mol Biol Cell. PubMed ID: 28904209
Summary:
MIC60/mitofilin constitutes a hetero-oligomeric complex on the inner mitochondrial membranes to maintain crista structure. However, little is known about its physiological functions. By characterizing Drosophila MIC60 mutants, this study defines its roles in vivo. MIC60 performs dual functions to maintain mitochondrial homeostasis. In addition to its canonical role in crista membrane structure, MIC60 regulates mitochondrial motility, likely by influencing protein levels of the outer mitochondrial membrane protein Miro that anchors mitochondria to the microtubule motors. Loss of MIC60 causes loss of Miro and mitochondrial arrest. At a cellular level, loss of MIC60 disrupts synaptic structure and function at the neuromuscular junctions. The double roles of MIC60 in both mitochondrial crista structure and motility position it as a crucial player for cellular integrity and survival.
Wang, Z., Oppegard, S. C., Eddington, D. T. and Cheng, J. (2017). Effect of localized hypoxia on Drosophila embryo development. PLoS One 12(9): e0185267. PubMed ID: 28934338
Summary:
Environmental stress, such as oxygen deprivation, affects various cellular activities and developmental processes. This study directly investigated Drosophila embryo development in vivo while cultured on a microfluidic device, which imposed an oxygen gradient on the developing embryos. The designed microfluidic device enabled both temporal and spatial control of the local oxygen gradient applied to the live embryos. Time-lapse live cell imaging was used to monitor the morphology and cellular migration patterns as embryos were placed in various geometries relative to the oxygen gradient. Results show that pole cell movement and tail retraction during Drosophila embryogenesis are highly sensitive to oxygen concentrations. Through modeling, the oxygen permeability across the Drosophila embryonic layers was also estimated for the first time using parameters measured on the oxygen control device.

Friday, November 10th

Sessions, A. O., Kaushik, G., Parker, S., Raedschelders, K., Bodmer, R., Van Eyk, J. E. and Engler, A. J. (2017). Extracellular matrix downregulation in the Drosophila heart preserves contractile function and improves lifespan. Matrix Biol 62: 15-27. PubMed ID: 27793636
Summary:
Aging is associated with extensive remodeling of the heart, including basement membrane (BM) components that surround cardiomyocytes. Remodeling is thought to impair cardiac mechanotransduction, but the contribution of specific BM components to age-related lateral communication between cardiomyocytes is unclear. Using a genetically tractable, rapidly aging model with sufficient cardiac genetic homology and morphology, e.g. Drosophila melanogaster, this study observed differential regulation of BM collagens between laboratory strains, correlating with changes in muscle physiology leading to cardiac dysfunction. Therefore, attempts were made to understand the extent to which BM proteins modulate contractile function during aging. Cardiac-restricted knockdown of ECM genes Pericardin, Laminin A, and Viking in Drosophila prevented age-associated heart tube restriction and increased contractility, even under viscous load. Most notably, reduction of Laminin A expression correlated with an overall preservation of contractile velocity with age and extension of organismal lifespan. Global heterozygous knockdown confirmed these data, which provides new evidence of a direct link between BM homeostasis, contractility, and maintenance of lifespan.
Rana, A., Oliveira, M. P., Khamoui, A. V., Aparicio, R., Rera, M., Rossiter, H. B. and Walker, D. W. (2017). Promoting Drp1-mediated mitochondrial fission in midlife prolongs healthy lifespan of Drosophila melanogaster. Nat Commun 8(1): 448. PubMed ID: 28878259
Summary:
The accumulation of dysfunctional mitochondria has been implicated in aging, but a deeper understanding of mitochondrial dynamics and mitophagy during aging is missing. This study shows that upregulating Drp1-a Dynamin-related protein that promotes mitochondrial fission-in midlife, prolongs Drosophila lifespan and healthspan. Short-term induction of Drp1, in midlife, is sufficient to improve organismal health and prolong lifespan, and observe a midlife shift toward a more elongated mitochondrial morphology, which is linked to the accumulation of dysfunctional mitochondria in aged flight muscle. Promoting Drp1-mediated mitochondrial fission, in midlife, facilitates mitophagy and improves both mitochondrial respiratory function and proteostasis in aged flies. Finally, autophagy is required for the anti-aging effects of midlife Drp1-mediated mitochondrial fission. These findings indicate that interventions that promote mitochondrial fission could delay the onset of pathology and mortality in mammals when applied in midlife. Mitochondrial fission and fusion are important mechanisms to maintain mitochondrial function. Here, the authors report that middle-aged flies have more elongated, or 'hyper-fused' mitochondria, and show that induction of mitochondrial fission in midlife, but not in early life, extends the health and life of flies.
Wu, Y. L., Chang, J. C., Lin, W. Y., Li, C. C., Hsieh, M., Chen, H. W., Wang, T. S., Liu, C. S. and Liu, K. L. (2017). Treatment with caffeic acid and resveratrol alleviates oxidative stress induced neurotoxicity in cell and Drosophila models of Spinocerebellar ataxia type3. Sci Rep 7(1): 11641. PubMed ID: 28912527
Summary:
Spinocerebellar ataxia type 3 (SCA3) is caused by the expansion of a polyglutamine (polyQ) repeat in the protein ataxin-3 which is involved in susceptibility to mild oxidative stress induced neuronal death. This study shows that caffeic acid (CA) and resveratrol (Res) decreased reactive oxygen species (ROS), mutant ataxin-3 and apoptosis and increased autophagy in the pro-oxidant tert-butyl hydroperoxide (tBH)-treated SK-N-SH-MJD78 cells containing mutant ataxin-3. Furthermore, CA and Res improved survival and locomotor activity and decreased mutant ataxin-3 and ROS levels in tBH-treated SCA3 Drosophila. CA and Res also altered p53 and nuclear factor-kappaB (NF-kappaB) activation and expression in tBH-treated cell and fly models of SCA3, respectively. Blockade of NF-kappaB activation annulled the protective effects of CA and Res on apoptosis, ROS, and p53 activation in tBH-treated SK-N-SH-MJD78 cells, which suggests the importance of restoring NF-kappaB activity by CA and Res. These findings suggest that CA and Res may be useful in the management of oxidative stress induced neuronal apoptosis in SCA3.
Thackray, A. M., Cardova, A., Wolf, H., Pradl, L., Vorberg, I., Jackson, W. S. and Bujdoso, R. (2017). Genetic human prion disease modelled in PrP transgenic Drosophila. Biochem J 474(19): 3253-3267. PubMed ID: 28814578
Summary:
Inherited human prion diseases, such as fatal familial insomnia (FFI) and familial Creutzfeldt-Jakob disease (fCJD), are associated with autosomal dominant mutations in the human prion protein gene PRNP and accumulation of PrPSc, an abnormal isomer of the normal host protein PrPC, in the brain of affected individuals. PrPSc is the principal component of the transmissible neurotoxic prion agent. Site-directed mutagenesis was used to generate Drosophila transgenic for murine or hamster PrP (prion protein) that carry single-codon mutations associated with genetic human prion disease. Mouse or hamster PrP harbouring an FFI (D178N) or fCJD (E200K) mutation showed mild Proteinase K resistance when expressed in Drosophila Adult Drosophila transgenic for FFI or fCJD variants of mouse or hamster PrP displayed a spontaneous decline in locomotor ability that increased in severity as the flies aged. Significantly, this mutant PrP-mediated neurotoxic fly phenotype was transferable to recipient Drosophila that expressed the wild-type form of the transgene. Collectively, these novel data are indicative of the spontaneous formation of a PrP-dependent neurotoxic phenotype in FFI- or CJD-PrP transgenic Drosophila and show that inherited human prion disease can be modelled in this invertebrate host.

Thursday, November 9th

Turrel, O., Goguel, V. and Preat, T. (2017). Drosophila neprilysin 1 rescues memory deficits caused by amyloid-beta peptide. J Neurosci [Epub ahead of print]. PubMed ID: 28931572
Summary:
Neprilysins are type-II metalloproteinases known to degrade and inactivate a number of small peptides, in particular the mammalian amyloid-beta peptide (Abeta). In Drosophila, several neprilysins expressed in the brain are required for middle-term (MTM) and long-term memory (LTM) in the dorsal paired medial (DPM) neurons, a pair of large neurons that broadly innervate the mushroom bodies (MB), the center of olfactory memory. These data indicate that one or several peptides need to be degraded for MTM and LTM. Previous work has shown that the fly amyloid precursor protein (APPL) is required for memory in the MB. This study shows that APPL is also required in adult DPM neurons for MTM and LTM formation. This finding prompted a search for an interaction between neprilysins and Drosophila Abeta (dAbeta), a cleavage product of APPL. To find out whether dAbeta was a neprilysin's target, inducible drivers were used to modulate neprilysin 1 (Nep1) and dAbeta expression in adult DPM neurons. Experiments were conducted either in both sexes or in females. The study shows that Nep1 inhibition makes dAbeta expression detrimental to both MTM and LTM. Conversely, memory deficits displayed by dAbeta-expressing flies are rescued by Nep1 overexpression. Consistent with behavioral data, biochemical analyses confirmed that Nep1 degrades dAbeta. Taken together, these findings establish that Nep1 and dAbeta expressed in DPM neurons are functionally linked for memory processes, suggesting that dAbeta is a physiological target for Nep1.
Subramanian, A., Siefert, M., Banerjee, S., Vishal, K., Bergmann, K. A., Curts, C. C. M., Dorr, M., Molina, C. and Fernandes, J. (2017). Remodeling of peripheral nerve ensheathment during the larval-to-adult transition in Drosophila. Dev Neurobiol 77(10): 1144-1160. PubMed ID: 28388016
Summary:
Over the course of a 4-day period of metamorphosis, the Drosophila larval nervous system is remodeled to prepare for adult-specific behaviors. One example is the reorganization of peripheral nerves in the abdomen, where five pairs of abdominal nerves (A4-A8) fuse to form the terminal nerve trunk. This reorganization is associated with selective remodeling of four layers that ensheath each peripheral nerve. The neural lamella (NL), is the first to dismantle; its breakdown is initiated by 6 hours after puparium formation, and is completely removed by the end of the first day. This layer begins to re-appear on the third day of metamorphosis. Perineurial glial (PG) cells situated just underneath the NL, undergo significant proliferation on the first day of metamorphosis, and at that stage contribute to 95% of the glial cell population. Cells of the two inner layers, Sub-Perineurial Glia (SPG) and Wrapping Glia (WG) increase in number on the second half of metamorphosis. Induction of cell death in perineurial glia via the cell death gene reaper and the Diptheria toxin (DT-1) gene, results in abnormal bundling of the peripheral nerves, suggesting that perineurial glial cells play a role in the process. A significant number of animals fail to eclose in both reaper and DT-1 targeted animals, suggesting that disruption of PG also impacts eclosion behavior. The studies will help to establish the groundwork for further work on cellular and molecular processes that underlie the co-ordinated remodeling of glia and the peripheral nerves they ensheath.
Shao, L., Saver, M., Chung, P., Ren, Q., Lee, T., Kent, C. F. and Heberlein, U. (2017). Dissection of the Drosophila neuropeptide F circuit using a high-throughput two-choice assay. Proc Natl Acad Sci U S A 114(38): E8091-e8099. PubMed ID: 28874527
Summary:
In their classic experiments, Olds and Milner showed that rats learn to lever press to receive an electric stimulus in specific brain regions. This led to the identification of mammalian reward centers. Interest in defining the neuronal substrates of reward perception in the fruit fly Drosophila melanogaster prompted the development of a simpler experimental approach wherein flies could implement behavior that induces self-stimulation of specific neurons in their brains. The high-throughput assay employs optogenetic activation of neurons when the fly occupies a specific area of a behavioral chamber, and the flies' preferential occupation of this area reflects their choosing to experience optogenetic stimulation. Flies in which neuropeptide F (NPF) neurons are activated display preference for the illuminated side of the chamber. Optogenetic activation of NPF neuron is rewarding in olfactory conditioning experiments, and the preference for NPF neuron activation is dependent on NPF signaling. Finally, a small subset of NPF-expressing neurons located in the dorsomedial posterior brain was identified that are sufficient to elicit preference. This assay provides the means for carrying out unbiased screens to map reward neurons in flies.
Tenenbaum, C. M., Misra, M., Alizzi, R. A. and Gavis, E. R. (2017). Enclosure of dendrites by epidermal cells restricts branching and permits coordinated development of spatially overlapping sensory neurons. Cell Rep 20(13): 3043-3056. PubMed ID: 28954223
Summary:
Spatial arrangement of different neuron types within a territory is essential to neuronal development and function. How development of different neuron types is coordinated for spatial coexistence is poorly understood. In Drosophila, dendrites of four classes of dendritic arborization (C1-C4da) neurons innervate overlapping receptive fields within the larval epidermis. These dendrites are intermittently enclosed by epidermal cells, with different classes exhibiting varying degrees of enclosure. The role of enclosure in neuronal development and its underlying mechanism remain unknown. This study shows that the membrane-associated protein Coracle acts in C4da neurons and epidermal cells to locally restrict dendrite branching and outgrowth by promoting enclosure. Loss of C4da neuron enclosure results in excessive branching and growth of C4da neuron dendrites and retraction of C1da neuron dendrites due to local inhibitory interactions between neurons. It is proposed that enclosure of dendrites by epidermal cells is a developmental mechanism for coordinated innervation of shared receptive fields.

Wednesday, November 8th

Ruth Archer, C., Basellini, U., Hunt, J., Simpson, S. J., Lee, K. P. and Baudisch, A. (2017). Diet has independent effects on the pace and shape of aging in Drosophila melanogaster.Biogerontology [Epub ahead of print]. PubMed ID: 28914388
Summary:
Studies examining how diet affects mortality risk over age typically characterise mortality using parameters such as aging rates, which condense how much and how quickly the risk of dying changes over time into a single measure. Demographers have suggested that decoupling the tempo and the magnitude of changing mortality risk may facilitate comparative analyses of mortality trajectories, but it is unclear what biologically meaningful information this approach offers. This study has determined how the amount and ratio of protein and carbohydrate ingested by female Drosophila melanogaster affects how much mortality risk increases over a time-standardised life-course (the shape of aging) and the tempo at which animals live and die (the pace of aging). Pace values increased as flies consumed more carbohydrate but declined with increasing protein consumption. Shape values were independent of protein intake but were lowest in flies consuming ~90 mug of carbohydrate daily. As protein intake only affected the pace of aging, varying protein intake rescaled mortality trajectories (i.e. stretched or compressed survival curves), while varying carbohydrate consumption caused deviation from temporal rescaling (i.e. changed the topography of time-standardised survival curves), by affecting pace and shape. Clearly, the pace and shape of aging may vary independently in response to dietary manipulation. This suggests that there is the potential for pace and shape to evolve independently of one another and respond to different physiological processes. Understanding the mechanisms responsible for independent variation in pace and shape, may offer insight into the factors underlying diverse mortality trajectories.
Tefit, M. A., Gillet, B., Joncour, P., Hughes, S. and Leulier, F. (2017). Stable association of a Drosophila-derived microbiota with its animal partner and the nutritional environment throughout a fly population's life cycle. J Insect Physiol [Epub ahead of print]. PubMed ID: 28916161
Summary:
In the past years, the fruit fly Drosophila melanogaster has been extensively used to study the relationship between animals and their associated microbes. Compared to the one of wild populations, the microbiota of laboratory-reared flies is less diverse, and comprises fewer bacterial taxa; nevertheless, the main commensal bacteria found in fly microbiota always belong to the Acetobacteraceae and Lactobacillaceae families. The bacterial communities associated with the fly are environmentally acquired, and the partners engage in a perpetual re-association process. Adult flies constantly ingest and excrete microbes from and onto their feeding substrate, which are then transmitted to the next generation developing within this shared habitat. This study was an attempt to analyze the potential changes in the bacterial community during its reciprocal transfer between the two compartments of the niche (i.e. the fly and the diet). To address this question, a diverse, wild-derived microbial community was used, and its relationship with the fly population and the nutritive substrate in a given habitat was examined. This study shows that the community was overall well maintained upon transmission to a new niche, to a new fly population and to their progeny, illustrating the stable association of a Drosophila-derived microbiota with its fly partner and the nutritional environment. These results highlight the preponderant role of the nutritional substrate in the dynamics of Drosophila/microbiota interactions, and the need to fully integrate this variable when performing such studies.
Thul, P. J., Tschapalda, K., Kolkhof, P., Thiam, A. R., Oberer, M. and Beller, M. (2017). Targeting of the Drosophila protein CG2254/Ldsdh1 to a subset of lipid droplets. 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 known to be essential for the regulation of 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 subsets of LDs by an as-yet-unknown mechanism. This finding makes LD targeting even more complex. This study characterize the Drosophila protein CG2254, which is targeted to subsets of LDs in cultured cells and in different larval Drosophila tissues, where the prevalence of subsets of LDs appears highly dynamic. An amphipathic amino acid stretch was found to mediates CG2254 LD localization. Additionally, a juxtaposed sequence stretch was found to limit CG2254 localization to a subset of LDs. 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 a subset of LDs. Based on its subcellular localization and annotated function, it is suggested that CG2254 is renamed Lipid droplet subset dehydrogenase 1 (Ldsdh1).
Rahman, M. M., Franch-Marro, X., Maestro, J. L., Martin, D. and Casali, A. (2017). Local Juvenile Hormone activity regulates gut homeostasis and tumor growth in adult Drosophila. Sci Rep 7(1): 11677. PubMed ID: 28916802
Summary:
Hormones play essential roles during development and maintaining homeostasis in adult organisms, regulating a plethora of biological processes. Generally, hormones are secreted by glands and perform a systemic action. This study shows that Juvenile Hormones (JHs), insect sesquiterpenoids synthesized by the corpora allata, are also synthesized by the adult Drosophila gut. This local, gut specific JH activity, is synthesized by and acts on the intestinal stem cell and enteroblast populations, regulating their survival and cellular growth through the JH receptors Gce/Met and the coactivator Tai. This local JH activity is important for damage response and is necessary for intestinal tumor growth driven by activating mutations in Wnt and EGFR/Ras pathways. Together, these results identify JHs as key hormonal regulators of gut homeostasis and open the possibility that analogous hormones may play a similar role in maintaining vertebrate adult intestinal stem cell population and sustaining tumor growth.

Tuesday, November 7th

Pan, C., Xiong, Y., Lv, X., Xia, Y., Zhang, S., Chen, H., Fan, J., Wu, W., Liu, F., Wu, H., Zhou, Z., Zhang, L. and Zhao, Y. (2017). UbcD1 regulates Hedgehog signaling by directly modulating Ci ubiquitination and processing. EMBO Rep. PubMed ID: 28887318
Summary:
The Hh pathway controls many morphogenetic processes in metazoans and plays important roles in numerous pathologies and in cancer. Hh signaling is mediated by the activity of the Gli/Ci family of transcription factors. Several studies in Drosophila have shown that ubiquitination by the ubiquitin E3 ligases Slimb and Rdx(Hib) plays a crucial role in controlling Ci stability dependent on the levels of Hh signals. If Hh levels are low, Slimb adds K11- and K48-linked poly-ubiquitin chains on Ci resulting in partial degradation. Ubiquitin E2 enzymes are pivotal in determining the topologies of ubiquitin chains. However, which E2 enzymes participate in the selective ubiquitination-degradation of Ci remains elusive. This study finds that the E2 enzyme UbcD1 negatively regulates Hh signaling activity in Drosophila wing discs. Genetic and biochemical analyses in wing discs and in cultured cells reveal that UbcD1 directly controls Ci stability. Interestingly, UbcD1 is found to be selectively involved in Slimb-mediated Ci degradation. Finally, it was shown that the homologs of UbcD1 play a conserved role in modulating Hh signaling in vertebrates.
Suresh, J., Harmston, N., Lim, K. K., Kaur, P., Jin, H. J., Lusk, J. B., Petretto, E. and Tolwinski, N. S. (2017). An embryonic system to assess direct and indirect Wnt transcriptional targets. Sci Rep 7(1): 11092. PubMed ID: 28894169
Summary:
During animal development, complex signals determine and organize a vast number of tissues using a very small number of signal transduction pathways. These developmental signaling pathways determine cell fates through a coordinated transcriptional response that remains poorly understood. The Wnt pathway is involved in a variety of these cellular functions, and its signals are transmitted in part through a beta-catenin/TCF transcriptional complex. This study reports an in vivo Drosophila assay that can be used to distinguish between activation, de-repression and repression of transcriptional responses, separating upstream and downstream pathway activation and canonical/non-canonical Wnt signals in embryos. Specific sets of genes were found downstream of both beta-catenin and TCF with an additional group of genes regulated by Wnt, while the non-canonical Wnt4 regulates a separate cohort of genes. Transcriptional changes were correlated with phenotypic outcomes of cell differentiation and embryo size, showing the model can be used to characterize developmental signaling compartmentalization in vivo.
Pascual, J., Jacobs, J., Sansores-Garcia, L., Natarajan, M., Zeitlinger, J., Aerts, S., Halder, G. and Hamaratoglu, F. (2017). Hippo reprograms the transcriptional response to Ras signaling. Dev Cell 42(6): 667-680.e664. PubMed ID: 28950103
Summary:
Hyperactivating mutations in Ras signaling are hallmarks of carcinomas. Ras signaling mediates cell fate decisions as well as proliferation during development. It is not known what dictates whether Ras signaling drives differentiation versus proliferation. This study shows that the Hippo pathway is critical for this decision. Loss of Hippo switches Ras activation from promoting cellular differentiation to aggressive cellular proliferation. Transcriptome analysis combined with genetic tests show that this excessive proliferation depends on the synergistic induction of Ras target genes. Using ChIP-nexus, Hippo signaling was found to keep Ras targets in check by directly regulating the expression of two key downstream transcription factors of Ras signaling: the ETS-domain transcription factor Pointed and the repressor Capicua. These results highlight how independent signaling pathways can impinge on each other at the level of transcription factors, thereby providing a safety mechanism to keep proliferation in check under normal developmental conditions.
Nakamura, M., Verboon, J. M. and Parkhurst, S. M. (2017). Prepatterning by RhoGEFs governs Rho GTPase spatiotemporal dynamics during wound repair. J Cell Biol [Epub ahead of print]. PubMed ID: 28923977
Summary:
Like tissues, single cells are subjected to continual stresses and damage. As such, cells have a robust wound repair mechanism comprised of dynamic membrane resealing and cortical cytoskeletal remodeling. One group of proteins, the Rho family of small guanosine triphosphatases (GTPases), is critical for this actin and myosin cytoskeletal response in which they form distinct dynamic spatial and temporal patterns/arrays surrounding the wound. A key mechanistic question, then, is how these GTPase arrays are formed. This study shows that in the Drosophila melanogaster cell wound repair model Rho GTPase arrays form in response to prepatterning by Rho guanine nucleotide exchange factors (RhoGEFs), a family of proteins involved in the activation of small GTPases. Furthermore, Annexin B9, a member of a class of proteins associated with the membrane resealing, was shown to be involved in an early, Rho family-independent, actin stabilization that is integral to the formation of one RhoGEF array. Thus, Annexin proteins may link membrane resealing to cytoskeletal remodeling processes in single cell wound repair.

Monday, November 6th

Qi, Y. X., Xu, G., Gu, G. X., Mao, F., Ye, G. Y., Liu, W. and Huang, J. (2017). A new Drosophila octopamine receptor responds to serotonin. Insect Biochem Mol Biol [Epub ahead of print]. PubMed ID: 28942992
Summary:
As the counterparts of the vertebrate adrenergic transmitters, octopamine and tyramine are important physiological regulators in invertebrates. They control and modulate many physiological and behavioral functions in insects. This study reports the pharmacological properties of a new alpha2-adrenergic-like octopamine receptor (CG18208) from Drosophila melanogaster, named DmOctalpha2R. This new receptor gene encodes two transcripts by alternative splicing. The long isoform DmOctalpha2R-L differs from the short isoform DmOctalpha2R-S by the presence of an additional 29 amino acids within the third intracellular loop. When heterologously expressed in mammalian cell lines, both receptors were activated by octopamine, tyramine, epinephrine and norepinephrine, resulting in the inhibition of cAMP production in a dose-dependent manner. The long form is more sensitive to the above ligands than the short form. The adrenergic agonists naphazoline, tolazoline and clonidine can stimulate DmOctalpha2R as full agonists. Surprisingly, serotonin and serotoninergic agonists can also activate DmOctalpha2R. Several tested adrenergic antagonists and serotonin antagonists blocked the action of octopamine or serotonin on DmOctalpha2R. The data presented in this study reported an adrenergic-like G protein-coupled receptor activated by serotonin, suggesting that the neurotransmission and neuromodulation in the nervous system could be more complex than previously thought.
Lim, J., Fernandez, A. I., Hinojos, S. J., Aranda, G. P., James, J., Seong, C. S. and Han, K. A. (2017). The mushroom body D1 dopamine receptor controls innate courtship drive. Genes Brain Behav [Epub ahead of print]. PubMed ID: 28902472
Summary:
Mating is critical for species survival and is profoundly regulated by neuromodulators and neurohormones to accommodate internal states and external factors. To identify the underlying neuromodulatory mechanisms, this study investigated the roles of dopamine receptors in various aspects of courtship behavior in Drosophila. The D1 dopamine receptor dDA1 regulates courtship drive in naive males. The wild-type naive males actively courted females regardless their appearance or mating status. On the contrary, the dDA1 mutant (dumb) males exhibited substantially reduced courtship toward less appealing females including decapitated, leg-less and mated females. The dumb male's reduced courtship activity was due to delay in courtship initiation and prolonged intervals between courtship bouts. The dampened courtship drive of dumb males was rescued by reinstated dDA1 expression in the mushroom body α/&beta& and γ neurons but not α/β or γ neurons alone, which is distinct from the previously characterized dDA1 functions in experience-dependent courtship or other learning and memory processes. It was also found that the dopamine receptors dDA1, DAMB and dD2R are dispensable for associative memory formation and short-term memory of conditioned courtship, thus courtship motivation and associative courtship learning and memory are regulated by distinct neuromodulatory mechanisms. Taken together, this study narrows the gap in the knowledge of the mechanism that dopamine regulates male courtship behavior.
Schatton, A. and Scharff, C. (2017). FoxP expression identifies a Kenyon cell subtype in the honeybee mushroom bodies linking them to fruitfly alphabetac neurons. Eur J Neurosci [Epub ahead of print]. PubMed ID: 28921711
Summary:
The arthropod mushroom bodies (MB) are a higher order sensory integration center. In insects, they play a central role in associative olfactory learning and memory. In Drosophila melanogaster (Dm), the highly ordered connectivity of heterogeneous MB neuron populations has been mapped using sophisticated molecular genetic and anatomical techniques. The MB-core subpopulation was recently shown to express the transcription factor FoxP with relevance for decision-making. This study reports the development and adult distribution of a FoxP-expressing neuron population in the MB of honeybees (Apis mellifera, Am) using in situ hybridization and a custom-made antiserum. The same expression pattern was found in adult bumblebees (Bombus terrestris, Bt). A new Dm transgenic line was designed that reports FoxP transcriptional activity in the MB-core region, clarifying previously conflicting data of two other reporter lines. Considering developmental, anatomical and molecular similarities, the data are consistent with the concept of deep homology of FoxP expression in neuron populations coding reinforcement-based learning and habit formation.
Li, X., Chen, R. and Zhu, S. (2017). bHLH-O proteins balance the self-renewal and differentiation of Drosophila neural stem cells by regulating Earmuff expression. Dev Biol [Epub ahead of print]. PubMed ID: 28899667
Summary:
Balancing self-renewal and differentiation of stem cells requires differential expression of self-renewing factors in two daughter cells generated from the asymmetric division of the stem cells. In Drosophila type II neural stem cell (or neuroblast, NB) lineages, the expression of the basic helix-loop-helix-Orange (bHLH-O) family proteins, including Deadpan (Dpn) and E(spl) proteins, is required for maintaining the self-renewal and identity of type II NBs, whereas the absence of these self-renewing factors is essential for the differentiation of intermediate neural progenitors (INPs) generated from type II NBs. This study demonstrates that Dpn maintains type II NBs by suppressing the expression of Earmuff (Erm). Evidence is provided that Dpn and E(spl) proteins suppress Erm by directly binding to C-sites and N-boxes in the cis-regulatory region of erm. Conversely, the absence of bHLH-O proteins in INPs allows activation of erm and Erm-mediated maturation of INPs. The results further suggest that Pointed P1 (PntP1) mediates the dedifferentiation of INPs resulting from the loss of Erm or overexpression of Dpn or E(spl) proteins. Taken together, these findings reveal mechanisms underlying the regulation of the maintenance of type II NBs and differentiation of INPs through the differential expression of bHLH-O family proteins.

Friday, October 3rd

Ninova, M., Griffiths-Jones, S. and Ronshaugen, M. (2017). Abundant expression of somatic transposon-derived piRNAs throughout Tribolium castaneum embryogenesis. Genome Biol 18(1): 184. PubMed ID: 28950880
Summary:
Piwi-interacting RNAs (piRNAs) are a class of short (~26-31-nucleotide) non-protein-coding RNAs expressed in the metazoan germline. The piRNA pathway in arthropods is best understood in the ovary of Drosophila melanogaster, where it acts to silence active transposable elements (TEs). Maternal loading of piRNAs in oocytes is further required for the inheritance of piRNA-mediated transposon defence. However, understanding of the diversity, evolution and function of the piRNA complement beyond drosophilids is limited. The red flour beetle, Tribolium castaneum, is an emerging model organism separated from Drosophila by ~ 350 million years of evolution that displays a number of features ancestral to arthropods, including short germ embryogenesis. This study characterized the maternally deposited and zygotically expressed small RNA and mRNA complements throughout T. castaneum embryogenesis. Beetle oocytes and embryos of all stages were found to be abundant in heterogeneous ~ 28-nucleotide RNAs. These small RNAs originate from discrete genomic loci enriched in TE sequences and display the molecular signatures of transposon-derived piRNAs. In addition to the maternally loaded primary piRNAs, Tribolium embryos produce secondary piRNAs by the cleavage of zygotically activated TE transcripts via the ping-pong mechanism. The two Tribolium piRNA pathway effector proteins, Tc-Piwi/Aub and Tc-Ago3, are also expressed throughout the soma of early embryos. These results show that the piRNA pathway in Tribolium is not restricted to the germline, but also operates in the embryo and may act to antagonize zygotically activated transposons. Taken together, these data highlight a functional divergence of the piRNA pathway between insects.
Katti, P., Thimmaya, D., Madan, A. and Nongthomba, U. (2017). Over-expression of miRNA-9 generates muscle hypercontraction through translational repression of the Troponin-T in Drosophila indirect flight muscles. G3 (Bethesda) [Epub ahead of print]. PubMed ID: 28866639
Summary:
miRNAs are small non-coding endogenous RNAs, typically 21-23 nucleotides long, that regulate gene expression, usually post-transcriptionally by binding to the 3'-UTR of target mRNA, thus blocking translation. The expression of several miRNAs is significantly altered during cardiac hypertrophy, myocardial ischemia, fibrosis, heart failure and other cardiac myopathies. Recent studies have implicated miR-9 in myocardial hypertrophy. However a detailed mechanism remains obscure. This study has addressed the roles of miR-9 in muscle development and function using the genetically tractable model system, the indirect flight muscles (IFMs) of Drosophila melanogaster. Bioinformatics analysis identified 135 potential miR-9a targets, of which 27 genes were associated with Drosophila muscle development. Troponin-T (TnT) was identified as major structural gene target of miR-9a. Flies over-expressing miR-9a in the IFMs have abnormal wing position and are flightless. These flies also exhibit loss of muscle integrity and sarcomeric organization causing an abnormal muscle condition known as "hypercontraction". Additionally, miR-9a over-expression resulted in the reduction of TnT protein levels while transcript levels were unaffected. Furthermore, muscle abnormalities associated with miR-9a over-expression were completely rescued by over-expression of TnT transgenes which lacked the miR-9a binding site. These findings indicate that miR-9a interacts with the 3'-UTR of the TnT mRNA and down-regulates the TnT protein levels by translational repression. The reduction in TnT levels leads to a cooperative down-regulation of other thin filament structural proteins. These findings have implications for understanding the cellular pathophysiology of cardiomyopathies associated with miR-9a over-expression.
Gotze, M., Dufourt, J., Ihling, C., Rammelt, C., Pierson, S., Sambrani, N., Temme, C., Sinz, A., Simonelig, M. and Wahle, E. (2017). Translational repression of the Drosophila nanos mRNA involves the RNA helicase Belle and RNA coating by Me31B and Trailer hitch. RNA 23(10): 1552-1568. PubMed ID: 28701521
Summary:
Translational repression of maternal mRNAs is an essential regulatory mechanism during early embryonic development. Repression of the Drosophila nanos mRNA, required for the formation of the anterior-posterior body axis, depends on the protein Smaug binding to two Smaug recognition elements (SREs) in the nanos 3' UTR. In a comprehensive mass spectrometric analysis of the SRE-dependent repressor complex, Smaug, Cup, Me31B, Trailer hitch, eIF4E, and PABPC were identified, in agreement with earlier data. As a novel component, the RNA-dependent ATPase Belle (DDX3) was found, and its involvement in deadenylation and repression of nanos was confirmed in vivo. Smaug, Cup, and Belle bound stoichiometrically to the SREs, independently of RNA length. Binding of Me31B and Tral was also SRE-dependent, but their amounts were proportional to the length of the RNA and equimolar to each other. It is suggested that "coating" of the RNA by a Me31B*Tral complex may be at the core of repression.
Liufu, Z., Zhao, Y., Guo, L., Miao, G., Xiao, J., Lyu, Y., Chen, Y., Shi, S., Tang, T. and Wu, C. I. (2017). Redundant and incoherent regulations of multiple phenotypes suggest microRNAs' role in stability control. Genome Res [Epub ahead of print]. PubMed ID: 28904014
Summary:
A "simple regulation" model for how microRNAs (miRNAs) function posits "one target-one phenotype" control under which most targeting is nonfunctional. In an alternative "coordinate regulation" model, multiple targets are assumed to control the same phenotypes coherently, and most targeting is functional. Both models have some empirical support but pose different conceptual challenges. This study concurrently analyzes multiple targets and phenotypes associated with the miRNA-310 family (miR310s) of Drosophila. Phenotypic rescue in the mir310s knockout background is achieved by promoter-directed RNA interference that restores wild-type expression. For one phenotype (eggshell morphology), redundant regulation was observed, hence rejecting "simple regulation" in favor of the "coordinate regulation" model. For other phenotypes (egg-hatching and male fertility), however, one gene shows full rescue, but three other rescues aggravate the phenotype. Overall, phenotypic controls by miR310s do not support either model. Like a thermostat that controls both heating and cooling elements to regulate temperature, redundancy and incoherence in regulation generally suggest some capacity in stability control. These results therefore support the published view that miRNAs play a role in the canalization of transcriptome and, hence, phenotypes.

Thursday, November 2nd

Newman, C. E., Toxopeus, J., Udaka, H., Ahn, S., Martynowicz, D. M., Graether, S. P., Sinclair, B. J. and Percival-Smith, A. (2017). CRISPR-induced null alleles show that Frost protects Drosophila melanogaster reproduction after cold exposure. J Exp Biol 220(Pt 18): 3344-3354. PubMed ID: 28705828
Summary:
The ability to survive and reproduce after cold exposure is important in all kingdoms of life. However, even in a sophisticated genetic model system like Drosophila melanogaster, few genes have been identified as functioning in cold tolerance. The accumulation of the Frost (Fst) gene transcript increases after cold exposure, making it a good candidate for a gene that has a role in cold tolerance. Despite extensive RNAi knockdown analysis, no role in cold tolerance has been assigned to Fst. CRISPR is an effective technique for completely knocking down genes, and is less likely to produce off-target effects than GAL4-UAS RNAi systems. CRISPR-mediated homologous recombination was used to generate Fst-null alleles, and these Fst alleles uncovered a requirement for FST protein in maintaining female fecundity following cold exposure. However, FST does not have a direct role in survival following cold exposure. FST mRNA accumulates in the Malpighian tubules, and the FST protein is a highly disordered protein with a putative signal peptide for export from the cell. Future work is needed to determine whether FST is exported from the Malpighian tubules and directly interacts with female reproductive tissues post-cold exposure, or whether it is required for other repair/recovery functions that indirectly alter energy allocation to reproduction.
Denecke, S., Fusetto, R., Martelli, F., Giang, A., Battlay, P., Fournier-Level, A., RA, O. H. and Batterham, P. (2017). Multiple P450s and variation in neuronal genes underpins the response to the insecticide Imidacloprid in a population of Drosophila melanogaster. Sci Rep 7(1): 11338. PubMed ID: 28900129
Summary:
Insecticide resistance is an economically important example of evolution in response to intense selection pressure. In this study, the genetics of resistance to the neonicotinoid insecticide imidacloprid is explored using the Drosophila Genetic Reference Panel, a collection of inbred Drosophila melanogaster genotypes derived from a single population in North Carolina. Imidacloprid resistance varied substantially among genotypes, and more resistant genotypes tended to show increased capacity to metabolize and excrete imidacloprid. Variation in resistance level was then associated with genomic and transcriptomic variation, implicating several candidate genes involved in central nervous system function and the cytochrome P450s Cyp6g1 and Cyp6g2. CRISPR-Cas9 mediated removal of Cyp6g1 suggested that it contributed to imidacloprid resistance only in backgrounds where it was already highly expressed. Cyp6g2, previously implicated in juvenile hormone synthesis via expression in the ring gland, was shown to be expressed in metabolically relevant tissues of resistant genotypes. Cyp6g2 overexpression was shown to both metabolize imidacloprid and confer resistance. These data collectively suggest that imidacloprid resistance is influenced by a variety of previously known and unknown genetic factors.
Evans, J. J., Xiao, C. and Robertson, R. M. (2017). AMP-activated protein kinase protects against anoxia in Drosophila melanogaster. Comp Biochem Physiol A Mol Integr Physiol 214: 30-39. PubMed ID: 28916374
Summary:
During anoxia, proper energy maintenance is essential in order to maintain neural operation. Starvation activates AMP-activated protein kinase (AMPK), an evolutionarily conserved indicator of cellular energy status, in a cascade which modulates ATP production and consumption. This study investigated the role of energetic status on anoxia tolerance in Drosophila and discovered that starvation or AMPK activation increases the speed of locomotor recovery from an anoxic coma. Using temporal and spatial genetic targeting, AMPK in the fat body was found to contribute to starvation-induced fast locomotor recovery, whereas, under fed conditions, disrupting AMPK in oenocytes prolongs recovery. By evaluating spreading depolarization in the fly brain during anoxia, AMPK activation was shown to reduce the severity of ionic disruption and prolongs recovery of electrical activity. Further genetic targeting indicates that glial, but not neuronal, AMPK affects locomotor recovery. Together, these findings support a model in which AMPK is neuroprotective in Drosophila.
Hussain, R., Shaukat, Z., Khan, M., Saint, R. and Gregory, S. L. (2017). Phosphoenolpyruvate carboxykinase maintains glycolysis-driven growth in Drosophila tumors. Sci Rep 7(1): 11531. PubMed ID: 28912546
Summary:
Tumors frequently fail to pass on all their chromosomes correctly during cell division, and this chromosomal instability (CIN) causes irregular aneuploidy and oxidative stress in cancer cells. This study's objective was to test knockdowns of metabolic enzymes in Drosophila to find interventions that could exploit the differences between normal and CIN cells to block CIN tumor growth without harming the host animal. Depleting by RNAi or feeding the host inhibitors against phosphoenolpyruvate carboxykinase (PEPCK) was able to block the growth of CIN tissue in a brat tumor explant model. Increasing NAD+ or oxidising cytoplasmic NADH was able to rescue the growth of PEPCK depleted tumors, suggesting a problem in clearing cytoplasmic NADH. Consistent with this, blocking the glycerol-3-phosphate shuttle blocked tumor growth, as well as lowering ROS levels. This work suggests that proliferating CIN cells are particularly vulnerable to inhibition of PEPCK, or its metabolic network, because of their compromised redox status.

Wednesday, November 1st

Nagel, A. C., Auer, J. S., Schulz, A., Pfannstiel, J., Yuan, Z., Collins, C. E., Kovall, R. A. and Preiss, A. (2017). Phosphorylation of Suppressor of Hairless impedes its DNA-binding activity. Sci Rep 7(1): 11820. PubMed ID: 28928428
Summary:
Notch signalling activity governs cellular differentiation in higher metazoa, where Notch signals are transduced by the transcription factor CSL, called Suppressor of Hairless [Su(H)] in Drosophila. Su(H) operates as molecular switch on Notch target genes: within activator complexes, including intracellular Notch, or within repressor complexes, including the antagonist Hairless. Mass spectrometry identified phosphorylation on Serine 269 in Su(H), potentially serving as a point of cross-regulation by other signalling pathways were generated. To address the biological significance, phospho-deficient [Su(H)S269A] and phospho-mimetic [Su(H)S269D] variants were generated: the latter displayed reduced transcriptional activity despite unaltered protein interactions with co-activators and -repressors. Based on the Su(H) structure, Ser269 phosphorylation may interfere with DNA-binding, which was confirmed by electro-mobility shift assay and isothermal titration calorimetry. Overexpression of Su(H)S269D during fly development demonstrated reduced transcriptional regulatory activity, similar to the previously reported DNA-binding defective mutant Su(H)R266H. As both are able to bind Hairless and Notch proteins, Su(H)S269D and Su(H)R266H provoked dominant negative effects upon overexpression. These data imply that Ser269 phosphorylation impacts Notch signalling activity by inhibiting DNA-binding of Su(H), potentially affecting both activation and repression. Ser269 is highly conserved in vertebrate CSL homologues, opening the possibility of a general and novel mechanism of modulating Notch signalling activity.
Khoshnood, B., Dacklin, I. and Grabbe, C. (2017). A proteomics approach to identify targets of the ubiquitin-like molecule Urm1 in Drosophila melanogaster. PLoS One 12(9): e0185611. PubMed ID: 28953965
Summary:
By covalently conjugating to target proteins, ubiquitin-like modifiers (UBLs) act as important regulators of target protein localization and activity. The most ancient and one of the least studied UBLs is Urm1, a dual-function protein that in parallel to performing similar functions as its prokaryotic ancestors in tRNA modification. Affinity purification followed by mass spectrometry were used to identify putative targets of Urm1 conjugation (urmylation) at three developmental stages of the Drosophila melanogaster lifecycle. Altogether 79 Urm1-interacting proteins were recovered in Drosophila, which include the already established Urm1 binding partners Prx5 and Uba4, together with 77 candidate urmylation targets that are completely novel in the fly. Among these, the majority was exclusively identified during either embryogenesis, larval stages or in adult flies. Biochemical evidence is presented that four of these proteins are covalently conjugated by Urm1, whereas the fifth verified Urm1-binding protein appears to interact with Urm1 via non-covalent means. Besides recapitulating the previously established roles of Urm1 in tRNA modification and during oxidative stress, functional clustering of the newly identified Urm1-associated proteins further positions Urm1 in protein networks that control other types of cellular stress, such as immunological threats and DNA damage. In addition, the functional characteristics of several of the candidate targets strongly match the phenotypes displayed by Urm1n123 null animals, including embryonic lethality, reduced fertility and shortened lifespan. In conclusion, this identification of candidate targets of urmylation significantly increases the knowledge of Urm1 and presents an excellent starting point for unravelling the role of Urm1 in the context of a complex living organism.
Martin, R., Pinal, N. and Morata, G. (2017). Distinct regenerative potential of trunk and appendages of Drosophila mediated by JNK signalling. Development. PubMed ID: 28935711
Summary:
The Drosophila body comprises a central part, the trunk, and outgrowths of the trunk, the appendages. Much is known about appendage regeneration, but little about the trunk. As the wing imaginal disc contains a trunk component, the notum, and a wing appendage, this study has investigated the response to ablation of these two components. In contrast with the strong regenerative response of the wing, the notum does not regenerate. Nevertheless, the elimination of the wing primordium elicits a proliferative response of notum cells, but they do not regenerate wing; they form a notum duplicate. Conversely, the wing cells cannot regenerate an ablated notum; they over-proliferate and generate a hinge overgrowth. These results suggest that trunk and appendages cannot be reprogrammed to generate each other. These experiments demonstrate that the proliferative response is mediated by JNK signalling from dying cells, but JNK functions differently in the trunk and the appendages, explaining their distinct regenerative potential.
Kulaberoglu, et al. (2017). Stable MOB1 interaction with Hippo/MST is not essential for development and tissue growth control. Nat Commun 8(1): 695. PubMed ID: 28947795
Summary:
The Hippo tumor suppressor pathway is essential for development and tissue growth control, encompassing a core cassette consisting of the Hippo (MST1/2), Warts (LATS1/2), and Tricornered (NDR1/2) kinases together with MOB1 as an important signaling adaptor. This study reports the crystal structure of the MOB1/NDR2 complex and define key MOB1 residues mediating MOB1's differential binding to Hippo core kinases, thereby establishing MOB1 variants with selective loss-of-interaction. By studying these variants in human cancer cells and Drosophila, it was uncovered that MOB1/Warts binding is essential for tumor suppression, tissue growth control, and development, while stable MOB1/Hippo binding is dispensable and MOB1/Trc binding alone is insufficient. Collectively, this study decrypts molecularly, cell biologically, and genetically the importance of the diverse interactions of Hippo core kinases with the pivotal MOB1 signal transducer. The Hippo tumor suppressor pathway is essential for development and tissue growth control. This study employs a multi-disciplinary approach to characterize the interactions of the three Hippo kinases with the signaling adaptor MOB1 and show how they differently affect development, tissue growth and tumor suppression.
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