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





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Saturday, October 31st, 2015

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Pan, L., Xie, W., Li, K.L., Yang, Z., Xu, J., Zhang, W., Liu, L.P., Ren, X., He, Z., Wu, J., Sun, J., Wei, H.M., Wang, D., Xie, W., Li, W., Ni, J.Q. and Sun, F.L. (2015). Heterochromatin remodeling by CDK12 contributes to learning in Drosophila. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 26508632
Summary:
Dynamic regulation of chromatin structure is required to modulate the transcription of genes in eukaryotes. However, the factors that contribute to the plasticity of heterochromatin structure are elusive. This study reports that cyclin-dependent kinase 12 (CDK12), a transcription elongation-associated RNA polymerase II (RNAPII) kinase, antagonizes heterochromatin enrichment in Drosophila chromosomes. Notably, loss of CDK12 induces the ectopic accumulation of heterochromatin protein 1 (HP1) on euchromatic arms, with a prominent enrichment on the X chromosome. Furthermore, ChIP and sequencing analysis reveals that the heterochromatin enrichment on the X chromosome mainly occurs within long genes involved in neuronal functions. Consequently, heterochromatin enrichment reduces the transcription of neuronal genes in the adult brain and results in a defect in Drosophila courtship learning. Taken together, these results define a previously unidentified role of CDK12 in controlling the epigenetic transition between euchromatin and heterochromatin and suggest a chromatin regulatory mechanism in neuronal behaviors.

Ryu, T., Spatola, B., Delabaere, L., Bowlin, K., Hopp, H., Kunitake, R., Karpen, G.H. and Chiolo, I. (2015). Heterochromatic breaks move to the nuclear periphery to continue recombinational repair. Nat Cell Biol [Epub ahead of print]. PubMed ID: 26502056
Summary:
Heterochromatin mostly comprises repeated sequences prone to harmful ectopic recombination during double-strand break (DSB) repair. In Drosophila cells, 'safe' homologous recombination (HR) repair of heterochromatic breaks relies on a specialized pathway that relocalizes damaged sequences away from the heterochromatin domain before strand invasion. This study shows that heterochromatic DSBs move to the nuclear periphery to continue HR repair. Relocalization depends on nuclear pores and inner nuclear membrane proteins (INMPs) that anchor repair sites to the nuclear periphery through the Smc5/Smc6-interacting proteins STUbL/RENi. Both the initial block to HR progression inside the heterochromatin domain, and the targeting of repair sites to the nuclear periphery, rely on SUMO and SUMO E3 ligases. This study reveals a critical role for SUMOylation in the spatial and temporal regulation of HR repair in heterochromatin, and identifies the nuclear periphery as a specialized site for heterochromatin repair in a multicellular eukaryote.

Abramov, Y.A., Shatskikh, A.S., Maksimenko, O.G., Bonaccorsi, S., Gvozdev, V.A. and Lavrov, S.A. (2015). The differences between cis- and trans- gene inactivation caused by heterochromatin in Drosophila. Genetics [Epub ahead of print]. PubMed ID: 26500261
Summary:
Position effect variegation (PEV) is the epigenetic disruption of gene expression near the de novo formed eu-heterochromatin border. Heterochromatic cis-inactivation may be accompanied by the trans-inactivation of genes on a normal homologous chromosome in trans-heterozygous combination with a PEV-inducing rearrangement. This study characterized a new genetic system, inversion In(2)A4, demonstrating cis-acting PEV as well as trans-inactivation of the reporter transgenes on the homologous non-rearranged chromosome. The cis-effect of heterochromatin in the inversion results not only in repression but also in activation of genes, and it varies at different developmental stages. While cis-actions affect only a few juxtaposed genes, trans-inactivation is observed in 500 kb region and demonstrates а non-uniform pattern of repression with intermingled regions where no transgene repression occurs. There is no repression around the histone gene cluster and in some other euchromatic sites. Trans-inactivation is accompanied by dragging of euchromatic regions into the heterochromatic compartment, but the histone gene cluster, located in the middle of the trans-inactivated region, was shown to be evicted from the heterochromatin. Trans-inactivation is followed by de novo HP1a accumulation in the affected transgene; trans-inactivation is specifically favored by the chromatin remodeler SAYP and prevented by Argonaute AGO2.

Dias, G. B., Heringer, P., Svartman, M. and Kuhn, G. C. (2015). Helitrons shaping the genomic architecture of Drosophila: enrichment of DINE-TR1 in alpha- and beta-heterochromatin, satellite DNA emergence, and piRNA expression. Chromosome Res [Epub ahead of print]. PubMed ID: 26408292
Summary:
Drosophila INterspersed Elements (DINEs) constitute an abundant but poorly understood group of Helitrons present in several Drosophila species. The general structure of DINEs includes two conserved blocks that may or not contain a region with tandem repeats in between. These central tandem repeats (CTRs) are similar within species but highly divergent between species. This study identified a subset of DINEs, termed DINE-TR1, which contain homologous CTRs of approximately 150 bp. DINE-TR1 are found in the sequenced genomes of several Drosophila species. However, interspecific high sequence identity (~88%) is limited to the first approximately 30 bp of each tandem repeat. Sequence analysis suggests vertical transmission. CTRs found within DINE-TR1 have independently expanded into satellite DNA-like arrays at least twice within Drosophila. By analyzing the genome of Drosophila virilis and Drosophila americana, it was shown that DINE-TR1 is highly abundant in pericentromeric heterochromatin boundaries, some telomeric regions and in the Y chromosome. It is also present in the centromeric region of one autosome from D. virilis and dispersed throughout several euchromatic sites in both species. DINE-TR1 was found to be abundant at piRNA clusters, and small DINE-TR1-derived RNA transcripts (~25 nt) are predominantly expressed in the testes and the ovaries, suggesting active targeting by the piRNA machinery. These features suggest potential piRNA-mediated regulatory roles for DINEs at local and genome-wide scales in Drosophila.

Friday, October 30th

Hudson, A. M., Mannix, K. M. and Cooley, L. (2015). Actin cytoskeletal organization in Drosophila germline ring canals depends on Kelch function in a Cullin-RING E3 ligase. Genetics [Epub ahead of print]. PubMed ID: 26384358
Summary:
The Drosophila Kelch protein is required to organize the ovarian ring canal cytoskeleton. Kelch binds and crosslinks F-actin in vitro, and it also functions with Cullin 3 (Cul3) as a component of a ubiquitin E3 ligase. How these two activities contribute to cytoskeletal remodeling in vivo is not known. This study used targeted mutagenesis to investigate the mechanism of Kelch function. A model was tested in which Cul3-dependent degradation of Kelch is required for its function, but no evidence was found to support this hypothesis. However, mutant Kelch deficient in its ability to interact with Cul3 failed to rescue the kelch cytoskeletal defects, suggesting that ubiquitin ligase activity is the principal activity required in vivo. It was also determined that the proteasome is required with Kelch to promote the ordered growth of the ring canal cytoskeleton. These results indicate that Kelch organizes the cytoskeleton in vivo by targeting a protein substrate for degradation by the proteasome.

Khuc Trong, P., Doerflinger, H., Dunkel, J., St Johnston, D. and Goldstein, R.E. (2015). Cortical microtubule nucleation can organise the cytoskeleton of Drosophila oocytes to define the anteroposterior axis. Elife 4. PubMed ID: 26406117
Summary:
Many cells contain non-centrosomal arrays of microtubules (MTs), but the assembly, organisation and function of these arrays are poorly understood. This study presents the first theoretical model for the non-centrosomal MT cytoskeleton in Drosophila oocytes, in which bicoid and oskar mRNAs become localised to establish the anterior-posterior body axis. Constrained by experimental measurements, the model shows that a simple gradient of cortical MT nucleation is sufficient to reproduce the observed MT distribution, cytoplasmic flow patterns and localisation of oskar and naive bicoid mRNAs. These simulations exclude a major role for cytoplasmic flows in localisation and reveal an organisation of the MT cytoskeleton that is more ordered than previously thought. Furthermore, modulating cortical MT nucleation induces a bifurcation in cytoskeletal organisation that accounts for the phenotypes of polarity mutants. Thus, this study's three-dimensional model explains many features of the MT network and highlights the importance of differential cortical MT nucleation for axis formation.

Trogden, K. P. and Rogers, S. L. (2015). TOG proteins are spatially regulated by Rac-GSK3β to control interphase microtubule dynamics. PLoS One 10: e0138966. PubMed ID: 26406596
Summary:
Microtubules are regulated by a diverse set of proteins that localize to microtubule plus ends (+TIPs) where they regulate dynamic instability and mediate interactions with the cell cortex, actin filaments, and organelles. Although individual +TIPs have been studied in depth and their basic contributions to microtubule dynamics are understood, there is a growing body of evidence that these proteins exhibit cross-talk and likely function to collectively integrate microtubule behavior and upstream signaling pathways. This study have identified a novel protein-protein interaction between the XMAP215 homologue in Drosophila, Mini spindles (Msps), and the CLASP homologue, Orbit. These proteins have been shown to promote and suppress microtubule dynamics, respectively. Microtubule dynamics are regionally controlled in cells by Rac acting to suppress GSK3β in the peripheral lamellae/lamellipodium. Phosphorylation of Orbit by GSK3β triggers a relocalization of Msps from the microtubule plus end to the lattice. Mutation of the Msps-Orbit binding site revealed that this interaction is required for regulating microtubule dynamic instability in the cell periphery. Based on these findings, it is proposed that Msps is a novel Rac effector that acts, in partnership with Orbit, to regionally regulate microtubule dynamics.

Radford, S. J., Hoang, T. L., Gluszek, A. A., Ohkura, H. and McKim, K. S. (2015). Lateral and end-on kinetochore attachments are coordinated to achieve bi-orientation in Drosophila oocytes. PLoS Genet 11: e1005605. PubMed ID: 26473960
Summary:
In oocytes, where centrosomes are absent, the chromosomes direct the assembly of a bipolar spindle. Interactions between chromosomes and microtubules are essential for both spindle formation and chromosome segregation. This study examined oocytes lacking two kinetochore proteins, NDC80 and SPC105R, and a centromere-associated motor protein, CENP-E, to characterize the impact of kinetochore-microtubule attachments on spindle assembly and chromosome segregation in Drosophila oocytes. The initiation of spindle assembly was shown to result from chromosome-microtubule interactions that are kinetochore-independent. Stabilization of the spindle, however, depends on both central spindle and kinetochore components. This stabilization coincides with changes in kinetochore-microtubule attachments and bi-orientation of homologs. It is proposed that the bi-orientation process begins with the kinetochores moving laterally along central spindle microtubules towards their minus ends. This movement depends on SPC105R, can occur in the absence of NDC80, and is antagonized by plus-end directed forces from the CENP-E motor. End-on kinetochore-microtubule attachments that depend on NDC80 are required to stabilize bi-orientation of homologs. A surprising finding was that SPC105R but not NDC80 is required for co-orientation of sister centromeres at meiosis I. Together, these results demonstrate that, in oocytes, kinetochore-dependent and -independent chromosome-microtubule attachments work together to promote the accurate segregation of chromosomes.

Thursday, October 29th

Merzetti, E.M. and Staveley, B.E. (2015). spargel, the PGC-1α homologue, in models of Parkinson disease in Drosophila melanogaster. BMC Neurosci 16: 70. PubMed ID: 26502946
Summary:
Parkinson disease (PD) is a progressive neurodegenerative disorder presenting with symptoms of resting tremor, bradykinesia, rigidity, postural instability and additional severe cognitive impairment over time. These symptoms arise from a decrease of available dopamine in the striatum of the brain resulting from the breakdown and death of dopaminergic (DA) neurons. A process implicated in the destruction of these neurons is mitochondrial breakdown and impairment. Upkeep and repair of mitochondria involves a number of complex and key components including Pink1, Parkin, and the PGC family of genes. PGC-1α has been characterized as a regulator of mitochondria biogenesis, insulin receptor signalling and energy metabolism, mutation of this gene has been linked to early onset forms of PD. The mammalian PGC family consists of three partially redundant genes making the study of full or partial loss of function difficult. The sole Drosophila melanogaster homologue of this gene family, spargel (srl), has been shown to function in similar pathways of mitochondrial upkeep and biogenesis. This study shows that the directed expression of srl-RNAi in the D. melanogaster eye causes abnormal ommatidia and bristle formation while eye specific expression of srl-EY does not produce the minor rough eye phenotype associated with high temperature GMR-Gal4 expression. Ddc-Gal4 mediated tissue specific expression of srl transgene constructs in D. melanogaster DA neurons causes altered lifespan and climbing ability. Expression of a srl-RNAi causes an increase in mean lifespan but a decrease in overall loco-motor ability while induced expression of srl-EY causes a severe decrease in mean lifespan and a decrease in loco-motor ability. The reduced lifespan and climbing ability associated with a tissue specific expression of srl in DA neurons provides a new model of PD in D. melanogaster which may be used to identify novel therapeutic approaches to human disease treatment and prevention.

Oswald, M. C., West, R. J., Lloyd-Evans, E. and Sweeney, S. T. (2015). Identification of dietary alanine toxicity and trafficking dysfunction in a Drosophila model of hereditary sensory and autonomic neuropathy type 1. Hum Mol Genet [Epub ahead of print]. PubMed ID: 26395456
Summary:
Hereditary sensory and autonomic neuropathy type 1 (HSAN1) is characterized by a loss of distal peripheral sensory and motorneuronal function, neuropathic pain and tissue necrosis. The most common cause of HSAN1 is due to dominant mutations in serine palmitoyl-transferase subunit 1 (SPT1). SPT catalyses the condensation of serine with palmitoyl-CoA, the initial step in sphingolipid biogenesis. Identified mutations in SPT1 are known to both reduce sphingolipid synthesis and generate catalytic promiscuity, incorporating alanine or glycine into the precursor sphingolipid to generate a deoxysphingoid base (DSB). Why either loss of function in SPT1, or generation of DSBs should generate deficits in distal sensory function remains unclear. To address these questions, a Drosophila model of HSAN1 was generated. Expression of dSpt1 bearing a disease-related mutation induced morphological deficits in synapse growth at the larval neuromuscular junction consistent with a dominant-negative action. Expression of mutant dSpt1 globally was found to be mildly toxic, but was completely toxic when the diet was supplemented with alanine, when DSBs were observed in abundance. Expression of mutant dSpt1 in sensory neurons generated developmental deficits in dendritic arborization with concomitant sensory deficits. A membrane trafficking defect was observed in soma of sensory neurons expressing mutant dSpt1, consistent with endoplasmic reticulum (ER) to Golgi block. It was possible to rescue sensory function in neurons expressing mutant dSpt1 by co-expressing an effector of ER-Golgi function, Rab1 suggesting compromised ER function in HSAN1 affected dendritic neurons. This Drosophila model identifies a novel strategy to explore the pathological mechanisms of HSAN1.

Tran, H., Almeida, S., Moore, J., Gendron, T. F., Chalasani, U., Lu, Y., Du, X., Nickerson, J. A., Petrucelli, L., Weng, Z. and Gao, F. B. (2015). Differential toxicity of nuclear RNA foci versus dipeptide repeat proteins in a Drosophila model of C9ORF72 FTD/ALS. Neuron 87: 1207-1214. PubMed ID: 26402604
Summary:
Dipeptide repeat (DPR) proteins are toxic in various models of Frontotemporal dementia/Amyotrophic Lateral Sclerosis (FTD/ALS) with GGGGCC (G4C2) repeat expansion. However, it is unclear whether nuclear G4C2 RNA foci also induce neurotoxicity. This study describes a Drosophila model expressing 160 G4C2 repeats (160R) flanked by human intronic and exonic sequences. Spliced intronic 160R formed nuclear G4C2 sense RNA foci in glia and neurons about ten times more abundantly than in human neurons; however, they had little effect on global RNA processing and neuronal survival. In contrast, highly toxic 36R in the context of poly(A)(+) mRNA were exported to the cytoplasm, where dipeptide repeat (DPR) proteins were produced at >100-fold higher level than in 160R flies. Moreover, the modest toxicity of intronic 160R expressed at higher temperature correlated with increased DPR production, but not RNA foci. Thus, nuclear RNA foci are neutral intermediates or possibly neuroprotective through preventing G4C2 RNA export and subsequent DPR production.

White, J. A., Anderson, E., Zimmerman, K., Zheng, K. H., Rouhani, R. and Gunawardena, S. (2015). Huntingtin differentially regulates the axonal transport of a sub-set of Rab-containing vesicles in vivo. Hum Mol Genet. PubMed ID: 26450517
Summary:
Loss of huntingtin (HTT), the Huntington's disease (HD) protein, was previously shown to cause axonal transport defects. Within axons, HTT can associate with kinesin-1 and dynein motors either directly or via accessory proteins for bi-directional movement. However, the composition of the vesicle-motor complex that contains HTT during axonal transport is unknown. This study analyzed the in vivo movement of 16 Rab GTPases within Drosophila larval axons and showed that HTT differentially influences the movement of a particular sub-set of these Rab-containing vesicles. While reduction of HTT perturbed the bi-directional motility of Rab3 and Rab19-containing vesicles, only the retrograde motility of Rab7-containing vesicles was disrupted with reduction of HTT. Interestingly, reduction of HTT stimulated the anterograde motility of Rab2-containing vesicles. Simultaneous dual-view imaging revealed that HTT and Rab2, 7 or 19 move together during axonal transport. Collectively, these findings indicate that HTT likely influences the motility of different Rab-containing vesicles and Rab-mediated functions. These findings have important implications for understanding of the complex role HTT plays within neurons normally, which when disrupted may lead to neuronal death and disease.

Wednesday, October 28th

Schmitt, S., Ugrankar, R., Greene, S.E., Prajapati, M. and Lehmann, M. (2015). Drosophila lipin interacts with insulin and TOR signaling pathways in the control of growth and lipid metabolism. J Cell Sci [Epub ahead of print]. PubMed ID: 26490996
Summary:
Lipin proteins have key functions in lipid metabolism, acting as both phosphatidate phosphatases (PAPs) and nuclear regulators of gene expression. This study shows that the insulin and TORC1 pathways independently control functions of Drosophila dLipin. Reduced signaling through the insulin receptor strongly enhances defects caused by dLipin deficiency in fat body development, whereas reduced signaling through TORC1 leads to translocation of dLipin into the nucleus. Reduced expression of dLipin results in decreased signaling through the insulin receptor-controlled PI3K/Akt pathway and increased hemolymph sugar levels. Consistent with this, downregulation of dLipin in fat body cell clones causes a strong growth defect. The PAP, but not the nuclear activity of dLipin is required for normal insulin pathway activity. Reduction of other enzymes of the glycerol-3 phosphate pathway similarly affects insulin pathway activity, suggesting an effect mediated by one or more metabolites associated with the pathway. Together, these data show that dLipin is subject to intricate control by the insulin and TORC1 pathways and that the cellular status of dLipin impacts how fat body cells respond to signals relayed through the PI3K/Akt pathway.

Wang, S. C., Hsu, H. J., Lin, G. W., Wang, T. F., Chang, C. C. and Lin, M. D. (2015). Germ plasm localisation of the HELICc of Vasa in Drosophila: analysis of domain sufficiency and amino acids critical for localisation. Sci Rep 5: 14703. PubMed ID: 26419889
Summary:
Formation of the germ plasm drives germline specification in Drosophila and some other insects such as aphids. Identification of the DEAD-box protein Vasa (Vas) as a conserved germline marker in flies and aphids suggests that they share common components for assembling the germ plasm. However, to which extent the assembly order is conserved and the correlation between functions and sequences of Vas remain unclear. Ectopic expression of the pea aphid Vas (ApVas1) in Drosophila did not drive its localisation to the germ plasm, but ApVas1 with a replaced C-terminal domain (HELICc) of Drosophila Vas (DmVas) became germ-plasm restricted. HELICc itself, through the interaction with Oskar (Osk), was sufficient for germ-plasm localisation. Similarly, HELICc of the grasshopper Vas could be recruited to the germ plasm in Drosophila. Nonetheless, germ-plasm localisation was not seen in the Drosophila oocytes expressing HELICcs of Vas orthologues from aphids, crickets, and mice. Glutamine (Gln) 527 within HELICc of DmVas was identified as critical for localisation, and its corresponding residue could also be detected in grasshopper Vas yet missing in the other three species. This suggests that Gln527 is a direct target of Osk or critical to the maintenance of HELICc conformation.

Sun, S., Reddy, B. V. and Irvine, K. D. (2015). Localization of Hippo signalling complexes and Warts activation in vivo. Nat Commun 6: 8402. PubMed ID: 26420589
Summary:
Hippo signalling controls organ growth and cell fate by regulating the activity of the kinase Warts. Multiple Hippo pathway components localize to apical junctions in epithelial cells, but the spatial and functional relationships among components have not been clarified, nor is it known where Warts activation occurs. This study reports that Hippo pathway components in Drosophila wing imaginal discs are organized into distinct junctional complexes, including separate distributions for Salvador, Expanded, Warts and Hippo. These complexes are reorganized on Hippo pathway activation, when Warts shifts from associating with its inhibitor Jub to its activator Expanded, and Hippo concentrates at Salvador sites. This study identify mechanisms promoting Warts relocalization, and using a phospho-specific antisera and genetic manipulations, where Warts activation occurs was identified: at apical junctions where Expanded, Salvador, Hippo and Warts overlap. These observations define spatial relationships among Hippo signalling components and establish the functional importance of their localization to Warts activation.

Zhou, Z., Yao, X., Li, S., Xiong, Y., Dong, X., Zhao, Y., Jiang, J. and Zhang, Q. (2015). Deubiquitination of Ci/Gli by Usp7/HAUSP Regulates Hedgehog Signaling. Dev Cell 34: 58-72. PubMed ID: 26120032
Summary:
Hedgehog (Hh) signaling plays essential roles in animal development and tissue homeostasis, and its misregulation causes congenital diseases and cancers. Regulation of the ubiquitin/proteasome-mediated proteolysis of Ci/Gli transcription factors is central to Hh signaling, but whether deubiquitinase is involved in this process remains unknown. This study shows that Hh stimulates the binding of a ubiquitin-specific protease Usp7 to Ci, which positively regulates Hh signaling activity through inhibiting Ci ubiquitination and degradation mediated by both Slimb-Cul1 and Hib-Cul3 E3 ligases. Furthermore, Usp7 forms a complex with GMP-synthetase (GMPS) to promote Hh pathway activity. Finally, it was shown that the mammalian counterpart of Usp7, HAUSP, positively regulates Hh signaling by modulating Gli ubiquitination and stability. These findings reveal a conserved mechanism by which Ci/Gli is stabilized by a deubiquitination enzyme and identify Usp7/HUASP as a critical regulator of Hh signaling and potential therapeutic target for Hh-related cancers.

Tuesday, October 27th

Picao-Osorio, J., Johnston, J., Landgraf, M., Berni, J. and Alonso, C.R. (2015). MicroRNA-encoded behavior in Drosophila. Science [Epub ahead of print]. PubMed ID: 26494171
Summary:
The relationship between microRNA regulation and the specification of behavior is only beginning to be explored. This study finds that mutation of a single microRNA locus (miR-iab4/8) in Drosophila larvae affects the animal's capacity to correct its orientation if turned upside-down (self-righting). One of the microRNA targets involved in this behavior is the Hox gene Ultrabithorax whose derepression in two metameric neurons leads to self-righting defects. In vivo neural activity analysis reveals that these neurons, the self-righting node (SRN), have different activity patterns in wild type and miRNA mutants while thermogenetic manipulation of SRN activity results in changes in self-righting behavior. These data thus reveal a microRNA-encoded behavior and suggests that other microRNAs might also be involved in behavioral control in Drosophila and other species.

Du, E. J., Ahn, T. J., Choi, M. S., Kwon, I., Kim, H. W., Kwon, J. Y. and Kang, K. (2015). The mosquito repellent citronellal directly potentiates Drosophila TRPA1, facilitating feeding suppression. Mol Cells [Epub ahead of print]. PubMed ID: 26447139
Summary:
Citronellal, a well-known plant-derived mosquito repellent, was previously reported to repel Drosophila melanogaster via olfactory pathways involving but not directly activating Transient Receptor Potential Ankyrin 1 (TRPA1). This study show that citronellal is a direct agonist for Drosophila and human TRPA1s (dTRPA1 and hTRPA1) as well as Anopheles gambiae TRPA1 (agTRPA1). Citronellal-induced activity is isoform-dependent for Drosophila and Anopheles gambiae TRPA1s. The recently identified dTRPA1(A) and agTRPA1(A) isoforms showed citronellal-provoked currents with EC50s of 1.0 +/- 0.2 and 0.1 +/- 0.03 mM, respectively, in Xenopus oocytes, while the sensitivities of TRPA1(B)s were much inferior to those of TRPA1(A)s. Citronellal dramatically enhanced the feeding-inhibitory effect of the TRPA1 agonist N-methylmaleimide (NMM) in Drosophila at an NMM concentration that barely repels flies. Thus, citronellal can promote feeding deterrence of fruit flies through direct action on gustatory dTRPA1, revealing the first isoform-specific function for TRPA1(A).

Scheidler, N. H., Liu, C., Hamby, K. A., Zalom, F. G. and Syed, Z. (2015). Volatile codes: Correlation of olfactory signals and reception in Drosophila-yeast chemical communication. Sci Rep 5: 14059. PubMed ID: 26391997
Summary:
Drosophila have evolved strong mutualistic associations with yeast communities that best support their growth and survival, resulting in the development of novel niches. It has been suggested that flies recognize their cognate yeasts primarily based on the rich repertoire of volatile organic compounds (VOCs) derived from the yeasts. Thus, it remained an exciting avenue to study whether fly species detect and discriminate yeast strains based on odor alone, and if so, how such resolution is achieved by the olfactory system in flies. This study used two fly species known to exploit different niches and harboring different yeasts, D. suzukii (a pest of fresh fruit) and D. melanogaster (a saprophytic fly and a neurogenetic model organism). It was initially established the behavioral preference of both fly species to six Drosophila-associated yeasts; then the VOC profile of each yeast esd chemically analyzed, revealing quantitative and qualitative differences; and finally the physiologically active constituents was isolated and identified from yeast VOCs for each drosophilid that potentially define attraction. By employing chemical, behavioral, and electrophysiological analyses, a comprehensive portrait was provided of the olfactory neuroethological correlates underlying fly-yeast coadaptation in two drosophilids with distinct habitats.

Lam, S. S. and Howell, K. S. (2015). Drosophila-associated yeast species in vineyard ecosystems. FEMS Microbiol Lett 362. PubMed ID: 26391524
Summary:
Yeast activity during wine fermentation directly contributes to wine quality, but the source and movement of yeasts in vineyards and winery environments have not been resolved. This study investigated the yeast species associated with the Drosophila insect vector to help understand yeast dispersal and persistence. Drosophila are commonly found in vineyards and are known to have a mutualistic relationship with yeasts in other ecosystems. Drosophilids were collected from vineyards, grape waste (marc) piles and wineries during grape harvest. Captured flies were identified morphologically, and their associated yeasts were identified. Drosophila melanogaster/D. simulans, D. hydei and Scaptodrosophila lativittata were identified in 296 captured Drosophila flies. These flies were associated with Metschnikowia pulcherrima, Hanseniaspora uvarum, Torulaspora delbrueckii and H. valbyensis yeasts. Yeast and Drosophila species diversity differed between collection locations (vineyard and marc: R = 0.588 for Drosophila and R = 0.644 for yeasts). Surprisingly, the primary wine fermentation yeast, Saccharomyces cerevisiae, was not isolated. Drosophila flies are preferentially associated with different yeast species in the vineyard and winery environments, and this association may help the movement and dispersal of yeast species in the vineyard and winery ecosystem.

Monday, October 26th

Vallejo, D.M., Juarez-Carreño, S., Bolivar, J., Morante, J. and Dominguez, M. (2015). A brain circuit that synchronizes growth and maturation revealed through Dilp8 binding to Lgr3. Science [Epub ahead of print]. PubMed ID: 26429885
Summary:
Body size constancy and symmetry are signs of developmental stability. Yet, it is unclear exactly how developing animals buffer size variation. Drosophila insulin-like peptide Dilp8 is responsive to growth perturbations and controls homeostatic mechanisms that co-ordinately adjust growth and maturation to maintain size within the normal range. This study shows that Lgr3 is a Dilp8 receptor. By functional and cAMP assays, a pair of Lgr3 neurons were found to mediate the homeostatic regulation. These neurons have extensive axonal arborizations, and genetic and GFP reconstitution across synaptic partners (GRASP) show these neurons connect with the insulin-producing cells and PTTH-producing neurons to attenuate growth and maturation. This previously unrecognized circuit suggests how growth and maturation rate are matched and co-regulated according to Dilp8 signals to stabilize organismal size.

Brigui, A., Hofmann, L., Arguelles, C., Sanial, M., Holmgren, R. A. and Plessis, A. (2015). Control of the dynamics and homeostasis of the Drosophila Hedgehog receptor Patched by two C2-WW-HECT-E3 Ubiquitin ligases. Open Biol 5. PubMed ID: 26446620
Summary:
The conserved Hedgehog (HH) signals control animal development, adult stem cell maintenance and oncogenesis. In Drosophila, the HH co-receptor Patched (PTC) controls both HH gradient formation and signalling. PTC is post-translationally downregulated by HH, which promotes its endocytosis and destabilization, but the mechanisms of PTC trafficking and its importance in the control of PTC remain to be understood. PTC interacts with E3 Ubiquitin (UB)-ligases of the C2-WW-HECT family; two of them-SMURF and NEDD4-are known to regulate its levels. Mutation of the PTC PY motif, which mediates binding of C2-WW-HECT family members, inhibits its internalization but not its autonomous and non-autonomous signalling activities. In addition, the two related UB-C2-WW-HECT ligases NEDD4 and SU(DX) regulate PTC trafficking and finely tune its accumulation through partially redundant but distinct functions. While both NEDD4 and SU(DX) promote PTC endocytosis, only SU(DX) is able to induce its lysosomal targeting and degradation. In conclusion, PTC trafficking and homeostasis are tightly regulated by a family of UB-ligases.

Guntur, A. R., Gu, P., Takle, K., Chen, J., Xiang, Y. and Yang, C. H. (2015). Drosophila TRPA1 isoforms detect UV light via photochemical production of H2O2. Proc Natl Acad Sci U S A 112: E5753-5761. PubMed ID: 26443856
Summary:
The transient receptor potential A1 (TRPA1) channel is an evolutionarily conserved detector of temperature and irritant chemicals. This study shows that two specific isoforms of TRPA1 in Drosophila are H2O2 sensitive and that they can detect strong UV light via sensing light-induced production of H2O2. Ectopic expression of these H2O2-sensitive Drosophila TRPA1 (dTRPA1) isoforms conferred UV sensitivity to light-insensitive HEK293 cells and Drosophila neurons, whereas expressing the H2O2-insensitive isoform did not. Curiously, when expressed in one specific group of motor neurons in adult flies, the H2O2-sensitive dTRPA1 isoforms were as competent as the blue light-gated channelrhodopsin-2 in triggering motor output in response to light. Corpus cardiacum (CC) cells, a group of neuroendocrine cells that produce the adipokinetic hormone (AKH) in the larval ring gland endogenously express these H2O2-sensitive dTRPA1 isoforms; they are UV sensitive. Sensitivity of CC cells required dTRPA1 and H2O2 production but not conventional phototransduction molecules. Thsese results suggest that specific isoforms of dTRPA1 can sense UV light via photochemical production of H2O2. It is speculated that UV sensitivity conferred by these isoforms in CC cells may allow young larvae to activate stress response-a function of CC cells-when they encounter strong UV, an aversive stimulus for young larvae.

Kumar, S. R., Patel, H. and Tomlinson, A. (2015). Wingless mediated apoptosis: How cone cells direct the death of peripheral ommatidia in the developing Drosophila eye. Dev Biol [Epub ahead of print]. PubMed ID: 26428511
Summary:
Morphogen gradients play pervasive roles in development, and understanding how they are established and decoded is a major goal of contemporary developmental biology. This study examined how a Wingless (Wg) morphogen gradient patterns the peripheral specialization of the fly eye. The outermost specialization is the pigment rim; a thick band of pigment cells that circumscribes the eye and optically insulates the sides of the retina. It results from the coalescence of pigment cells that survive the death of the outermost row of developing ommatidia. This study investigated here how the Wg target genes expressed in the moribund ommatidia direct the intercellular signaling, the morphogenetic movements, and ultimately the ommatidial death. A salient feature of this process is the secondary expression of the Wg morphogen elicited in the ommatidia by the primary Wg signal. Neither the primary nor secondary sources of Wg alone are able to promote ommatidial death, but together they suffice to drive the apoptosis. This represents an unusual gradient read-out process in which a morphogen induces its own expression in its target cells to generate a concentration spike required to push the local cellular responses to the next threshold response.

Sunday, October 25th

Praxenthaler, H., Smylla, T. K., Nagel, A. C., Preiss, A. and Maier, D. (2015). Generation of new hairless alleles by genomic engineering at the Hairless locus in Drosophila melanogaster.. PLoS One 10: e0140007. PubMed ID: 26448463
Summary:
Hairless (H) is the major antagonist within the Notch signalling pathway of Drosophila melanogaster. By binding to Suppressor of Hairless [Su(H)] and two co-repressors, H induces silencing of Notch target genes in the absence of Notch signals. We have applied genomic engineering to create several new H alleles. To this end the endogenous H locus was replaced with an attP site by homologous recombination, serving as a landing platform for subsequent site directed integration of different H constructs. This way a complete H knock out allele HattP was generated, reintroduced a wild type H genomic and a cDNA-construct (Hgwt, Hcwt) as well as two constructs encoding H proteins defective of Su(H) binding (HLD, HiD). Phenotypes regarding viability, bristle and wing development were recorded, and the expression of Notch target genes wingless and cut was analysed in mutant wing discs or in mutant cell clones. Moreover, genetic interactions with Notch (N5419) and Delta (DlB2) mutants were addressed. Overall, phenotypes were largely as expected: both HLD and HiD were similar to the HattP null allele, indicating that most of H activity requires the binding of Su(H). Both rescue constructs Hgwt and Hcwt were homozygous viable without phenotype. Unexpectedly, the hemizygous condition uncovered that they were not identical to the wild type allele: notably Hcwt showed a markedly reduced activity, suggesting the presence of as yet unidentified regulatory or stabilizing elements in untranslated regions of the H gene. Interestingly, Hgwt homozygous cells expressed higher levels of H protein, perhaps unravelling gene-by-environment interactions.

Huu, N.T., Yoshida, H. and Yamaguchi, M. (2015). Tumor suppressor gene OSCP1/NOR1 regulates apoptosis, proliferation, differentiation, and ROS generation during eye development of Drosophila melanogaster. FEBS J [Epub ahead of print]. PubMed ID: 26411401
Summary:
OSCP1/NOR1 (Organic solute carrier partner 1/Oxidored-nitro domain-containing protein 1) is a known tumor suppressor protein. OSCP1 has been reported to mediate transport of various organic solutes into cells, however its role during development has not yet been addressed. This study reports the results of studies with dOSCP1 (the Drosophila orthologue of hOSCP1) knockdown flies to elucidate the role of OSCP1/NOR1 during development. Knockdown of dOSCP1 in the eye imaginal discs induces a rough eye phenotype in adult flies. This phenotype results from an induction of caspase-dependent apoptosis followed by a compensatory proliferation and ROS generation in eye imaginal discs. The induction of apoptosis appears to be associated with down-regulation of the anti-apoptotic Buffy gene and up-regulation of the pro-apoptotic Debcl gene. These effects of knockdown of dOSCP1 lead to mitochondrial fragmentation, degradation, and a shortfall in ATP production. It was also found that knockdown of dOSCP1 causes a defect in the cone cell and pigment cell differentiation of pupal retinae. Moreover, mutations in EGFR pathway-related genes, such as Spitz and Drk enhance the rough eye phenotype induced by dOSCP1-knockdown. These results suggest that dOSCP1 positively regulates EGFR signaling pathway. Overall these findings indicate that dOSCP1 plays multiple roles during eye development of Drosophila

Yan, Y., Wang, H., Chen, H., Lindström-Battle, A. and Jiao, R. (2015). Ecdysone and insulin signaling play essential roles in readjusting the altered body size caused by the dGPAT4 mutation in Drosophila. J Genet Genomics 42: 487-494. PubMed ID: 26408093
Summary:
The ability of the animals to develop into a normal-sized adult after the challenges of genetic alterations and/or environmental stresses reveals a robustness of body size control. This study shows that the mutation of dGPAT4, a de novo synthase of lysophosphatidic acid, is a genetic alteration that triggers such a robust response of the animals to body size challenges in Drosophila. Loss of dGPAT4 leads to a severe delay of development, slow growth and resultant small-sized animals during the larval stages, but results in normal-sized adult flies. The robust body size adjustment of the dGPAT4 mutant is likely achieved by corresponding changes in ecdysone and insulin signaling, which is also manifested by compromised food intake. Thus, the study proposes that a strategy has been evolved by the animals to reach final body size when challenged by genetic alterations, which requires the coordinated ecdysone and insulin signaling

Sobala, L. F., Wang, Y. and Adler, P. N. (2015). ChtVis-Tomato, a genetic reporter for in vivo visualization of chitin deposition in Drosophila. Development [Epub ahead of print]. PubMed ID: 26395478
Summary:
Chitin is a polymer of N-acetylglucosamine that is abundant and widely found in the biological world. It is an important constituent of the cuticular exoskeleton that plays such key role in the insect life style. A limitation in the study of chitin deposition during cuticle formation has been the lack of a way to detect it in living organisms. To get around this, ChtVis-Tomato, an in vivo reporter for chitin was developed in Drosophila. ChtVis-Tomato encodes a fusion protein that contains an apical secretion signal, a chitin binding domain, a fluorescent protein and a cleavage site to release it from the plasma membrane. The chitin reporter facilitates study of chitin deposition in time lapse experiments, and using it unexpected deposits of chitin fibers were identified in Drosophila pupae. Cht-Vis-Tomato should facilitate future studies on chitin in Drosophila and other insects.

Saturday, October 24th

Natarajan, R., Barber, K., Buckley, A., Cho, P., Egbejimi, A. and Wairkar, Y. P. (2015). Tricornered kinase regulates synapse development by regulating the levels of Wiskott-Aldrich Syndrome protein. PLoS One 10: e0138188. PubMed ID: 26393506
Summary:
Precise regulation of synapses during development is essential to ensure accurate neural connectivity and function of nervous system. mTOR, a kinase, is shared between two functionally distinct multi-protein complexes- mTORC1 and mTORC2, that act downstream of Tuberous Sclerosis Complex (TSC). Studies have suggested an important role for TSC in synapse development at the Drosophila neuromuscular junction (NMJ) synapses. In addition, the data suggested that the regulation of the NMJ synapse numbers in Drosophila largely depends on signaling via mTORC2. In the present study, this observation was furthered by identifying Tricornered (Trc) kinase, a serine/threonine kinase as a likely mediator of TSC signaling. trc genetically interacts with Tsc2 to regulate the number of synapses. In addition, Tsc2 and trc mutants exhibit a dramatic reduction in synaptic levels of WASP, an important regulator of actin polymerization. Trc regulates the WASP levels largely, by regulating the transcription of WASP. Finally, this study shows that overexpression of WASP (Wiskott-Aldrich Syndrome Protein) in trc mutants can suppress the increase in the number of synapses observed in trc mutants, suggesting that WASP regulates synapses downstream of Trc. Thus, these data provide a novel insight into how Trc may regulate the genetic program that controls the number of synapses during development.

Hasanagic, M., van Meel, E., Luan, S., Aurora, R., Kornfeld, S. and Eissenberg, J. C. (2015). The lysosomal enzyme receptor protein (LERP) is not essential, but is implicated in lysosomal function in Drosophila melanogaster. Biol Open. PubMed ID: 26405051
Summary:
The lysosomal enzyme receptor protein (LERP) of Drosophila is the ortholog of the mammalian cation-independent mannose 6-phosphate (Man 6-P) receptor, which mediates trafficking of newly synthesized lysosomal acid hydrolases to lysosomes. However, flies lack the enzymes necessary to make the Man 6-P mark, and the amino acids implicated in Man 6-P binding by the mammalian receptor are not conserved in LERP. Thus, the function of LERP in sorting of lysosomal enzymes to lysosomes in Drosophila is unclear. This study analyzed the consequence of LERP depletion in S2 cells and intact flies. RNAi-mediated knockdown of LERP in S2 cells had little or no effect on the cellular content or secretion of several lysosomal hydrolases. A novel Lerp null mutation, LerpF6, was generated that abolishes LERP protein expression. Lerp mutants have normal viability and fertility and display no overt phenotypes other than reduced body weight. Lerp mutant flies exhibit a 30-40% decrease in the level of several lysosomal hydrolases, and are hypersensitive to dietary chloroquine and starvation, consistent with impaired lysosome function. Loss of LERP also enhances an eye phenotype associated with defective autophagy. These findings implicate Lerp in lysosome function and autophagy.

Wong, C. O., Palmieri, M., Li, J., Akhmedov, D., Chao, Y., Broadhead, G. T., Zhu, M. X., Berdeaux, R., Collins, C. A., Sardiello, M. and Venkatachalam, K. (2015). Diminished MTORC1-dependent JNK activation underlies the neurodevelopmental defects associated with lysosomal dysfunction. Cell Rep 12: 2009-2020. PubMed ID: 26387958
Summary:
This study evaluated the mechanisms underlying the neurodevelopmental deficits in Drosophila and mouse models of lysosomal storage diseases (LSDs). Lysosomes promote the growth of neuromuscular junctions (NMJs) via Rag GTPases and mechanistic target of rapamycin complex 1 (MTORC1). However, rather than employing S6K/4E-BP1, MTORC1 stimulates NMJ growth via JNK, a determinant of axonal growth in Drosophila and mammals. This role of lysosomal function in regulating JNK phosphorylation is conserved in mammals. Despite requiring the amino-acid-responsive kinase MTORC1, NMJ development is insensitive to dietary protein. This paradox is attributed to anaplastic lymphoma kinase (ALK), which restricts neuronal amino acid uptake, and the administration of an ALK inhibitor couples NMJ development to dietary protein. These findings provide an explanation for the neurodevelopmental deficits in LSDs and suggest an actionable target for treatment.

Majdi, S., Berglund, E. C., Dunevall, J., Oleinick, A. I., Amatore, C., Krantz, D. E. and Ewing, A. G. (2015). Electrochemical measurements of optogenetically stimulated quantal amine release from single nerve cell varicosities in Drosophila larvae. Angew Chem Int Ed Engl [Epub ahead of print]. PubMed ID: 26387683
Summary:
The nerve terminals found in the body wall of Drosophila larvae are readily accessible to experimental manipulation. This study used the light-activated ion channel, channelrhodopsin-2, which is expressed by genetic manipulation in Type II varicosities to study octopamine release in Drosophila. A method was developed to measure neurotransmitter release from exocytosis events at individual varicosities in the Drosophila larval system by amperometry. A microelectrode was placed in a region of the muscle containing a varicosity and held at a potential sufficient to oxidize octopamine and the terminal stimulated by blue light. Optical stimulation of Type II boutons evokes exocytosis of octopamine, which is detected through oxidization at the electrode surface. 22700 +/- 4200 molecules of octopamine were released per vesicle. This system provides a genetically accessible platform to study the regulation of amine release at an intact synapse.

Friday, October 23rd

Wu, C., Chen, Y., Wang, F., Chen, C., Zhang, S., Li, C., Li, W., Wu, S. and Xue, L. (2015). Pelle modulates dFoxO-mediated cell death in Drosophila. PLoS Genet 11: e1005589. PubMed ID: 26474173
Summary:
Interleukin-1 receptor-associated kinases (IRAKs) are crucial mediators of the IL-1R/TLR signaling pathways that regulate the immune and inflammation response in mammals. Recent studies also suggest a critical role of IRAKs in tumor development, though the underlying mechanism remains elusive. Pelle is the sole Drosophila IRAK homolog implicated in the conserved Toll pathway that regulates Dorsal/Ventral patterning, innate immune response, muscle development and axon guidance. This study reports a novel function of pll in modulating apoptotic cell death, which is independent of the Toll pathway. It was found that loss of pll results in reduced size in wing tissue, which is caused by a reduction in cell number but not cell size. Depletion of pll up-regulates the transcription of pro-apoptotic genes, and triggers caspase activation and cell death. The transcription factor dFoxO is required for loss-of-pll induced cell death. Furthermore, loss of pll activates dFoxO, promotes its translocation from cytoplasm to nucleus, and up-regulates the transcription of its target gene Thor/4E-BP. Finally, Pll physically interacts with dFoxO and phosphorylates dFoxO directly. This study not only identifies a previously unknown physiological function of pll in cell death, but also sheds light on the mechanism of IRAKs in cell survival/death during tumorigenesis. 

Bader, C. A., Shandala, T., Ng, Y. S., Johnson, I. R. and Brooks, D. A. (2015). Atg9 is required for intraluminal vesicles in amphisomes and autolysosomes. Biol Open [Epub ahead of print]. PubMed ID: 26353861
Summary:
Autophagy is an intracellular recycling and degradation process, which is important for energy metabolism, lipid metabolism, physiological stress response and organism development. During Drosophila development, autophagy is up-regulated in fat body and midgut cells, to control metabolic function and to enable tissue remodelling. Atg9 is the only transmembrane protein involved in the core autophagy machinery and is thought to have a role in autophagosome formation. During Drosophila development, Atg9 co-located with Atg8 autophagosomes, Rab11 endosomes and Lamp1 endosomes-lysosomes. RNAi silencing of Atg9 reduced both the number and the size of autophagosomes during development and caused morphological changes to amphisomes/autolysosomes. In control cells there was compartmentalised acidification corresponding to intraluminal Rab11/Lamp-1 vesicles, but in Atg9 depleted cells there were no intraluminal vesicles and the acidification was not compartmentalised. It is concluded that Atg9 is required to form intraluminal vesicles and for localised acidification within amphisomes/autolysosomes, and consequently when depleted, reduced the capacity to degrade and remodel gut tissue during development.

Arefin, B., Kucerova, L., Krautz, R., Kranenburg, H., Parvin, F. and Theopold, U. (2015). Apoptosis in hemocytes induces a shift in effector mechanisms in the Drosophila immune system and leads to a pro-inflammatory state. PLoS One 10: e0136593. PubMed ID: 26322507
Summary:
Apart from their role in cellular immunity via phagocytosis and encapsulation, Drosophila hemocytes release soluble factors such as antimicrobial peptides, and cytokines to induce humoral responses. In addition, they participate in coagulation and wounding, and in development. To assess their role during infection with entomopathogenic nematodes, plasmatocytes and1 crystal cells, the two classes of hemocytes present in naive larvae were deleted by expressing proapoptotic proteins in order to produce hemocyte-free (Hml-apo, originally called Hemoless) larvae. Surprisingly, Hml-apo larvae are still resistant to nematode infections. When further elucidating the immune status of Hml-apo larvae, a shift was observed in immune effector pathways including massive lamellocyte differentiation and induction of Toll- as well as repression of imd signaling. This leads to a pro-inflammatory state, characterized by the appearance of melanotic nodules in the hemolymph and to strong developmental defects including pupal lethality and leg defects in escapers. Further analysis suggests that most of the phenotypes that were observed in Hml-apo larvae are alleviated by administration of antibiotics and by changing the food source indicating that they are mediated through the microbiota. Biochemical evidence identifies nitric oxide as a key phylogenetically conserved regulator in this process. Finally it was shown that the nitric oxide donor L-arginine similarly modifies the response against an early stage of tumor development in fly larvae.

Meehan, T. L., Kleinsorge, S. E., Timmons, A. K., Taylor, J. D. and McCall, K. (2015). Polarization of the epithelial layer and apical localization of integrins are required for engulfment of apoptotic cells. Dis Model Mech [Epub ahead of print]. PubMed ID: 26398951
Summary:
Inefficient clearance of dead cells or debris by epithelial cells can lead to or exacerbate debilitating conditions such as retinitis pigmentosa, macular degeneration, chronic obstructive pulmonary disease, and asthma. Despite the importance of engulfment by epithelial cells, little is known about the molecular changes that are required within these cells. The misregulation of integrins has previously been associated with disease states, suggesting that a better understanding of the regulation of receptor trafficking may be key to treating diseases caused by defects in phagocytosis. This study demonstrates that the integrin heterodimer αPS3/βPS becomes apically enriched and is required for engulfment by the epithelial follicle cells of the Drosophila ovary. Integrin heterodimer localization and function is largely directed by the α subunit. Moreover, proper cell polarity promotes asymmetric integrin enrichment, suggesting that αPS3/βPS trafficking occurs in a polarized fashion. Several genes previously known for their roles in trafficking and cell migration are also required for engulfment. Moreover, as in mammals, the same α integrin subunit is required by professional and non-professional phagocytes and migrating cells in Drosophila. These findings suggest that migrating and engulfing cells may use common machinery and demonstrate a critical role for integrin function and polarized trafficking of integrin subunits during engulfment. This study also establishes the epithelial follicle cells of the Drosophila ovary as a powerful model for understanding the molecular changes required for engulfment by a polarized epithelium.

Sudmeier, L.J., Samudrala, S.S., Howard, S.P. and Ganetzky, B. (2015). Persistent activation of the innate immune response in adult Drosophila following radiation exposure during larval development. G3 (Bethesda) [Epub ahead of print]. PubMed ID: 26333838
Summary:
This study investigates the role of the innate immune system in response to radiation exposure. It was shown that the innate immune response and NF-ĸB target gene expression is activated in the adult Drosophila brain following radiation exposure during larval development and that this response is sustained in adult flies weeks after radiation exposure. Preliminary data suggest that innate immunity is radioprotective during Drosophila development. Together these data suggest that activation of the innate immune response may be beneficial initially for survival following radiation exposure but result in long-term deleterious consequences, with chronic inflammation leading to impaired neuronal function and viability at later stages. This work lays the foundation for future studies of how the innate immune response is triggered by radiation exposure and its role in mediating the biological responses to radiation.

Yang, H., Kronhamn, J., Ekström, J.O., Korkut, G.G. and Hultmark, D. (2015). JAK/STAT signaling in Drosophila muscles controls the cellular immune response against parasitoid infection. EMBO Rep [Epub ahead of print]. PubMed ID: 26412855
Summary:
The role of JAK/STAT signaling in the cellular immune response of Drosophila is not well understood. This study shows that parasitoid wasp infection activates JAK/STAT signaling in somatic muscles of the Drosophila larva, triggered by secretion of the cytokines Upd2 and Upd3 from circulating hemocytes. Deletion of upd2 or upd3, but not the related os (upd1) gene, reduces the cellular immune response, and suppression of the JAK/STAT pathway in muscle cells reduces the encapsulation of wasp eggs and the number of circulating lamellocyte effector cells. These results suggest that JAK/STAT signaling in muscles participates in a systemic immune defense against wasp infection.

Thursday, October 22nd

Kwong, P.N., Chambers, M., Vashisht, A.A., Turki-Judeh, W., Yau, T.Y., Wohlschlegel, J.A. and Courey, A.J. (2015). The central region of the Drosophila co-repressor Groucho as a regulatory hub. J Biol Chem [Epub ahead of print]. PubMed ID: 26483546
Summary:
Groucho (Gro) is a Drosophila co-repressor that regulates the expression of a large number of genes, many of which are involved in developmental control. Previous studies have shown that its central region is essential for function, even though its three domains are poorly conserved and intrinsically disordered. Using these disordered domains as affinity reagents, this study identified multiple embryonic Gro-interacting proteins. The interactors include protein complexes involved in chromosome organization, mRNA processing, and signaling. Further investigation of the interacting proteins using a reporter assay showed that many of them modulate Gro-mediated repression either positively or negatively. The positive regulators include components of the spliceosomal subcomplex U1 small nuclear ribonucleoprotein (U1 snRNP). A co-immunoprecipitation ex periment confirms this finding and suggests that a sizable fraction of nuclear U1 snRNP is associated with Gro. The use of RNA-seq to analyze the gene expression profile of cells subjected to knockdown of Gro or snRNP-U1-C (a component of U1 snRNP) shows a significant overlap between genes regulated by these two factors. Furthermore, comparison of RNA-seq data to Gro and Pol II ChIP data led to a number of insights including the finding that Gro-repressed genes are enriched for promoter proximal Pol II. The study concludes that the Gro central domains mediate multiple interactions required for repression thus functioning as a regulatory hub. Furthermore, interactions with the spliceosome may contribute to repression by Gro.

Kramer, M. C., Liang, D., Tatomer, D. C., Gold, B., March, Z. M., Cherry, S. and Wilusz, J. E. (2015). Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins. Genes Dev [Epub ahead of print]. PubMed ID: 26450910
Summary:
Thousands of eukaryotic protein-coding genes are noncanonically spliced to produce circular RNAs. Bioinformatics has indicated that long introns generally flank exons that circularize in Drosophila, but the underlying mechanisms by which these circular RNAs are generated are largely unknown. This study, using extensive mutagenesis of expression plasmids and RNAi screening, revealed that circularization of the Drosophila laccase2 gene is regulated by both intronic repeats and trans-acting splicing factors. Analogous to what has been observed in humans and mice, base-pairing between highly complementary transposable elements facilitates backsplicing. Long flanking repeats (approximately 400 nucleotides [nt]) promote circularization cotranscriptionally, whereas pre-mRNAs containing minimal repeats (<40 nt) generate circular RNAs predominately after 3' end processing. Unlike the previously characterized Muscleblind (Mbl) circular RNA, which requires the Mbl protein for its biogenesis, it was found that Laccase2 circular RNA levels are not controlled by Mbl or the Laccase2 gene product but rather by multiple hnRNP (heterogeneous nuclear ribonucleoprotein) and SR (serine-arginine) proteins acting in a combinatorial manner. hnRNP and SR proteins also regulate the expression of other Drosophila circular RNAs, including Plexin A (PlexA), suggesting a common strategy for regulating backsplicing. Furthermore, the laccase2 flanking introns support efficient circularization of diverse exons in Drosophila and human cells, providing a new tool for exploring the functional consequences of circular RNA expression across eukaryotes.

Molla-Herman, A., Vallés, A.M., Ganem-Elbaz, C., Antoniewski, C. and Huynh, J.R. (2015). tRNA processing defects induce replication stress and Chk2-dependent disruption of piRNA transcription. EMBO J 34(24):3009-27. PubMed ID: 26471728
Summary:
RNase P is a conserved endonuclease that processes the 5' trailer of tRNA precursors. This study isolated mutations in Rpp30, a subunit of RNase P, and found that these induce complete sterility in Drosophila females. It was shown that sterility is not due to a shortage of mature tRNAs, but that atrophied ovaries result from the activation of several DNA damage checkpoint proteins, including p53, Claspin, and Chk2. Indeed, tRNA processing defects lead to increased replication stress and de-repression of transposable elements in mutant ovaries. Transcription of major piRNA sources collapse in mutant germ cells and that this correlates with a decrease in heterochromatic H3K9me3 marks on the corresponding piRNA-producing loci. These data thus link tRNA processing, DNA replication, and genome defense by small RNAs. This unexpected connection reveals constraints that could shape genome organization during evolution.

Huang, W., Carbone, M.A., Magwire, M.M., Peiffer, J.A., Lyman, R.F., Stone, E.A., Anholt, R.R. and Mackay, T.F. (2015). Genetic basis of transcriptome diversity in Drosophila melanogaster. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 26483487
Summary:
This study quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila Genetic Reference Panel (DGRP), increasing the annotated Drosophila transcriptome by 11%, including thousands of novel transcribed regions (NTRs). It was found that 42% of the Drosophila transcriptome is genetically variable in males and females, including the NTRs, and is organized into modules of genetically correlated transcripts. NTRs often are negatively correlated with the expression of protein-coding genes, which was exploited to annotate NTRs functionally. Regulatory variants for the mean and variance of gene expression were identified, which have largely independent genetic control. Expression quantitative trait loci (eQTLs) for the mean, but not for the variance, of gene expression are concentrated near genes. Notably, the variance eQTLs often interacted epistatically with local variants in these genes to regulate gene expression. This comprehensive characterization of population-scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation.

Wednesday, October 21st

Plavicki, J.S., Squirrell, J.M., Eliceiri, K.W. and Boekhoff-Falk, G. (2015). Expression of the Drosophila homeobox gene, Distal-less supports an ancestral role in neural development. Dev Dyn [Epub ahead of print]. PubMed ID: 26472170
Summary:
Distal-less (Dll) encodes a homeodomain transcription factor expressed in developing appendages of organisms throughout metazoan phylogeny. Based on earlier observations in the limbless nematode Caenorhabditis elegans and the primitive chordate amphioxus, it was proposed that Dll has an ancestral function in nervous system development. Consistent with this hypothesis, Dll is necessary for the development of both peripheral and central components of the Drosophila olfactory system. Furthermore, vertebrate homologs of Dll, the Dlx genes, play critical roles in mammalian brain development. This study shows that Dll is expressed in the embryonic, larval and adult CNS and PNS in embryonic and larval neurons, brain and ventral nerve cord (VNC) glia, as well as in PNS structures associated with chemosensation. In adult flies, Dll expression is expressed in the optic lobes, central brain regions and the antennal lobes. Characterization of Dll expression in the developing nervous system supports a role of Dll in neural development and function and establishes an important basis for determining the specific functional roles of Dll in Drosophila development and for comparative studies of Drosophila Dll functions with those of its vertebrate counterparts.

Zhou, C., Franconville, R., Vaughan, A. G., Robinett, C. C., Jayaraman, V. and Baker, B. S. (2015). Central neural circuitry mediating courtship song perception in male Drosophila. Elife 4. PubMed ID: 26390382
Summary:
Animals use acoustic signals across a variety of social behaviors, particularly courtship. In Drosophila, song is detected by antennal mechanosensory neurons and further processed by second-order aPN1/aLN(al) neurons. However, little is known about the central pathways mediating courtship hearing. This study identified a male-specific pathway for courtship hearing via third-order ventrolateral protocerebrum Projection Neuron 1 (vPN1) neurons and fourth-order pC1 neurons. Genetic inactivation of vPN1 or pC1 disrupts song-induced male-chaining behavior. Calcium imaging reveals that vPN1 responds preferentially to pulse song with long inter-pulse intervals (IPIs), while pC1 responses to pulse song closely match the behavioral chaining responses at different IPIs. Moreover, genetic activation of either vPN1 or pC1 induced courtship chaining, mimicking the behavioral response to song. These results outline the aPN1-vPN1-pC1 pathway as a labeled line for the processing and transformation of courtship song in males.

Silva, B., Molina-Fernandez, C., Ugalde, M. B., Tognarelli, E. I., Angel, C. and Campusano, J. M. (2015). Muscarinic ACh receptors contribute to aversive olfactory learning in Drosophila.. Neural Plast 2015: 658918. PubMed ID: 26380118
Summary:
The most studied form of associative learning in Drosophila consists in pairing an odorant, the conditioned stimulus (CS), with an unconditioned stimulus (US). The timely arrival of the CS and US information to a specific Drosophila brain association region, the mushroom bodies (MB), can induce new olfactory memories. Thus, the MB is considered a coincidence detector. It has been shown that olfactory information is conveyed to the MB through cholinergic inputs that activate acetylcholine (ACh) receptors, while the US is encoded by biogenic amine (BA) systems. This study evaluates the proposition that, as in mammals, GPCR muscarinic ACh receptors (mAChRs) contribute to memory formation in Drosophila. The results show that pharmacological and genetic blockade of mAChRs in MB disrupts olfactory aversive memory in larvae. This effect is not explained by an alteration in the ability of animals to respond to odorants or to execute motor programs. These results show that mAChRs in MB contribute to generating olfactory memories in Drosophila (Silva, 2015).

Bailey, A.P., Koster, G., Guillermier, C., Hirst, E.M., MacRae, J.I., Lechene, C.P., Postle, A.D. and Gould, A.P. (2015). Antioxidant role for lipid droplets in a stem cell niche of Drosophila. Cell 163: 340-353. PubMed ID: 26451484
Summary:
Stem cells reside in specialized microenvironments known as niches. During Drosophila development, glial cells provide a niche that sustains the proliferation of neural stem cells (neuroblasts) during starvation. This study finds that the glial cell niche also preserves neuroblast proliferation under conditions of hypoxia and oxidative stress. Lipid droplets that form in niche glia during oxidative stress limit the levels of reactive oxygen species (ROS) and inhibit the oxidation of polyunsaturated fatty acids (PUFAs). These droplets protect glia and also neuroblasts from peroxidation chain reactions that can damage many types of macromolecules. The underlying antioxidant mechanism involves diverting PUFAs, including diet-derived linoleic acid, away from membranes to the core of lipid droplets, where they are less vulnerable to peroxidation. The study reveals an antioxidant role for lipid droplets that could be relevant in many different biological contexts.

Sitaraman, D., Aso, Y., Jin, X., Chen, N., Felix, M., Rubin, G.M. and Nitabach, M.N. (2015). Propagation of homeostatic sleep signals by segregated synaptic microcircuits of the Drosophila mushroom body. Curr Biol [Epub ahead of print]. PubMed ID: 26455303
Summary:
The Drosophila mushroom body (MB) is a key associative memory center that has also been implicated in the control of sleep. However, the identity of MB neurons underlying homeostatic sleep regulation, as well as the types of sleep signals generated by specific classes of MB neurons, has remained poorly understood. Two MB output neuron (MBON) classes whose axons convey sleep control signals from the MB to converge in the same downstream target region: a cholinergic sleep-promoting MBON class and a glutamatergic wake-promoting MBON class have been previously identified. This study deploys a combination of neurogenetic, behavioral, and physiological approaches to identify and mechanistically dissect sleep-controlling circuits of the MB. The existence of two segregated excitatory synaptic microcircuits that propagate homeostatic sleep information from different populations of intrinsic MB "Kenyon cells" (KCs) to specific sleep-regulating MBONs was revealed: sleep-promoting KCs increase sleep by preferentially activating the cholinergic MBONs, while wake-promoting KCs decrease sleep by preferentially activating the glutamatergic MBONs. Importantly, activity of the sleep-promoting MB microcircuit is increased by sleep deprivation and is necessary for homeostatic rebound sleep (i.e., the increased sleep that occurs after, and in compensation for, sleep lost during deprivation). These findings reveal for the first time specific functional connections between subsets of KCs and particular MBONs and establish the identity of synaptic microcircuits underlying transmission of homeostatic sleep signals in the MB.

Walker, S.J., Corrales-Carvajal, V.M. and Ribeiro, C. (2015). Postmating circuitry modulates salt taste processing to increase reproductive output in Drosophila. Curr Biol [Epub ahead of print]. PubMed ID: 26412135
Summary:
To optimize survival and reproduction, animals must match their nutrient intake to their current needs. Reproduction profoundly changes nutritional requirements, with many species showing an appetite for sodium during reproductive periods. How this internal state modifies neuronal information processing to ensure homeostasis is not understood. This study shows that dietary sodium levels positively affect reproductive output in Drosophila melanogaster; to satisfy this requirement, females develop a strong, specific appetite for sodium following mating. It was shown that mating modulates gustatory processing to increase the probability of initiating feeding on salt. This postmating effect is not due to salt depletion by egg production, since abolishing egg production leaves the sodium appetite intact. Rather, the salt appetite is induced need-independently by male-derived Sex Peptide acting on the Sex Peptide Receptor in female reproductive tract neurons. Further, postmating appetites for both salt and yeast are driven by the resultant silencing of downstream SAG neurons. Surprisingly, unlike the postmating yeast appetite, the salt appetite does not require octopamine, suggesting a divergence in the postmating circuitry. These findings demonstrate that the postmating circuit supports reproduction by increasing the palatability of specific nutrients. Such a feedforward regulation of sensory processing may represent a common mechanism through which reproductive state-sensitive circuits modify complex behaviors across species.

Tuesday, October 20th

Ramírez, F., Lingg, T., Toscano, S., Lam, K.C., Georgiev, P., Chung, H.R., Lajoie, B.R., de Wit, E., Zhan, Y., de Laat, W., Dekker, J., Manke, T. and Akhtar, A. (2015). High-affinity sites form an interaction network to facilitate spreading of the MSL complex across the X chromosome in Drosophila. Mol Cell 60: 146-162. PubMed ID: 26431028
Summary:
Dosage compensation mechanisms provide a paradigm to study the contribution of chromosomal conformation toward targeting and spreading of epigenetic regulators over a specific chromosome. By using Hi-C and 4C analyses, this study shows that high-affinity sites (HAS), landing platforms of the male-specific lethal (MSL) complex, are enriched around topologically associating domain (TAD) boundaries on the X chromosome and harbor more long-range contacts in a sex-independent manner. Ectopically expressed roX1 and roX2 RNAs target HAS on the X chromosome in trans and, via spatial proximity, induce spreading of the MSL complex in cis, leading to increased expression of neighboring autosomal genes. It was shown that the MSL complex regulates nucleosome positioning at HAS, therefore acting locally rather than influencing the overall chromosomal architecture. The study proposes that the sex-independent, three-dimensional conformation of the X chromosome poises it for exploitation by the MSL complex, thereby facilitating spreading in males.

Miles, W.O., Lepesant, J.M., Bourdeaux, J., Texier, M., Kerenyi, M.A., Nakakido, M., Hamamoto, R., Orkin, S.H., Dyson, N.J. and Di Stefano, L. (2015). The LSD1 family of histone demethylases and the PUMILIO post-transcriptional repressor function in a complex regulatory feedback loop. Mol Cell Biol [Epub ahead of print]. PubMed ID: 26438601
Summary:
The Lysine (K)-specific demethylase (LSD1) family of histone demethylases regulates chromatin structure and the transcriptional potential of genes. LSD1 is frequently deregulated in tumors and depletion of LSD1 family members causes developmental defects. This study reports that reductions in the expression of the Pumilio (PUM) translational repressor complex enhances phenotypes due to dLsd1 depletion in Drosophila. The PUM complex is a target of LSD1 regulation in fly and mammalian cells and its expression is inversely correlated with LSD1 levels in human bladder carcinoma. Unexpectedly, PUM was found to post-transcriptionally regulate LSD1 family protein levels in flies and human cells indicating the existence of feedback loops between the LSD1 family and the PUM complex. These results highlight a new post-transcriptional mechanism regulating LSD1 activity and suggest that the feedback loop between LSD1 family and the PUM complex may be functionally important during development and in human malignancies.

Reubens, M. C., Biller, M. D., Bedsole, S. E., Hopkins, L. T., Ables, E. T. and Christensen, T. W. (2015). Mcm10 is required for oogenesis and early embryogenesis in Drosophila. Mech Dev [Epub ahead of print]. PubMed ID: 26369283
Summary:
Efficient replication of the genome and the establishment of endogenous chromatin states are processes that are essential to eukaryotic life. It is well documented that Mcm10 is intimately linked to both of these important biological processes; therefore, it is not surprising that Mcm10 is commonly misregulated in many human cancers. This study sought to identify the potential biological functions of Mcm10 in the context of a complex multicellular organism by continuing our analysis in Drosophila using three novel hypomorphic alleles. Observation of embryonic nuclear morphology and quantification of embryo hatch rates reveal that maternal loading of Mcm10 is required for embryonic nuclear stability, and suggest a role for Mcm10 post zygotic transition. Contrary to the essential nature of Mcm10 depicted in the literature, it does not appear to be required for adult viability in Drosophila if embryonic requirements are met. Although not required for adult somatic viability, analysis of fecundity and ovarian morphology in mutant females suggest that Mcm10 plays a role in maintenance of the female germline. Taken together, these results demonstrate critical roles for Mcm10 during early embryogenesis, and mark the first data linking Mcm10 to female specific reproduction in multicellular eukaryotes.

Chereji, R.V.,et al. (2015). Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster. Nucleic Acids Res [Epub ahead of print]. PubMed ID: 26429969
Summary:
Nucleosomal DNA is thought to be generally inaccessible to DNA-binding factors, such as micrococcal nuclease (MNase). This study digested Drosophila chromatin with high and low concentrations of MNase to reveal two distinct nucleosome types: MNase-sensitive and MNase-resistant. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C-containing dinucleotides, whereas MNase-sensitive nucleosomes form on A/T-rich sequences found at transcription start and termination sites, enhancers and DNase I hypersensitive sites. Estimates of nucleosome formation energies indicate that MNase-sensitive nucleosomes tend to be less stable than MNase-resistant ones. Strikingly, a decrease in cell growth temperature of about 10°C makes MNase-sensitive nucleosomes less accessible, suggesting that observed variations in MNase sensitivity are related to either thermal fluctuations of chromatin fibers or the activity of enzymatic machinery. In the vicinity of active genes and DNase I hypersensitive sites nucleosomes are organized into periodic arrays, likely due to 'phasing' off potential barriers formed by DNA-bound factors or by nucleosomes anchored to their positions through external interactions. The latter idea is substantiated by a biophysical model of nucleosome positioning and energetics, which predicts that nucleosomes immediately downstream of transcription start sites are anchored and recapitulates nucleosome phasing at active genes significantly better than sequence-dependent models.

Monday, October 19th

Conduit, P. T. and Raff, J. W. (2015). Different Drosophila cell types exhibit differences in mitotic centrosome assembly dynamics. Curr Biol 25: R650-651. PubMed ID: 26241137
Summary:
Centrosomes are major microtubule organising centres comprising a pair of centrioles surrounded by pericentriolar material (PCM). The PCM expands dramatically as cells enter mitosis, and we previously showed that two key PCM components, Centrosomin (Cnn) and Spd-2, cooperate to form a scaffold structure around the centrioles that recruits the mitotic PCM in Drosophila; the SPD-5 and SPD-2 proteins appear to play a similar function in C. elegans. In fly syncytial embryos, Cnn and Spd-2 are initially recruited into a central region of the PCM and then flux outwards. This centrosomal flux is potentially important, but it has so far not been reported in any other cell type. This study examine the dynamic behaviour of Cnn and Spd-2 in Drosophila larval brain cells. Spd-2 fluxes outwards from the centrioles in both brains and embryos in a microtubule-independent manner. In contrast, although Cnn is initially incorporated into the region of the PCM occupied by Spd-2 in both brains and embryos, Cnn fluxes outwards along microtubules in embryos, but not in brain cells, where it remains concentrated around the centrosomal Spd-2. Thus, the microtubule-independent centrosomal-flux of Spd-2 occurs in multiple fly cell types, while the microtubule-dependent outward flux of Cnn appears to be restricted to the syncytial embryo.

Mirkovic, M., Hutter, L.H., Novák, B. and Oliveira, R.A. (2015). Premature sister chromatid separation is poorly detected by the spindle assembly checkpoint as a result of system-level feedback. Cell Rep [Epub ahead of print]. PubMed ID: 26456822
Summary:
Sister chromatid cohesion, mediated by the cohesin complex, is essential for faithful mitosis. Nevertheless, evidence suggests that the surveillance mechanism that governs mitotic fidelity, the spindle assembly checkpoint (SAC), is not robust enough to halt cell division when cohesion loss occurs prematurely. The mechanism behind this poor response is not properly understood. Using developing Drosophila brains, this study shows that full sister chromatid separation elicits a weak checkpoint response resulting in abnormal mitotic exit after a short delay. Quantitative live-cell imaging approaches combined with mathematical modeling indicate that weak SAC activation upon cohesion loss is caused by weak signal generation. This is further attenuated by several feedback loops in the mitotic signaling network. The study proposes that multiple feedback loops involving cyclin-dependent kinase 1 (Cdk1) gradually impair error-correction efficiency and accelerate mitotic exit upon premature loss of cohesion. These findings explain how cohesion defects may escape SAC surveillance.

Baker, C.C., Gim, B.S. and Fuller, M.T. (2015). Cell type-specific translational repression of Cyclin B during meiosis in males. Development 142: 3394-3402. PubMed ID: 26443637
Summary:
The unique cell cycle dynamics of meiosis are controlled by layers of regulation imposed on core mitotic cell cycle machinery components by the program of germ cell development. Although the mechanisms that regulate Cdk1/Cyclin B activity in meiosis in oocytes have been well studied, little is known about the trans-acting factors responsible for developmental control of these factors in male gametogenesis. During meiotic prophase in Drosophila males, transcript for the core cell cycle protein Cyclin B1 (CycB) is expressed in spermatocytes, but the protein does not accumulate in spermatocytes until just before the meiotic divisions. This study shows that two interacting proteins, Rbp4 and Fest, expressed at the onset of spermatocyte differentiation under control of the developmental program of male gametogenesis, function to direct cell type- and stage-specific repression of translation of the core G2/M cell cycle component cycB during the specialized cell cycle of male meiosis. Binding of Fest to Rbp4 requires a 31-amino acid region within Rbp4. Rbp4 and Fest are required for translational repression of cycB in immature spermatocytes, with Rbp4 binding sequences in a cell type-specific shortened form of the cycB 3' UTR. Finally, it was shown that Fest is required for proper execution of meiosis I.

Christophorou, N., Rubin, T., Bonnet, I., Piolot, T., Arnaud, M. and Huynh, J.R. (2015). Microtubule-driven nuclear rotations promote meiotic chromosome dynamics. Nat Cell Biol [Epub ahead of print]. PubMed ID: 26458247
Summary:
At the onset of meiosis, each chromosome needs to find its homologue and pair to ensure proper segregation. In Drosophila, pairing occurs during the mitotic cycles preceding meiosis. This study shows that germ cell nuclei undergo marked movements during this developmental window. It was demonstrated that microtubules and Dynein drive nuclear rotations and are required for centromere pairing and clustering. It was further found that Klaroid (SUN) and Klarsicht (KASH) co-localize with centromeres at the nuclear envelope and are required for proper chromosome motions and pairing. Mud (NuMA in vertebrates) was identified as co-localizing with centromeres, Klarsicht and Klaroid. Mud is also required to maintain the integrity of the nuclear envelope and for the correct assembly of the synaptonemal complex. These findings reveal a mechanism for chromosome pairing in Drosophila, and indicate that microtubules, centrosomes and associated proteins play a crucial role in the dynamic organization of chromosomes inside the nucleus.

Sunday, October 18th

Fan, X., Liang, Q., Lian, T., Wu, Q., Gaur, U., Li, D., Yang, D., Mao, X., Jin, Z., Li, Y. and Yang, M. (2015). Rapamycin preserves gut homeostasis during Drosophila aging. Oncotarget [Epub ahead of print]. PubMed ID: 26431326
Summary:
Gut homeostasis plays an important role in maintaining the overall body health during aging. Rapamycin, a specific inhibitor of mTOR, exerts prolongevity effects in evolutionarily diverse species. However, its impact on the intestinal homeostasis remains poorly understood. This study demonstrates that rapamycin can slow down the proliferation rate of intestinal stem cells (ISCs) in the aging guts and induce autophagy in the intestinal epithelium in Drosophila. Rapamycin can also significantly affect the FOXO associated genes in intestine and up-regulate the negative regulators of IMD/Rel pathway, consequently delaying the microbial expansion in the aging guts. Collectively, these findings reveal that rapamycin can delay the intestinal aging by inhibiting mTOR and thus keeping stem cell proliferation in check. These results further explain the mechanism of healthspan and lifespan extension by rapamycin in Drosophila.

Lin, W.S., et al. (2015). Reduced gut acidity induces an obese-like phenotype in Drosophila melanogaster and in mice. PLoS One 10: e0139722. PubMed ID: 26436771
Summary:
In order to identify genes involved in stress and metabolic regulation, this study carried out a Drosophila P-element-mediated mutagenesis screen for starvation resistance. A mutant, m2, was isolated that showed a 23% increase in survival time under starvation conditions. The P-element insertion was mapped to the region upstream of the vha16-1 gene, which encodes the c subunit of the vacuolar-type H+-ATPase. It was found that vha16-1 is highly expressed in the fly midgut, and that m2 mutant flies are hypomorphic for vha16-1 and also exhibit reduced midgut acidity. This deficit is likely to induce altered metabolism and contribute to accelerated aging, since vha16-1 mutant flies are short-lived and display increases in body weight and lipid accumulation. Similar phenotypes were also induced by pharmacological treatment, through feeding normal flies and mice with a carbonic anhydrase inhibitor (acetazolamide) or proton pump inhibitor (PPI, lansoprazole) to suppress gut acid production. This study may thus provide a useful model for investigating chronic acid suppression in patients.

Suzuki, M., et al. (2015). Glucocerebrosidase deficiency accelerates the accumulation of proteinase K-resistant alpha-synuclein and aggravates neurodegeneration in a Drosophila model of Parkinson's disease. Hum Mol Genet [Epub ahead of print]. PubMed ID: 26362253
Summary:
Α-synuclein (αSyn) plays a central role in the pathogenesis of Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Genetic studies have revealed that mutations in the glucocerebrosidase 1 (GBA1) gene, which are responsible for Gaucher's disease, are strong risk factors for PD and DLB. This study employed Drosophila models to examine the link between the loss of glucocerebrosidase (GCase) and the toxicity of αSyn. Knockdown of the Drosophila homolog of GBA1 (dGBA1) exacerbates the locomotor dysfunction, loss of dopaminergic neurons and retinal degeneration of αSyn-expressing flies. This phenotypic aggravation was associated with the accumulation of proteinase K (PK)-resistant αSyn, rather than with changes in the total amount of αSyn, raising the possibility that glucosylceramide (GlcCer), a substrate of GCase, accelerates the misfolding of αSyn. Indeed, in vitro experiments revealed that GlcCer directly promotes the conversion of recombinant αSyn into the PK-resistant form, representing a toxic conformational change. Similar to dGBA1 knockdown, knockdown of the Drosophila homolog of β-galactosidase (β-Gal) also aggravated locomotor dysfunction of the αSyn flies, and its substrate GM1 ganglioside accelerated the formation of PK-resistant αSyn. These findings suggest that the functional loss of GCase or β-Gal promotes the toxic conversion of αSyn via aberrant interactions between αSyn and their substrate glycolipids, leading to the aggravation of αSyn-mediated neurodegeneration.

Yu, Z., Goodman, L. D., Shieh, S. Y., Min, M., Teng, X., Zhu, Y. and Bonini, N. M. (2015). A fly model for the CCUG-repeat expansion of myotonic dystrophy type 2 reveals a novel interaction with MBNL1. Hum Mol Genet 24: 954-962. PubMed ID: 25305073
Summary:
Expanded non-coding RNA repeats of CUG and CCUG are the underlying genetic causes for myotonic dystrophy type 1 (DM1) and type 2 (DM2), respectively. A gain-of-function of these pathogenic repeat expansions is mediated at least in part by their abnormal interactions with RNA-binding proteins such as MBNL1 (see Drosophila Muscleblind) and resultant loss of activity of these proteins. To study pathogenic mechanisms of CCUG-repeat expansions in an animal model, a fly model of DM2 was created that expresses pure, uninterrupted CCUG-repeat expansions ranging from 16 to 720 repeats in length. This fly model for DM2 recapitulates key features of human DM2 including RNA repeat-induced toxicity, ribonuclear foci formation and changes in alternative splicing. Interestingly, expression of two isoforms of MBNL1, MBNL135 and MBNL140, leads to cleavage and concurrent upregulation of the levels of the RNA-repeat transcripts, with MBNL140 having more significant effects than MBNL135. This property is shared with a fly CUG-repeat expansion model. These results suggest a novel mechanism for interaction between the pathogenic RNA repeat expansions of myotonic dystrophy and MBNL1.

Saturday, October 17th

Van De Bor, V., Zimniak, G., Papone, L., Cerezo, D., Malbouyres, M., Juan, T., Ruggiero, F. and Noselli, S. (2015). Companion blood cells control ovarian stem cell niche microenvironment and homeostasis. Cell Rep [Epub ahead of print]. PubMed ID: 26456819
Summary:
The extracellular matrix plays an essential role for stem cell differentiation and niche homeostasis. Yet, the origin and mechanism of assembly of the stem cell niche microenvironment remain poorly characterized. This study uncovers an association between the niche and blood cells, leading to the formation of the Drosophila ovarian germline stem cell niche basement membrane. A distinct pool of plasmatocytes tightly associated with the developing ovaries from larval stages onward was identified. Expressing tagged collagen IV tissue specifically, it was shown that the germline stem cell niche basement membrane is produced by these "companion plasmatocytes" in the larval gonad and persists throughout adulthood, including the reproductive period. Eliminating companion plasmatocytes or specifically blocking their collagen IV expression during larval stages results in abnormal adult niches with excess stem cells, a phenotype due to aberrant BMP signaling. Thus, local interactions between the niche and blood cells during gonad development are essential for adult germline stem cell niche microenvironment assembly and homeostasis.

Wang, S., Gao, Y., Song, X., Ma, X., Zhu, X., Mao, Y., Yang, Z., Ni, J., Li, H., Malanowski, K.E., Anoja, P., Park, J., Haug, J. and Xie, T. (2015). Wnt signaling-mediated redox regulation maintains the germ line stem cell differentiation niche. Elife 4. PubMed ID: 26452202
Summary:
Adult stem cells continuously undergo self-renewal and generate differentiated cells. In the Drosophila ovary, two separate niches control germ line stem cell (GSC) self-renewal and differentiation processes. Compared to the self-renewing niche, relatively little is known about the maintenance and function of the differentiation niche. This study shows that the cellular redox state regulated by Wnt signaling is critical for the maintenance and function of the differentiation niche to promote GSC progeny differentiation. Defective Wnt signaling causes the loss of the differentiation niche and the upregulated BMP signaling in differentiated GSC progeny, thereby disrupting germ cell differentiation. Mechanistically, Wnt signaling controls the expression of multiple glutathione-S-transferase family genes and the cellular redox state. Finally, Wnt2 and Wnt4 function redundantly to maintain active Wnt signaling in the differentiation niche. Therefore, this study reveals a novel strategy for Wnt signaling in regulating the cellular redox state and maintaining the differentiation niche.

Loyer, N., Kolotuev, I., Pinot, M. and Le Borgne, R. (2015). DrosophilaE-cadherin is required for the maintenance of ring canals anchoring to mechanically withstand tissue growth. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 26424451
Summary:
Intercellular bridges called "ring canals" (RCs) resulting from incomplete cytokinesis play an essential role in intercellular communication in somatic and germinal tissues. During Drosophila oogenesis, RCs connect the maturing oocyte to nurse cells supporting its growth. Despite numerous genetic screens aimed at identifying genes involved in RC biogenesis and maturation, how RCs anchor to the plasma membrane (PM) throughout development remains unexplained. This study reports that the clathrin adaptor protein 1 (AP-1) complex, although dispensable for the biogenesis of RCs, is required for the maintenance of the anchorage of RCs to the PM to withstand the increased membrane tension associated with the exponential tissue growth at the onset of vitellogenesis. It was shown that AP-1 regulates the localization of the intercellular adhesion molecule E-cadherin and that loss of AP-1 causes the disappearance of the E-cadherin-containing adhesive clusters surrounding the RCs. E-cadherin itself is shown to be required for the maintenance of the RCs' anchorage, a function previously unrecognized because of functional compensation by N-cadherin. Scanning block-face EM combined with transmission EM analyses reveals the presence of interdigitated, actin- and Moesin-positive, microvilli-like structures wrapping the RCs. Thus, by modulating E-cadherin trafficking, it was shown that the sustained E-cadherin-dependent adhesion organizes the microvilli meshwork and ensures the proper attachment of RCs to the PM, thereby counteracting the increasing membrane tension induced by exponential tissue growth.

Felix, M., Chayengia, M., Ghosh, R., Sharma, A. and Prasad, M. (2015). dPak3 regulates apical-basal polarity in migrating border cells during Drosophila oogenesis. Development [Epub ahead of print]. PubMed ID: 26395489
Summary:
During group cell migration collectively moving cells are physically attached to each other and retain some degree of apical-basal polarity during the migratory phase. Though much is known about direction sensing, it is far from clear how polarity is regulated in diverse instances of multicellular movement. This study reports the role of dPak3, a group I p21 activated serine-threonine protein kinase, in maintaining apical-basal polarity in migrating border cell cluster during Drosophila oogenesis. dPak3 is enriched in border cells and downregulation of its function impedes border cell movement. Time-lapse imaging suggests that dPak3 affects protrusive behavior of the border cell cluster specifically regulating the stability and directionality of the protrusions. This study shows that dPak3 functions downstream of the guidance receptor signaling to regulate the level and distribution of F-actin in the migrating border cells. Further evidence is provided that dPak3 genetically interacts with lateral polarity marker Scribble and regulates c-Jun N-terminal kinase (JNK) signaling in the moving border cells. Since dPak3 depletion results in mislocalization of several apical-basal polarity markers including Stardust, Crumbs and Coracle and overexpression of D-jun rescues the polarity of the dPak3-depleted cluster, it is proposed that dPak3 functions through the JNK signaling to modulate the apical-basal polarity of the migrating border cell cluster. Interestingly, loss of apical-basal polarity was also observed in Rac1 depleted border cell cluster suggesting that the guidance receptor signaling functions through Rac GTPase and dPak3 to regulate overall polarity of the cluster to mediate efficient collective movement of the border cells to the oocyte boundary.

Friday, October 16th

Dequéant, M.L., Fagegaltier, D., Hu, Y., Spirohn, K., Simcox, A., Hannon, G.J. and Perrimon, N. (2015). Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 26438832
Summary:
The use of time series profiling to identify groups of functionally related genes (synexpression groups) is a powerful approach for the discovery of gene function. This study applies this strategy during RasV12 immortalization of Drosophila embryonic cells, a phenomenon not well characterized. Using high-resolution transcriptional time-series datasets, a gene network based on temporal expression profile similarities was generated. This analysis revealed that common immortalized cells are related to adult muscle precursors (AMPs), a stem cell-like population contributing to adult muscles and sharing properties with vertebrate satellite cells. Remarkably, the immortalized cells retain the capacity for myogenic differentiation when treated with the steroid hormone ecdysone.

Kuhn, H., Sopko, R., Coughlin, M., Perrimon, N. and Mitchison, T. (2015). The Atg1-Tor pathway regulates yolk catabolism in Drosophila embryos. Development [Epub ahead of print]. PubMed ID: 26395483
Summary:
Yolk provides an important source of nutrients during the early development of oviparous organisms. It is composed mainly of vitellogenin proteins packed into membrane-bound compartments called yolk platelets. Catabolism of yolk is initiated by acidification of the yolk platelet, leading to the activation of Cathepsin-like proteinases, but it is unknown how this process is triggered. Yolk catabolism initiates at cellularization in Drosophila melanogaster embryos. Using maternal shRNA technology this, study found that yolk catabolism depends on the Tor pathway and on the autophagy-initiating kinase Atg1. While Atg1 was required for a burst of spatially-regulated autophagy during late cellularization, autophagy was not required for initiating yolk catabolism. It is proposed that the conserved Tor metabolic sensing pathway regulates yolk catabolism, similar to Tor-dependent metabolic regulation on the lysosome.

Bergstralh, D.T., Lovegrove, H.E. and St Johnston, D. (2015). Lateral adhesion drives reintegration of misplaced cells into epithelial monolayers. Nat Cell Biol [Epub ahead of print]. PubMed ID: 26414404
Summary:
Cells in simple epithelia orient their mitotic spindles in the plane of the epithelium so that both daughter cells are born within the epithelial sheet. This is assumed to be important to maintain epithelial integrity and prevent hyperplasia, because misaligned divisions give rise to cells outside the epithelium. This study tests this assumption in three types of Drosophila epithelium; the cuboidal follicle epithelium, the columnar early embryonic ectoderm, and the pseudostratified neuroepithelium. Ectopic expression of Inscuteable in these tissues reorients mitotic spindles, resulting in one daughter cell being born outside the epithelial layer. Live imaging reveals that these misplaced cells reintegrate into the tissue. Reducing the levels of the lateral homophilic adhesion molecules Neuroglian or Fasciclin 2 disrupts reintegration, giving rise to extra-epithelial cells, whereas disruption of adherens junctions has no effect. Thus, the reinsertion of misplaced cells seems to be driven by lateral adhesion, which pulls cells born outside the epithelial layer back into it. These findings reveal a robust mechanism that protects epithelia against the consequences of misoriented divisions.

Yadav, R., Kundu, S. and Sarkar, S. (2015). Drosophila glob1 expresses dynamically and is required for development and oxidative stress response. Genesis [Epub ahead of print]. PubMed ID: 26426154
Summary:
The globin protein family is conservation through archaea to human. Globin(s) have been "classically" studied as oxygen binding protein(s). Drosophila possesses three globin genes (glob1, glob2, glob3) located at different cytogenetic positions. This study investigated the expression and function of glob1. Glob1 is coded maternally. Zygotic transcription occurs in somatic muscles, gut primordia, fat bodies, tracheal cells, etc. Similarly, dynamic expression of glob1 was evident in most of the larval tissues, interestingly with high expression in dividing cells. Reduced expression of glob1 leads to various impairments and lethality during embryogenesis and larval development. A substantial increase in cellular ROS occurs upon reduced expression of glob1 leading to locomotor impairment and early aging in surviving adult flies. Thus, in addition to oxygen management, globin gene(s) are also involved in regulating various aspects of development in Drosophila.

Thursday, October 15th

Mishra, A.K., Sachan, N., Mutsuddi, M. and Mukherjee, A. (2015). Kinase active Misshapen regulates Notch signaling in Drosophila melanogaster. Exp Cell Res [Epub ahead of print]. PubMed ID: 26431585
Summary:
Notch signaling pathway represents a principal cellular communication system that plays a pivotal role during development of metazoans. Drosophila misshapen (msn) encodes a protein kinase, which is related to the budding yeast Ste20p (sterile 20 protein) kinase. In a genetic screen, using candidate gene approach to identify novel kinases involved in Notch signaling, this study identified msn as a novel regulator of Notch signaling. Overexpression of kinase active form of Msn exhibits phenotypes similar to Notch loss-of-function condition and msn genetically interacts with components of Notch signaling pathway. Kinase active form of Msn associates with Notch receptor and regulates its signaling activity. It was further shown that kinase active Misshapen leads to accumulation of membrane-tethered form of Notch. Moreover, activated Msn also depletes Armadillo and DE-Cadherin from adherens junctions. Thus, this study provides a yet unknown mode of regulation of Notch signaling by Misshapen.

Ni, L., Zheng, Y., Hara, M., Pan, D. and Luo, X. (2015). Structural basis for Mob1-dependent activation of the core Mst-Lats kinase cascade in Hippo signaling. Genes Dev 29: 1416-1431. PubMed ID: 26108669
Summary:
The Mst-Lats kinase cascade is central to the Hippo tumor-suppressive pathway that controls organ size and tissue homeostasis. The adaptor protein Mob1 promotes Lats activation by Mst, but the mechanism remains unknown. This study shows that human Mob1 binds to autophosphorylated docking motifs in active Mst2. This binding enables Mob1 phosphorylation by Mst2. Phosphorylated Mob1 undergoes conformational activation and binds to Lats1. We determine the crystal structures of phospho-Mst2-Mob1 and phospho-Mob1-Lats1 complexes, revealing the structural basis of both phosphorylation-dependent binding events. Further biochemical and functional analyses demonstrate that Mob1 mediates Lats1 activation through dynamic scaffolding and allosteric mechanisms. Thus, Mob1 acts as a phosphorylation-regulated coupler of kinase activation by virtue of its ability to engage multiple ligands. It is proposed that stepwise, phosphorylation-triggered docking interactions of nonkinase elements enhance the specificity and robustness of kinase signaling cascades.

Li, C., Kan, L., Chen, Y., Zheng, X., Li, W., Zhang, W., Cao, L., Lin, X., Ji, S., Huang, S., Zhang, G., Liu, X., Tao, Y., Wu, S. and Chen, D. (2015). Ci antagonizes Hippo signaling in the somatic cells of the ovary to drive germline stem cell differentiation. Cell Res [Epub ahead of print]. PubMed ID: 26403189
Summary:
Many stem cell populations are tightly regulated by their local microenvironment (niche), which comprises distinct types of stromal cells. However, little is known about mechanisms by which niche subgroups coordinately determine the stem cell fate. This study identified that Yki, the key Hippo pathway component, is essential for escort cell (EC) function in promoting germline differentiation in Drosophila ovary. Hedgehog (Hh) signals emanating primarily from cap cells support the function of ECs, where Cubitus interruptus (Ci), the Hh signaling effector, acts to inhibit Hippo kinase cascade activity. Mechanistically, Ci competitively interacts with Hpo and impairs the Hpo-Wts signaling complex formation, thereby promoting Yki nuclear localization. The actions of Ci ensure effective Yki signaling to antagonize Sd/Tgi/Vg-mediated default repression in ECs. This study uncovers a mechanism explaining how subgroups of niche cells coordinate to determine the stem cell fate via Hh-Hippo signaling crosstalk, and enhances understanding of mechanistic regulations of the oncogenic Yki/YAP signaling.

Balmer, S., Dussert, A., Collu, G. M., Benitez, E., Iomini, C. and Mlodzik, M. (2015). Components of intraflagellar transport Complex A function independently of the cilium to regulate canonical Wnt signaling in Drosophila. Dev Cell 34: 705-718. PubMed ID: 26364750
Summary:
The development of multicellular organisms requires the precisely coordinated regulation of an evolutionarily conserved group of signaling pathways. Temporal and spatial control of these signaling cascades is achieved through networks of regulatory proteins, segregation of pathway components in specific subcellular compartments, or both. In vertebrates, dysregulation of primary cilia function has been strongly linked to developmental signaling defects, yet it remains unclear whether cilia sequester pathway components to regulate their activation or cilia-associated proteins directly modulate developmental signaling events. To elucidate this question, an RNAi-based screen was conducted in Drosophila non-ciliated cells to test for cilium-independent loss-of-function phenotypes of ciliary proteins in developmental signaling pathways. The results show no effect on Hedgehog signaling. In contrast, the screen identified several cilia-associated proteins as functioning in canonical Wnt signaling. Further characterization of specific components of Intraflagellar Transport complex A uncovered a cilia-independent function in potentiating Wnt signals by promoting β-catenin/Armadillo activity.

Wednesday, October 14th

Karaiskos, S., Naqvi, A. S., Swanson, K. E. and Grigoriev, A. (2015). Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets. Biol Direct 10: 51. PubMed ID: 26374501
Summary:

Development of sequencing technologies and supporting computation enable discovery of small RNA molecules that previously escaped detection or were ignored due to low count numbers. This study describes Drosophila melanogaster tRFs, which appear to have a number of structural and functional features similar to those of miRNAs but are less abundant. As is the case with miRNAs, (1) tRFs seem to have distinct isoforms preferentially originating from 5' or 3' end of a precursor molecule (in this case, tRNA), (2) ends of tRFs appear to contain short "seed" sequences matching conserved regions across 12 Drosophila genomes, preferentially in 3' UTRs but also in introns and exons; (3) tRFs display specific isoform loading into Ago1 Ago2 and thus likely function in RISC complexes; (4) levels of loading in Ago1 and Ago2 differ considerably; and (5) both tRF expression and loading appear to be age-dependent, indicating potential regulatory changes from young to adult organisms. Drosophila tRF reads mapped to both nuclear and mitochondrial tRNA genes for all 20 amino acids, while previous studies have usually reported fragments from only a few tRNAs. These tRFs show a number of similarities with miRNAs, including seed sequences. Based on complementarity with conserved Drosophila regions such seed sequences and their possible targets were identified with matches in the 3'UTR regions. Strikingly, the potential target genes of the most abundant tRFs show significant Gene Ontology enrichment in development and neuronal function. The latter suggests that involvement of tRFs in the RNA interfering pathway may play a role in brain activity or brain changes with age.

Coyne, A. N., Yamada, S. B., Siddegowda, B. B., Estes, P. S., Zaepfel, B. L., Johannesmeyer, J. S., Lockwood, D. B., Pham, L. T., Hart, M. P., Cassel, J. A., Freibaum, B., Boehringer, A. V., Taylor, J. P., Reitz, A. B., Gitler, A. D. and Zarnescu, D. C. (2015). Fragile X protein mitigates TDP-43 toxicity by remodeling RNA granules and restoring translation. Hum Mol Genet. PubMed ID: 26385636
Summary:
RNA dysregulation is a newly recognized disease mechanism in amyotrophic lateral sclerosis (ALS). This study identified Drosophila fragile X mental retardation protein (dFMRP) as a robust genetic modifier of TDP-43-dependent toxicity in a Drosophila model of ALS. dFMRP overexpression (dFMRP OE) mitigates TDP-43 dependent locomotor defects and reduced lifespan in Drosophila. TDP-43 and FMRP form a complex in flies and human cells. In motor neurons, TDP-43 expression increases the association of dFMRP with stress granules and colocalizes with polyA binding protein in a variant-dependent manner. Furthermore, dFMRP dosage modulates TDP-43 solubility and molecular mobility with overexpression of dFMRP resulting in a significant reduction of TDP-43 in the aggregate fraction. Polysome fractionation experiments indicate that dFMRP OE also relieves the translation inhibition of futsch mRNA, a TDP-43 target mRNA, which regulates neuromuscular synapse architecture. Restoration of futsch translation by dFMRP OE mitigates Futsch-dependent morphological phenotypes at the neuromuscular junction including synaptic size and presence of satellite boutons. These data suggest a model whereby dFMRP is neuroprotective by remodeling TDP-43 containing RNA granules, reducing aggregation and restoring the translation of specific mRNAs in motor neurons.

Ramaswami, G., Deng, P., Zhang, R., Anna Carbone, M., Mackay, T. F. and Billy Li, J. (2015). Genetic mapping uncovers cis-regulatory landscape of RNA editing. Nat Commun 6: 8194. PubMed ID: 26373807
Summary:
Adenosine-to-inosine (A-to-I) RNA editing, catalysed by ADAR enzymes, plays an important role in neurological functions. This study applied a quantitative trait loci (QTL) mapping approach to identify genetic variants associated with variability in RNA editing. With very accurate measurement of RNA editing levels at 789 sites in 131 Drosophila melanogaster strains, this study identified 545 editing QTLs (edQTLs) associated with differences in RNA editing. Many edQTLs can act through changes in the local secondary structure for edited dsRNAs. Furthermore, edQTLs located outside of the edited dsRNA duplex were found to be enriched in secondary structure, suggesting that distal dsRNA structure beyond the editing site duplex affects RNA editing efficiency. Thus work will facilitate the understanding of the cis-regulatory code of RNA editing.

Weng, R. and Cohen, S. M. (2015). Control of Drosophila type I and type II central brain neuroblast proliferation by bantam microRNA. Development [Epub ahead of print]. PubMed ID: 26395494
Summary:
Post-transcriptional regulation of stem cell self-renewal by microRNAs is emerging as an important mechanism controlling tissue homeostasis. This report providse evidence that the bantam microRNA controls neuroblast number and proliferation in the Drosophila central brain. bantam also supports proliferation of the transit-amplifying intermediate neural progenitor cells in type II neuroblast lineages. The stem cell factors brat, prospero are identified as bantam targets acting on different aspects of these processes. Thus bantam appears to act in multiple regulatory steps in the maintenance and proliferation of neuroblasts and their progeny to regulate growth of the central brain.

Tuesday, October 13th

Lavrynenko, O., Rodenfels, J., Carvalho, M., Dye, N. A., Lafont, R., Eaton, S. and Shevchenko, A. (2015). The Ecdysteroidome of Drosophila: influence of diet and development. Development [Epub ahead of print]. PubMed ID: 26395481
Summary:
Ecdysteroids are the hormones regulating development, physiology and fertility in arthropods, which synthesize them exclusively from dietary sterols. But how dietary sterol diversity influences the ecdysteroid profile, how animals ensure the production of desired hormones and whether there are functional differences between different ecdysteroids produced in vivo, remains unknown. This is because currently there is no analytical technology for unbiased, comprehensive and quantitative assessment of the full complement of endogenous ecdysteroids. This study developed a new LC-MS/MS method to screen the entire chemical space of ecdysteroid-related structures and to quantify known and newly discovered hormones and their catabolites. The ecdysteroidome was quantitated in Drosophila melanogaster. and how the ecdysteroid profile varies with diet and development was investigated. Drosophila can produce 4 different classes of ecdysteroids, which are obligatorily derived from 4 types of dietary sterol precursors. Drosophila produces makisterone A from plant sterols and epi-makisterone A from ergosterol, the major yeast sterol. However they prefer to selectively utilize scarce ergosterol precursors to make a novel hormone 24,28-dehydromakisterone A and trace cholesterol to synthesize 20-hydroxyecdysone. Interestingly, epi-makisterone A supports only larval development, while all other ecdysteroids allow full adult development. It is suggests that evolutionary pressure against producing epi-C24 ecdysteroids may explain selective utilization of ergosterol precursors and the puzzling preference for cholesterol.

Alex, A., et al. (2015). A circadian clock gene, cry, affects heart morphogenesis and function in Drosophila as revealed by optical coherence microscopy. PLoS One 10: e0137236. PubMed ID: 26348211
Summary:
Circadian rhythms are endogenous, entrainable oscillations of physical, mental and behavioural processes in response to local environmental cues. The role that circadian clock genes play in heart development and function are poorly understood. The Drosophila cryptochrome (dCry) is a circadian clock gene that encodes a major component of the circadian clock negative feedback loop. Compared to the embryonic stage, the relative expression levels of dCry showed a significant increase (>100-fold) in Drosophila during the pupa and adult stages. This study performed analysis of functional and morphological changes in the Drosophila heart throughout its post-embryonic lifecycle. The Drosophila heart exhibited major morphological and functional alterations during its development. Notably, heart rate (HR) and cardiac activity period (CAP) of Drosophila showed significant variations during the pupa stage, when heart remodeling took place. From the M-mode (2D + time) OCM images, cardiac structural and functional parameters of Drosophila at different developmental stages were quantitatively determined. In order to study the functional role of dCry on Drosophila heart development, dCry was silenced by RNAi in the Drosophila heart and mesoderm, and quantitatively measured heart morphology and function in those flies throughout its development. Silencing of dCry resulted in slower HR, reduced CAP, smaller heart chamber size, pupal lethality and disrupted posterior segmentation that was related to increased expression of a posterior compartment protein, Wingless. Collectively, these studies provided novel evidence that the circadian clock gene, dCry, plays an essential role in heart morphogenesis and function.

Singh, S., Sanchez-Herrero, E. and Shashidhara, L. S. (2015). Critical role for Fat/Hippo and IIS/Akt pathways downstream of Ultrabithorax during haltere specification in Drosophila. Mech Dev [Epub ahead of print]. PubMed ID: 26299254
Summary:
In Drosophila, differential development of wing and haltere, which differ in cell size, number and morphology, is dependent on the function of Hox gene Ultrabithorax (Ubx). This study reports studies on Ubx-mediated regulation of the Fat/Hippo and IIS/dAkt pathways, which control cell number and cell size during development. Over-expression of Yki or down regulation of negative components of the Fat/Hippo pathway, such as expanded, caused considerable increase in haltere size, mainly due to increase in cell number. These phenotypes were also associated with the activation of Akt pathways in developing haltere. Although activation of Akt alone did not affect the cell size or the organ size, dramatic increase was seen in haltere size when Akt was activated in the background where expanded is down regulated. This was associated with the increase in both cell size and cell number. The organ appeared flatter than wildtype haltere and the trichome morphology and spacing resembled that of wing suggesting homeotic transformations. Thus, these results suggest a link between cellular growth and pattern formation and the final differentiated state of the organ.

Wicker-Thomas, C., et al. (2015). Flexible origin of hydrocarbon/pheromone precursors in Drosophila melanogaster.J Lipid Res [Epub ahead of print]. PubMed ID: 26353752
Summary:
In terrestrial insects, cuticular hydrocarbons (CHCs) provide protection from desiccation. Specific CHCs can also act as pheromones, which are important for successful mating. Oenocytes are abdominal cells thought to act as specialized units for CHC biogenesis that consists of long-chain fatty-acid (LCFA) synthesis, optional desaturation(s), elongation to very-long-chain fatty acids (VLCFAs) and removal of the carboxyl group. By investigating CHC biogenesis in Drosophila melanogaster, this study showed that VLCFA synthesis takes place only within the oenocytes. Conversely, several pathways, which may compensate for one another, can feed the oenocyte pool of LCFAs, suggesting that this step is a critical node for regulating CHC synthesis. Importantly, flies deficient in LCFA-synthesis sacrificed their triacylglycerol stores while maintaining some CHC production. Moreover, pheromone production was lower in adult flies that emerged from larvae that were fed excess dietary lipids and their mating success was lower. Further, pheromone production in the oenocytes was shown to depends on lipid metabolism in the fat tissue and that FATP, a bipartite acyl-CoA-synthase(ACS)/fatty-acid-transporter, likely acts through its ACS domain in the oenocyte pathway of CHC biogenesis. This study highlights the importance of environmental and physiological inputs in regulating LCFA synthesis to eventually control sexual communication in a polyphagous animal.

Monday, October 12th

Kruger, E., Mena, W., Lahr, E. C., Johnson, E. C. and Ewer, J. (2015). Genetic analysis of Eclosion hormone action during Drosophila larval ecdysis. Development [Epub ahead of print]. PubMed ID: 26395475
Summary:
Insect growth is punctuated by molts, during which the animal produces a new exoskeleton. The molt culminates with ecdysis, an ordered sequence of behaviors that causes the old cuticle to be shed. This sequence is activated by Ecdysis Triggering Hormone (ETH), which acts on the CNS to activate neurons that produce neuropeptides implicated in ecdysis, including Eclosion hormone (EH), Crustacean Cardioactive Peptide (CCAP), and bursicon. Despite over 40 years of research on ecdysis, understanding of the precise roles of these neurohormones remains rudimentary. Of particular interest is EH, whose role beyond the well-accepted action of massively upregulating ETH release has remained elusive. This study reports on the isolation of an eh null mutant in Drosophila, and it's use to investigate the role of EH in larval ecdysis. Null mutant animals invariably died at around the time of ecdysis, revealing an essential role in its control. Unexpectedly, however, they failed to express the preparatory behavior of pre-ecdysis while directly expressing the motor program of ecdysis. In addition, although ETH release could not be detected in these animals, the lack of pre-ecdysis could not be rescued by injections of ETH, suggesting that EH is required within the CNS for ETH to trigger the normal ecdysial sequence. Using a genetically-encoded calcium probe it was shown that EH configures the response of the CNS to ETH. These findings show that EH plays an essential role in the Drosophila CNS in the control of ecdysis, in addition to its known role in the periphery of triggering ETH release.

Cavanaugh, D. J., Vigderman, A. S., Dean, T., Garbe, D. S. and Sehgal, A. (2015). The circadian clock gates sleep through time-of-day dependent modulation of sleep-promoting neurons. Sleep [Epub ahead of print]. PubMed ID: 26350473
Summary:
Sleep is under the control of homeostatic and circadian processes, which interact to determine sleep timing and duration, but the mechanisms through which the circadian system modulates sleep are largely unknown. This study used adult-specific, temporally controlled neuronal activation and inhibition to identify an interaction between the circadian clock and a novel population of sleep-promoting neurons in Drosophila. In this study, transgenic flies expressed either dTRPA1, a neuronal activator, or Shibirets1, an inhibitor of synaptic release, in small subsets of neurons. Sleep, as determined by activity monitoring and video tracking, was assessed before and after temperature-induced activation or inhibition using these effector molecules. This study compared the effect of these manipulations in control flies and in mutant flies that lacked components of the molecular circadian clock. Adult-specific activation or inhibition of a population of neurons that projects to the sleep-promoting dorsal Fan-Shaped Body resulted in bidirectional control over sleep. Interestingly, the magnitude of the sleep changes were time-of-day dependent. Activation of sleep-promoting neurons was maximally effective during the middle of the day and night, and was relatively ineffective during the day-to-night and night-to-day transitions. These time-of-day specific effects were absent in flies that lacked functional circadian clocks. In conclusion, the circadian system functions to gate sleep through active inhibition at specific times of day. These data identify a mechanism through which the circadian system prevents premature sleep onset in the late evening, when homeostatic sleep drive is high.

Ahmad, M., Chaudhary, S.U., Afzal, A.J. and Tariq, M. (2015). Starvation-induced dietary behaviour in Drosophila melanogaster larvae and adults. Sci Rep 5: 14285. PubMed ID: 26399327
Summary:
Drosophila melanogaster larvae are classified as herbivores and known to feed on non-carnivorous diet under normal conditions. However, when nutritionally challenged these larvae exhibit cannibalistic behaviour by consuming a diet composed of larger conspecifics. This study reports that cannibalism in Drosophila larvae is confined not only to scavenging on conspecifics that are larger in size, but also on their eggs. Moreover, such cannibalistic larvae develop as normally as those grown on standard cornmeal medium. When stressed, Drosophila melanogaster larvae can also consume a carnivorous diet derived from carcasses of organisms belonging to diverse taxonomic groups, including Musca domestica, Apis mellifera, and Lycosidae sp. While adults are ill-equipped to devour conspecific carcasses, they selectively oviposit on them and also consume damaged cadavers of conspecifics. Thus, these results suggest that nutritionally stressed Drosophila show distinct as well as unusual feeding behaviours that can be classified as detritivorous, cannibalistic and/or carnivorous.

Stern, U., He, R. and Yang, C. H. (2015). Analyzing animal behavior via classifying each video frame using convolutional neural networks. Sci Rep 5: 14351. PubMed ID: 26394695
Summary:
High-throughput analysis of animal behavior requires software to analyze videos. Such software analyzes each frame individually, detecting animals' body parts. But the image analysis rarely attempts to recognize "behavioral states"-e.g., actions or facial expressions-directly from the image instead of using the detected body parts. This study shows that convolutional neural networks (CNNs)-a machine learning approach that recently became the leading technique for object recognition, human pose estimation, and human action recognition-were able to recognize directly from images whether Drosophila were "on" (standing or walking) or "off" (not in physical contact with) egg-laying substrates for each frame of the videos. Nultiple nets and image transformations were to optimize accuracy for the classification task, achieving a surprisingly low error rate of just 0.072%. Classifying one of the 8 h videos took less than 3 h using a fast GPU. The approach enabled uncovering a novel egg-laying-induced behavior modification in Drosophila. Furthermore, it should be readily applicable to other behavior analysis tasks.

Sunday, October 11th

Carvalho, A.B., Vicoso, B., Russo, C.A., Swenor, B. and Clark, A.G. (2015). Birth of a new gene on the Y chromosome of Drosophila melanogaster. Proc Natl Acad Sci U S A 112(40):12450-5. PubMed ID: 26385968
Summary:
Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. This study shows how these genes were acquired. It was found that a previously unidentified gene (flagrante delicto Y, FDY) originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.

Kao, J. Y., Lymer, S., Hwang, S. H., Sung, A. and Nuzhdin, S. V. (2015). Postmating reproductive barriers contribute to the incipient sexual isolation of the United States and Caribbean Drosophila melanogaster. Ecol Evol 5: 3171-3182. PubMed ID: 26357543
Summary:
The nascent stages of speciation start with the emergence of sexual isolation. Understanding the influence of reproductive barriers in this evolutionary process is an ongoing effort. This paper presents a study of Drosophila melanogaster admixed populations from the southeast United States and the Caribbean islands known to be a secondary contact zone of European- and African-derived populations undergoing incipient sexual isolation. The existence of premating reproductive barriers has been previously established, but these types of barriers are not the only source shaping sexual isolation. To assess the influence of postmating barriers, this study investigated putative postmating barriers of female remating and egg-laying behavior, as well as hatchability of eggs laid and female longevity after mating. In the central region of the putative hybrid zone of American and Caribbean populations, lower hatchability of eggs laid was observed accompanied by increased resistance to harm after mating to less-related males. These results illustrate that postmating reproductive barriers act alongside premating barriers and genetic admixture such as hybrid incompatibilities and influence early phases of sexual isolation.

Hollis, B., Houle, D. and Kawecki, T. J. (2015). Evolution of reduced postcopulatory molecular interactions in Drosophila populations lacking sperm competition. J Evol Biol [Epub ahead of print]. PubMed ID: 26395588
Summary:
In many species with internal fertilization, molecules transferred in the male ejaculate trigger and interact with physiological changes in females. It is controversial to what extent these interactions between the sexes act synergistically to mediate the female switch to a reproductive state or instead reflect sexual antagonism evolved as a byproduct of sexual selection on males. To address this question, this study eliminated sexual selection by enforcing monogamy in populations of Drosophila melanogaster for 65 generations and then measured the expression of male seminal fluid protein genes and genes involved in the female response to mating. In the absence of sperm competition, male and female reproductive interests are perfectly aligned and any antagonism should be reduced by natural selection. Consistent with this idea, males from monogamous populations showed reduced expression of seminal fluid protein genes, 16% less on average than in polygamous males. After mating, females with an evolutionary history of monogamy exhibited lower relative expression of genes that were upregulated in response to mating and higher expression of genes that were downregulated. Surprisingly, these genes showed a similar pattern even before mating, suggesting that monogamous females evolved to be less poised for mating and the accompanying receipt of male seminal fluid proteins. This reduced investment by both monogamous males and females in molecules involved in postcopulatory interactions points to a pervasive role of sexual conflict in shaping these interactions.

Huang, Y., Stinchcombe, J. R. and Agrawal, A. F. (2015). Quantitative genetic variance in experimental fly populations evolving with or without environmental heterogeneity. Evolution 69(10):2735-46. PubMed ID: 26362112
Summary:
Heterogeneous environments are typically expected to maintain more genetic variation in fitness within populations than homogeneous environments. However, the accuracy of this claim depends on the form of heterogeneity as well as the genetic basis of fitness traits and how similar the assay environment is to the environment of past selection. This study measured quantitative genetic (QG) variance for three traits important for fitness using replicated experimental populations of Drosophila melanogaster evolving under four selective regimes: constant salt-enriched medium (Salt), constant cadmium-enriched medium (Cad), and two heterogeneous regimes that vary either temporally (Temp) or spatially (Spatial). As theory predicts, Spatial populations tended to harbor more genetic variation than Temp populations or those maintained in a constant environment that is the same as the assay environment. Contrary to expectation, Salt populations tend to have more genetic variation than Cad populations in both assay environments. The patterns for QG variances across regimes in relation to previously reported data on genome-wide sequence diversity. For some traits, the QG patterns are similar to the diversity patterns of ecological selected SNPs, whereas the QG patterns for some other traits resembled that of neutral SNPs.

Saturday, October 10th

Carnes, M. U., et al. 2015. The genomic basis of postponed senescence in Drosophila melanogaster. PLoS One 10: e0138569. PubMed ID: 26378456
Summary:
Natural populations harbor considerable genetic variation for lifespan. While evolutionary theory provides general explanations for the existence of this variation, knowledge of the genes harboring naturally occurring polymorphisms affecting lifespan is limited. This study assessed the genetic divergence between five Drosophila melanogaster lines selected for postponed senescence for over 170 generations (O lines) and five lines from the same base population maintained at a two week generation interval for over 850 generations (B lines). On average, O lines live 70% longer than B lines, are more productive at all ages, and have delayed senescence for other traits than reproduction. Population sequencing of pools of individuals was performed from all B and O lines, and 6,394 genetically divergent variants were identified in or near 1,928 genes at a false discovery rate of 0.068. A 2.6 Mb region at the tip of the X chromosome contained many variants fixed for alternative alleles in the two populations, suggestive of a hard selective sweep. Genome wide gene expression of O and B lines at one and five weeks of age was also analyzed using RNA sequencing, and genes were identified with significant effects on gene expression with age, population and the age by population interaction, separately for each sex. Transcripts were identified that exhibited the transcriptional signature of postponed senescence, and the gene expression and genetic divergence data were integrated to identify 98 (175) top candidate genes in females (males) affecting postponed senescence and increased lifespan. While several of these genes have been previously associated with Drosophila lifespan, most are novel and constitute a rich resource for future functional validation.

Dubos, A., et al. (2015). Conditional depletion of intellectual disability and Parkinsonism candidate gene ATP6AP2 in fly and mouse induces cognitive impairment and neurodegeneration. Hum Mol Genet [Epub ahead of print]. PubMed ID: 26376863
Summary:
ATP6AP2, an essential accessory component of the vacuolar H+ ATPase (V-ATPase), has been associated with intellectual disability (ID) and Parkinsonism. ATP6AP2 has been implicated in several signalling pathways; however, little is known regarding its role in the nervous system. To decipher its function in behaviour and cognition, conditional knockdowns of ATP6AP2 were generated and characterized in the nervous system of Drosophila and mouse models. In Drosophila, ATP6AP2 knockdown induced defective phototaxis and vacuolated photoreceptor neurons and pigment cells when depleted in eyes and altered short- and long-term memory when depleted in the mushroom body. In mouse, conditional Atp6ap2 deletion in glutamatergic neurons caused increased spontaneous locomotor activity and altered fear memory. Both Drosophila ATP6AP2 knockdown and deletion mice presented with presynaptic transmission defects, and with an abnormal number and morphology of synapses. In addition, deletion mice showed autophagy defects that led to axonal and neuronal degeneration in the cortex and hippocampus. Surprisingly, axon myelination was affected in the mutant mice, and axonal transport alterations were observed in Drosophila. In accordance with the identified phenotypes across species, genome-wide transcriptome profiling of deletion mouse hippocampi revealed dysregulation of genes involved in myelination, action potential, membrane-bound vesicles and motor behaviour. In summary, ATP6AP2 disruption in mouse and fly leads to cognitive impairment and neurodegeneration, mimicking aspects of the neuropathology associated with ATP6AP2 mutations in humans. These results identify ATP6AP2 as an essential gene for the nervous system.

Khanna, M. R. and Fortini, M. E. (2015). Transcriptomic analysis of Drosophila mushroom body neurons lacking Amyloid-beta precursor-like protein activity. J Alzheimers Dis 46: 913-928. PubMed ID: 26402626
Summary:
The amyloid-&beta: protein precursor (AbetaPP; see Drosophila Appl) is subjected to sequential intramembrane proteolysis by α-, &beta:-, and γ-secretases, producing secreted amyloid-&beta: (A&beta:) peptides and a cytoplasmically released A&beta:PP Intracellular Domain (AICD). AICD complexes with transcription factors in the nucleus, suggesting that this AβPP fragment serves as an active signaling effector that regulates downstream genes, although its nuclear targets are poorly defined. To further understand this potential signaling mechanism mediated by AβPP, a transcriptomic identification of the Drosophila genome that is regulated by the fly AβPP orthologue was performed in fly mushroom body neurons, which control learning- and memory-based behaviors. Significant changes were found in expression of 245 genes, representing approximately 1.6% of the Drosophila genome, with the changes ranging from +6 fold to -40 fold. The largest class of responsive targets corresponds to non-protein coding genes and includes microRNAs that have been previously implicated in Alzheimer's disease pathophysiology. Several genes were identified in the Drosophila microarray analyses that have also emerged as putative AβPP targets in similar mammalian transcriptomic studies. These results also indicate a role for AβPP in cellular pathways involving the regulation of Drosophila Casein Kinase II, mitochondrial oxidative phosphorylation, RNA processing, and innate immunity. These findings provide insights into the intracellular events that are regulated by AβPP activity in healthy neurons and that might become dysregulated as a result of abnormal AβPP proteolysis in AD.

Cutler, T., Sarkar, A., Moran, M., Steffensmeier, A., Puli, O. R., Mancini, G., Tare, M., Gogia, N. and Singh, A. (2015). Drosophila eye model to study neuroprotective role of CREB binding protein (CBP) in Alzheimer's disease. PLoS One 10: e0137691. PubMed ID: 26367392
Summary:
This study utilized Gal4/UAS system to develop a transgenic fruit fly model for Aβ42 (see Drosophila Appl) mediated neurodegeneration. Targeted misexpression of human Aβ42 in the differentiating photoreceptor neurons of the developing eye of transgenic fly triggers neurodegeneration. This progressive neurodegenerative phenotype resembles Alzheimer's like neuropathology. A histone acetylase, CREB Binding Protein (CBP), was identified as a genetic modifier of Aβ42 mediated neurodegeneration. Targeted misexpression of CBP along with Aβ42 in the differentiating retina can significantly rescue neurodegeneration. Gain-of-function of CBP rescues Aβ42 mediated neurodegeneration by blocking cell death. Misexpression of Aβ42 affects the targeting of axons from retina to the brain but misexpression of full length CBP along with Aβ42 can restore this defect. The CBP protein has multiple domains and is known to interact with many different proteins. This structure function analysis using truncated constructs lacking one or more domains of CBP protein, in transgenic flies revealed that Bromo, HAT and polyglutamine (BHQ) domains together are required for the neuroprotective function of CBP. This BHQ domain of CBP has not been attributed to promote survival in any other neurodegenerative disorders. This study has identified CBP as a genetic modifier of Aβ42 mediated neurodegeneration. Furthermore, this study had identified BHQ domain of CBP is being responsible for its neuroprotective function. These studies may have significant bearing on understanding of genetic basis of AD.

Friday, October 9th

Kulshammer, E., Mundorf, J., Kilinc, M., Frommolt, P., Wagle, P. and Uhlirova, M. (2015). Interplay among Drosophila transcription factors Ets21c, Fos and Ftz-F1 drives JNK-mediated tumor malignancy. Dis Model Mech 8: 1279-1293. PubMed ID: 26398940
Summary:
This study defines TF network that triggers an abnormal gene expression program promoting malignancy of clonal tumors, generated in Drosophila imaginal disc epithelium by gain of oncogenic Ras (RasV12) and loss of the tumor suppressor Scribble (scrib1). Malignant transformation of the rasV12scrib1 tumors requires TFs of distinct families, namely the bZIP protein Fos, the ETS-domain factor Ets21c and the nuclear receptor Ftz-F1, all acting downstream of Jun-N-terminal kinase (JNK). Depleting any of the three TFs improves viability of tumor-bearing larvae, and this positive effect can be enhanced further by their combined removal. Although both Fos and Ftz-F1 synergistically contribute to rasV12scrib1 tumor invasiveness, only Fos is required for JNK-induced differentiation defects and Matrix metalloprotease (MMP1) upregulation. In contrast, the Fos-dimerizing partner Jun is dispensable for JNK to exert its effects in rasV12scrib1 tumors. Interestingly, Ets21c and Ftz-F1 are transcriptionally induced in these tumors in a JNK- and Fos-dependent manner, thereby demonstrating a hierarchy within the tripartite TF network, with Fos acting as the most upstream JNK effector. Of the three TFs, only Ets21c can efficiently substitute for loss of polarity and cooperate with Ras(V12) in inducing malignant clones that, like rasV12scrib1 tumors, invade other tissues and overexpress MMP1 and the Drosophila insulin-like peptide 8 (Dilp8). While rasV12ets21c tumors require JNK for invasiveness, the JNK activity is dispensable for their growth. In conclusion, this study delineates both unique and overlapping functions of distinct TFs that cooperatively promote aberrant expression of target genes, leading to malignant tumor phenotypes.

Housden, B. E., Valvezan, A. J., Kelley, C., Sopko, R., Hu, Y., Roesel, C., Lin, S., Buckner, M., Tao, R., Yilmazel, B., Mohr, S. E., Manning, B. D. and Perrimon, N. (2015). Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi. Sci Signal 8: rs9. PubMed ID: 26350902
Summary:
The tuberous sclerosis complex (TSC) family of tumor suppressors, TSC1 and TSC2, function together in an evolutionarily conserved protein complex that is a point of convergence for major cell signaling pathways that regulate mTOR complex 1 (mTORC1). Mutation or aberrant inhibition of the TSC complex is common in various human tumor syndromes and cancers. The discovery of novel therapeutic strategies to selectively target cells with functional loss of this complex is therefore of clinical relevance to patients with nonmalignant TSC and those with sporadic cancers. This study developed a CRISPR-based method to generate homogeneous mutant Drosophila cell lines. By combining TSC1 or TSC2 mutant cell lines with RNAi screens against all kinases and phosphatases, synthetic interactions with TSC1 and TSC2 were identified. Individual knockdown of three candidate genes (mRNA-cap, Pitslre, and CycT; orthologs of RNGTT, CDK11, and CCNT1 in humans) reduced the population growth rate of Drosophila cells lacking either TSC1 or TSC2 but not that of wild-type cells. Moreover, individual knockdown of these three genes had similar growth-inhibiting effects in mammalian TSC2-deficient cell lines, including human tumor-derived cells, illustrating the power of this cross-species screening strategy to identify potential drug targets.

Talbert, M. E., Barnett, B., Hoff, R., Amella, M., Kuczynski, K., Lavington, E., Koury, S., Brud, E. and Eanes, W. F. (2015). Genetic perturbation of key central metabolic genes extends lifespan in Drosophila and affects response to dietary restriction. Proc Biol Sci 282. PubMed ID: 26378219
Summary:
There is a connection between nutrient inputs, energy-sensing pathways, lifespan variation and aging. Despite the role of metabolic enzymes in energy homeostasis and their metabolites as nutrient signals, little is known about how their gene expression impacts lifespan. This report uses P-element mutagenesis in Drosophila to study the effect on lifespan of reductions in expression of seven central metabolic enzymes, and contrast the effects on normal diet and dietary restriction. The major observation is that for five of seven genes, the reduction of gene expression extends lifespan on one or both diets. Two genes are involved in redox balance, and it was observed that lower activity genotypes significantly extend lifespan. The hexokinases also show extension of lifespan with reduced gene activity. Since both affect the ATP/ADP ratio, this connects with the role of AMP-activated protein kinase as an energy sensor in regulating lifespan and mediating caloric restriction. These genes possess significant expression variation in natural populations, and the experimental genotypes in this study span this level of natural activity variation. These studies link the readout of energy state with the perturbation of the genes of central metabolism and demonstrate their effect on lifespan.

Kopp, Z. A., et al. (2015). Heart-specific Rpd3 downregulation enhances cardiac function and longevity. Aging (Albany NY) 7: 648-663. PubMed ID: 26399365
Summary:
Downregulation of Rpd3, a homologue of mammalian Histone Deacetylase 1 (HDAC1), extends lifespan in Drosophila melanogaster. Once revealed that long-lived fruit flies exhibit limited cardiac decline, whether Rpd3 downregulation would improve stress resistance and/or lifespan when targeted in the heart was investigated. Contested against three different stressors (oxidation, starvation and heat), heart-specific Rpd3 downregulation significantly enhanced stress resistance in flies. However, these higher levels of resistance were not observed when Rpd3 downregulation was targeted in other tissues or when other long-lived flies were tested in the heart-specific manner. Interestingly, the expressions of anti-aging genes such as Sod2, foxo and Thor, were systemically increased as a consequence of heart-specific Rpd3 downregulation. Showing higher resistance to oxidative stress, the heart-specific Rpd3 downregulation concurrently exhibited improved cardiac functions, demonstrating an increased heart rate, decreased heart failure and accelerated heart recovery. Conversely, Rpd3 upregulation in cardiac tissue reduced systemic resistance against heat stress with decreased heart function, also specifying phosphorylated Rpd3 levels as a significant modulator. Continual downregulation of Rpd3 throughout aging increased lifespan, implicating that Rpd3 deacetylase in the heart plays a significant role in cardiac function and longevity to systemically modulate the fly's response to the environment.

Thursday, October 8th

Deligiannaki, M., Casper, A. L., Jung, C. and Gaul, U. (2015). Pasiflora proteins are novel core components of the septate junction. Development 142: 3046-3057. PubMed ID: 26329602
Summary:
Epithelial sheets play essential roles as selective barriers insulating the body from the environment and establishing distinct chemical compartments within it. In invertebrate epithelia, septate junctions (SJs) consist of large multi-protein complexes that localize at the apicolateral membrane and mediate barrier function. This study reports the identification of two novel SJ components, Pasiflora1 (CG7713) and Pasiflora2 (CG8121), through a genome-wide glial RNAi screen in Drosophila. Pasiflora mutants show permeable blood-brain and tracheal barriers, overelongated tracheal tubes and mislocalization of SJ proteins. Consistent with the observed phenotypes, the genes are co-expressed in embryonic epithelia and glia and are required cell-autonomously to exert their function. Pasiflora1 and Pasiflora2 belong to a previously uncharacterized family of tetraspan membrane proteins conserved across the protostome-deuterostome divide. Both proteins localize at SJs and their apicolateral membrane accumulation depends on other complex components. In fluorescence recovery after photobleaching experiments, pasiflora proteins were found to be core SJ components as they are required for complex formation and exhibit restricted mobility within the membrane of wild-type epithelial cells, but rapid diffusion in cells with disrupted SJs. Taken together, these results show that Pasiflora1 and Pasiflora2 are novel integral components of the SJ and implicate a new family of tetraspan proteins in the function of these ancient and crucial cell junctions.

Ordan, E. and Volk, T. (2015). A non-signaling role of Robo2 in tendons is essential for Slit processing and muscle patterning. Development 142(20):3512-8. PubMed ID: 26400093
Summary:
Coordinated locomotion of an organism relies on the development of proper musculoskeletal connections. In Drosophila, the Slit-Robo signaling pathway guides muscles to tendons. This study shows that the Slit receptor Roundabout 2 (Robo2) plays a non-cell-autonomous role in directing muscles to their corresponding tendons. Robo2 is expressed by tendons, and its non signaling activity in these cells promotes Slit cleavage producing a cleaved Slit-N-terminal guiding signal, which provides short-range signaling into muscles. Consistently, robo2 mutant embryos exhibited a muscle phenotype similar to that of slit, which could not be rescued by a muscle-specific Robo2 expression but rather by an ectodermally derived Robo2. Alternatively this muscle phenotype could be induced by tendon-specific robo2RNAi. Membrane immobilization of Slit, or its N-terminal cleaved form on tendons bypasses the functional requirement for Robo2 in tendons, verifying that the major role of Robo2 is to promote the association of Slit with the tendon cell membrane. Cleaved Slit (Slit-N) tends to oligomerize whereas full-length uncleavable Slit does not. It is therefore proposed that Slit-N oligomers produced at the tendon membrane by Robo2 signal to the approaching muscle by combined Robo;Robo3 activity. These findings establish a Robo2-mediated mechanism, independent of signaling essential to limiting Slit distribution, which might be relevant to the regulation of Slit-mediated short-range signaling in additional systems.

Fear, J. M., Arbeitman, M. N., Salomon, M. P., Dalton, J. E., Tower, J., Nuzhdin, S. V. and McIntyre, L. M. (2015). The Wright stuff: Reimagining path analysis reveals novel components of the sex determination hierarchy in Drosophila melanogaster. BMC Syst Biol 9: 53. PubMed ID: 26335107
Summary:
This study used a structural equation modeling approach, leveraging natural genetic variation from two studies on Drosophila female head tissues to expand understanding of the sex hierarchy gene regulatory network (GRN). The GRN was expanded adding novel links among genes, including a link from fruitless (fru) to Sex-lethal (Sxl). This link is further supported by the presence of fru binding sites in the Sxl locus. 754 candidate genes were added to the pathway, including the splicing factors male-specific lethal 2 and Rm62 as downstream targets of Sxl. Independent studies of doublesex and transformer mutants support evidence for a link between the sex hierarchy and metabolism, via Insulin-like receptor. The genes added in one population were enriched for genes with sex-biased splicing and components of the spliceosome. Using natural alleles this approach not only identifies novel relationships, but using supervised approaches can order genes into a regulatory hierarchy.

Dong, Q., Brenneman, B., Fields, C. and Srivastava, A. (2015). A Cathepsin-L is required for invasive behavior during air sac primordium development in Drosophila melanogaster. FEBS Lett 589(20 Pt B):3090-7. PubMed ID: 26341534
Summary:
The Drosophila Air Sac Primordium (ASP) has emerged as an important structure where cellular, genetic and molecular events responsible for invasive behavior and branching morphogenesis can be studied. This report presents data which demonstrate that a Cathepsin-L encoded by the gene Cysteine proteinase-1 (CP1) in Drosophila is necessary for invasive behavior during ASP development. CP1 is expressed in ASP and knockdown of CP1 results in suppression of migratory and invasive behavior observed during ASP development. It was further shown that CP1 possibly regulates invasive behavior by promoting degradation of Basement Membrane. These data provide clues to the possible role of Cathepsin L in human lung development and tumor invasion, especially, given the similarities between human lung and Drosophila ASP development.

Wednesday, October 7th

Zanet, J., Benrabah, E., Li, T., Pelissier-Monier, A., Chanut-Delalande, H., Ronsin, B., Bellen, H. J., Payre, F. and Plaza, S. (2015). Pri sORF peptides induce selective proteasome-mediated protein processing. Science 349: 1356-1358. PubMed ID: 26383956
Summary:
A wide variety of RNAs encode small open-reading-frame (smORF/sORF) peptides, but their functions are largely unknown. This study shows that Drosophila polished-rice (pri) sORF peptides trigger proteasome-mediated protein processing, converting the Shavenbaby (Svb) transcription repressor into a shorter activator. A genome-wide RNA interference screen identifies an E2-E3 ubiquitin-conjugating complex, UbcD6-Ubr3, which targets Svb to the proteasome in a pri-dependent manner. Upon interaction with Ubr3, Pri peptides promote the binding of Ubr3 to Svb. Ubr3 can then ubiquitinate the Svb N terminus, which is degraded by the proteasome. The C-terminal domains protect Svb from complete degradation and ensure appropriate processing. These data show that Pri peptides control selectivity of Ubr3 binding, which suggests that the family of sORF peptides may contain an extended repertoire of protein regulators.

Zheng, Y., Wang, W., Liu, B., Deng, H., Uster, E. and Pan, D. (2015). Identification of Happyhour/MAP4K as alternative Hpo/Mst-like kinases in the Hippo kinase cascade. Dev Cell 34(6):642-55. PubMed ID: 26364751
Summary:
In Drosophila and mammals, the canonical Hippo kinase cascade is mediated by Hpo/Mst acting through the intermediary kinase Wts/Lats to phosphorylate the transcriptional coactivator Yki/YAP/TAZ. However, the underlying mechanisms linking Yki/YAP/TAZ activity to the actin cytoskeleton are poorly understood. Using Drosophila imaginal discs as an in vivo model, this study shows that Wts, but not Hpo, is genetically indispensable for cytoskeleton-mediated subcellular localization of Yki. Through a systematic screen, the Ste-20 kinase Happyhour (Hppy) and its mammalian counterpart MAP4K1/2/3/5 were identified as an alternative kinase that phosphorylates the hydrophobic motif of Wts/Lats in a similar manner as Hpo/Mst. Consistent with their redundant function as activating kinases of Wts/Lats, combined loss of Hpo/Mst and Hppy/MAP4K abolishes cytoskeleton-mediated regulation of Yki/YAP subcellular localization, as well as YAP cytoplasmic translocation induced by contact inhibition.

Lebreton, G. and Casanova, J. (2015). Ligand-binding and constitutive FGF receptors in single Drosophila tracheal cells. Implications for the role of FGF in collective migration. Dev Dyn [Epub ahead of print]. PubMed ID: 26342211
Summary:
The migration of individual cells relies on their capacity to evaluate differences across their bodies and to move either towards or against a chemoattractant or a chemorepellent signal respectively. However, the direction of collective migration is believed to depend on the internal organisation of the cell cluster while the role of the external signal is limited to single out some cells in the cluster, confering them with motility properties. This study analysed the role of Fibroblast Growth Factor (FGF) signalling in collective migration in the Drosophila trachea. While ligand-binding FGF receptor (FGFR) activity in a single cell can drive migration of a tracheal cluster, this study shows that activity from a constitutively activated FGFR cannot - an observation that contrasts with previously analysed cases. These results indicate that individual cells in the tracheal cluster can 'read' differences in the distribution of FGFR activity and lead migration of the cluster accordingly. Thus, FGF can act as a chemoattractant rather than as a motogen in collective cell migration. This finding has many implications in both development and pathology.

Kim, K., Yoon, J., Yim, J. and Kim, H. J. (2015). Deneddylase 1 regulates Deneddylase activity of the Cop9 signalosome in Drosophila melanogaster. Insect Sci [Epub ahead of print]. PubMed ID: 26332639
Summary:
NEDD8 conjugation of Cullin has an important role in ubiquitin-mediated protein degradation. The COP9 signalosome, of which CSN5 is the major catalytic subunit, is a major Cullin deneddylase. Another deneddylase, Deneddylase 1, has also been shown to process the Nedd8 precursor. In Drosophila, the DEN1 mutants do not have increased levels of Cullin neddylation, but instead show a significant decrease in neddylated Cullin. This characteristic decrease in neddylated Cullins in the DEN1null background can be rescued by UAS-dDEN1WT overexpression but not by overexpression of mature NEDD8, indicating that this phenotype is distinct from the NEDD8-processing function of DEN1. This study examined the role of DEN1-CSN interaction in regulating Cullin neddylation. Overexpression of DEN1 in a CSN5hypo background slightly reduced unneddylated Cullin levels. The CSN5, DEN1 double mutation partially rescues the premature lethality associated with the CSN5 single mutation. These results suggest that DEN1 regulates Cullin neddylation by suppressing CSN deneddylase activity.

Tuesday, October 6th

Chen, S., Gendelman, H. K., Roche, J. P., Alsharif, P. and Graf, E. R. (2015). Mutational analysis of Rab3 function for controlling active zone protein composition at the Drosophila neuromuscular junction. PLoS One 10: e0136938. PubMed ID: 26317909
Summary:
At synapses, the release of neurotransmitter is regulated by molecular machinery that aggregates at specialized presynaptic release sites termed active zones. The complement of active zone proteins at each site is a determinant of release efficacy and can be remodeled to alter synapse function. The small GTPase Rab3 plays a novel role that controls the distribution of active zone proteins to individual release sites at the Drosophila neuromuscular junction. Rab3 has been extensively studied for its role in the synaptic vesicle cycle; however, the mechanism by which Rab3 controls active zone development remains unknown. To explore this mechanism, a mutational analysis was conducted to determine the molecular and structural requirements of Rab3 function at Drosophila synapses. GTP-binding was found to be required for Rab3 to traffick to synapses and distribute active zone components across release sites. Conversely, the hydrolytic activity of Rab3 is unnecessary for this function. Through a structure-function analysis specific residues were identified within the effector-binding switch regions that are required for Rab3 function, and it was determined that membrane attachment is essential. These findings suggest that Rab3 controls the distribution of active zone components via a vesicle docking mechanism that is consistent with standard Rab protein function.

Ullrich, A., Bohme, M. A., Schoneberg, J., Depner, H., Sigrist, S. J. and Noe, F. (2015). Dynamical organization of Syntaxin-1A at the presynaptic active zone. PLoS Comput Biol 11: e1004407. PubMed ID: 26367029
Summary:
Synaptic vesicle fusion is mediated by SNARE proteins forming in between synaptic vesicle (v-SNARE) and plasma membrane (t-SNARE), one of which is Syntaxin-1A. Although exocytosis mainly occurs at active zones, Syntaxin-1A appears to cover the entire neuronal membrane. By using STED super-resolution light microscopy and image analysis of Drosophila neuro-muscular junctions, this study shows that Syntaxin-1A clusters are more abundant and have an increased size at active zones. A computational particle-based model of syntaxin cluster formation and dynamics is developed. The model is parametrized to reproduce Syntaxin cluster-size distributions found by STED analysis, and successfully reproduces existing FRAP results. The model shows that the neuronal membrane is adjusted in a way to strike a balance between having most syntaxins stored in large clusters, while still keeping a mobile fraction of syntaxins free or in small clusters that can efficiently search the membrane or be traded between clusters. This balance is subtle and can be shifted toward almost no clustering and almost complete clustering by modifying the syntaxin interaction energy on the order of only 1 kBT. This capability appears to be exploited at active zones. The larger active-zone syntaxin clusters are more stable and provide regions of high docking and fusion capability, whereas the smaller clusters outside may serve as flexible reserve pool or sites of spontaneous ectopic release.

Beck, K., Ehmann, N., Andlauer, T. F., Ljaschenko, D., Strecker, K., Fischer, M., Kittel, R. J. and Raabe, T. (2015). Loss of the Coffin-Lowry syndrome associated gene RSK2 alters ERK activity, synaptic function and axonal transport in Drosophila motoneurons. Dis Model Mech 8(11):1389-400. PubMed ID: 26398944
Summary:
Plastic changes in synaptic properties are considered as fundamental for adaptive behaviors. Extracellular-signal-regulated kinase (ERK)-mediated signaling (see Drosophila Rolled) has been implicated in regulation of synaptic plasticity. Ribosomal S6 kinase 2 (RSK2) acts as a regulator and downstream effector of ERK. In the brain, RSK2 is predominantly expressed in regions required for learning and memory. Loss-of-function mutations in human RSK2 cause Coffin-Lowry Syndrome, which is characterized by severe mental retardation and low IQ scores in male patients. Knockout of RSK2 in mice or the RSK ortholog in Drosophila (see S6K) result in a variety of learning and memory defects. However, overall brain structure in these animals is not affected, leaving open the question of the pathophysiological consequences. Using the fly neuromuscular system as a model for excitatory glutamatergic synapses, this study shows that removal of RSK function causes distinct defects in motoneurons and at the neuromuscular junction. Based on histochemical and electrophysiological analyses it is concluded that RSK is required for normal synaptic morphology and function. Furthermore, loss of RSK function interferes with ERK signaling at different levels. Elevated ERK activity was evident in the somata of motoneurons, whereas decreased ERK activity was observed in axons and the presynapse. In addition, a novel function of RSK in anterograde axonal transport was uncovered. These results emphasize the importance of fine tuning ERK activity in neuronal processes underlying higher brain functions. In this context, RSK acts as a modulator of ERK signaling.

Ziegler, A. B., Menage, C., Gregoire, S., Garcia, T., Ferveur, J. F., Bretillon, L. and Grosjean, Y. (2015). Lack of dietary polyunsaturated fatty acids causes synapse dysfunction in the Drosophila visual system. PLoS One 10: e0135353. PubMed ID: 26308084
Summary:
Polyunsaturated fatty acids (PUFAs) are essential nutrients for animals and necessary for the normal functioning of the nervous system. A lack of PUFAs can result from the consumption of a deficient diet or genetic factors, which impact PUFA uptake and metabolism. Both can cause synaptic dysfunction, which is associated with numerous disorders. However, there is a knowledge gap linking these neuronal dysfunctions and their underlying molecular mechanisms. Because of its genetic manipulability and its easy, fast, and cheap breeding, Drosophila melanogaster has emerged as an excellent model organism for genetic screens, helping to identify the genetic bases of such events. As a first step towards the understanding of PUFA implications in Drosophila synaptic physiology a breeding medium containing only very low amounts of PUFAs was designed. The fly's visual system, a well-established model for studying signal transmission and neurological disorders, was used to measure the effects of a PUFA deficiency on synaptic function. Using both visual performance and eye electrophysiology, it was found that PUFA deficiency strongly affected synaptic transmission in the fly's visual system. These defects were rescued by diets containing omega-3 or omega-6 PUFAs alone or in combination. In summary, manipulating PUFA contents in the fly's diet was powerful to investigate the role of these nutrients on the fly's visual synaptic function. This study aims at showing how the first visual synapse of Drosophila can serve as a simple model to study the effects of PUFAs on synapse function. A similar approach could be further used to screen for genetic factors underlying the molecular mechanisms of synaptic dysfunctions associated with altered PUFA levels.

Monday, October 5th

Clemens, J., Girardin, C. C., Coen, P., Guan, X. J., Dickson, B. J. and Murthy, M. (2015). Connecting neural codes with behavior in the auditory system of Drosophila. Neuron 87: 1332-1343. PubMed ID: 26365767
Summary:
Brains are optimized for processing ethologically relevant sensory signals. However, few studies have characterized the neural coding mechanisms that underlie the transformation from natural sensory information to behavior. This study focused on acoustic communication in Drosophila melanogaster and used computational modeling to link natural courtship song, neuronal codes, and female behavioral responses to song. Melanogaster females are sensitive to long timescale song structure (on the order of tens of seconds). From intracellular recordings, models were generated that recapitulate neural responses to acoustic stimuli. These neural codes were linked with female behavior by generating model neural responses to natural courtship song. Using a simple decoder, female behavioral responses were predicted to the same song stimuli with high accuracy. This modeling approach reveals how long timescale song features are represented by the Drosophila brain and how neural representations can be decoded to generate behavioral selectivity for acoustic communication signals.

Rabinovich, D., Mayseless, O. and Schuldiner, O. (2015). Long term ex vivo culturing of Drosophila brain as a method to live image pupal brains: insights into the cellular mechanisms of neuronal remodeling. Front Cell Neurosci 9: 327. PubMed ID: 26379498
Summary:
Research on the stereotypic remodeling of Drosophila mushroom body (MB) γ neurons has contributed to knowledge of the molecular mechanisms of remodeling but knowledge of the cellular mechanisms remain poorly understood. A major hurdle in understanding various dynamic processes that occur during metamorphosis is the lack of time-lapse resolution. The pupal case and opaque fat bodies that enwrap the central nervous system (CNS) make live-imaging of the central brain in-vivo impossible. This study describes an ex vivo long-term brain culture system that supports the development and neuronal remodeling of pupal brains. By optimizing culture conditions and dissection protocols, development was observed in culture at kinetics similar to what occurs in vivo. Using this new method, the first time-lapse sequence of MB gamma neurons undergoing remodeling was observed in up to a single cell resolution. Axon pruning was found to be initiated by blebbing, followed by one-two nicks that seem to initiate a more widely spread axon fragmentation. The long-term ex vivo brain culture system could be used to study dynamic aspects of neurodevelopment of any Drosophila neuron.

Smith-Trunova, S., Prithviraj, R., Spurrier, J., Kuzina, I., Gu, Q. and Giniger, E. (2015). Cdk5 regulates developmental remodeling of mushroom body neurons in Drosophila. Dev Dyn [Epub ahead of print]. PubMed ID: 26394609
Summary:
During metamorphosis, axons and dendrites of the mushroom body (MB) in the Drosophila central brain are remodeled extensively to support the transition from larval to adult behaviors. This study shows that the neuronal cyclin-dependent kinase, Cdk5, regulates the timing and rate of mushroom body remodeling: reduced Cdk5 activity causes a delay in pruning of MB neurites, while hyperactivation accelerates it. It was shown that Cdk5 cooperates with the ubiquitin-proteasome system in this process. Finally, Cdk5 modulates the first overt step in neurite disassembly, dissolution of the neuronal tubulin cytoskeleton, and it also acts at additional steps of MB pruning. These data show that Cdk5 regulates the onset and extent of remodeling of the Drosophila MB. Given the wide phylogenetic conservation of Cdk5, the study suggests that it is likely to play a role in developmental remodeling in other systems, as well. Moreover, it can be speculated that the well-established role of Cdk5 in neurodegeneration may involve some of the same cellular mechanisms that it employs during developmental remodeling.

Valmalette, J. C., Raad, H., Qiu, N., Ohara, S., Capovilla, M. and Robichon, A. (2015). Nano-architecture of gustatory chemosensory bristles and trachea in Drosophila wings. Sci Rep 5: 14198. PubMed ID: 26381332
Summary:
In the Drosophila wing anterior margin, the dendrites of gustatory neurons occupy the interior of thin and long bristles that present tiny pores at their extremities. The functions of this gustatory activity remain elusive and controversial. This study investigated the architecture of the wing chemosensory bristles and wing trachea using Raman spectroscopy and fluorescence microscopy. It was hypothesized that the wing gustatory hair, an open-ended capillary tube, and the wing trachea constitute biological systems similar to nano-porous materials. Evidence is presented that argues in favour of the existence of a layer or a bubble of air beneath the pore inside the gustatory hair. These hollow hairs and wing tracheal tubes fulfill conditions for which the physics of fluids applied to open-ended capillaries and porous materials are relevant. The wing gustatory hair and tracheal architectures were shown to be capable of trapping volatile molecules from the environment, which might increase the efficiency of their spatial detection by way of wing vibrations or during flight.

Sunday, October 4th

Newton, F. G., Harris, R. E., Sutcliffe, C. and Ashe, H. L. (2015). Coordinate post-transcriptional repression of Dpp-dependent transcription factors attenuates signal range during development. Development 142(19):3362-73. PubMed ID: 26293305
Summary:
Precise control of the range of signalling molecule action is critical for correct cell fate patterning during development. For example, Drosophila ovarian germline stem cells (GSCs) are maintained by exquisitely short-range BMP signalling from the niche. In the absence of BMP signalling, one GSC daughter differentiates into a cystoblast (CB) and this fate is stabilised by Brain Tumour (Brat) and Pumilio (Pum)-mediated post-transcriptional repression of mRNAs, including that encoding the Dpp transducer, Mad. However, the identity of other repressed mRNAs and the mechanism of post-transcriptional repression are currently unknown. This study identified the Medea and schnurri mRNAs, which encode transcriptional regulators required for activation and/or repression of Dpp target genes, as additional Pum-Brat targets suggesting that tripartite repression of the transducers is deployed to desensitise the CB to Dpp. In addition, this study shows that repression by Pum-Brat requires recruitment of the CCR4 and Pop2 deadenylases, with knockdown of deadenylases in vivo giving rise to ectopic GSCs. Consistent with this, Pum-Brat repression leads to poly(A) tail shortening and mRNA degradation in tissue culture cells and a reduced number of Mad and shn transcripts in the CB relative to the GSC based on single molecule mRNA quantitation. Finally, the generality of the mechanism was shown by demonstrating that Brat also attenuates pMad and Dpp signalling range in the early embryo. Together these data serve as a platform for understanding how post-transcriptional repression restricts interpretation of BMPs and other cell signals in order to allow robust cell fate patterning during development.

Marco, A. (2015). Selection against maternal microRNA target sites in maternal transcripts. G3 (Bethesda) 5(10):2199-207. PubMed ID: 26306531
Summary:
In animals, before the zygotic genome is expressed, the egg already contains gene products deposited by the mother. These maternal products are crucial during the initial steps of development. In Drosophila melanogaster a large number of maternal products are found in the oocyte, some of which are indispensable. Many of these products are RNA molecules, such as gene transcripts and ribosomal RNAs. Recently, microRNAs - small RNA gene regulators - have been detected early during development and are important in these initial steps. The presence of some microRNAs in unfertilized eggs has been reported, but whether they have a functional impact in the egg or early embryo has not being explored. This study extracted and sequenced small RNAs from Drosophila unfertilized eggs. The unfertilized egg is rich in small RNAs and contains multiple microRNA products. Maternal microRNAs are often encoded within the intron of maternal genes, suggesting that many maternal microRNAs are the product of transcriptional hitch-hiking. Comparative genomics analyses suggest that maternal transcripts tend to avoid target sites for maternal microRNAs. A microRNA target mutation model was developed to study the functional impact of polymorphisms at microRNA target sites. The analysis of Drosophila populations suggests that there is selection against maternal microRNA target sites in maternal transcripts. A potential role of the maternal microRNA mir-9c in maternal-to-zygotic transition is also discussed. In conclusion, maternal microRNAs in Drosophila have a functional impact in maternal protein-coding transcripts.

Wang, W., Han, B. W., Tipping, C., Ge, D. T., Zhang, Z., Weng, Z. and Zamore, P. D. (2015). Slicing and binding by Ago3 or Aub trigger Piwi-bound piRNA production by distinct mechanisms. Mol Cell 59: 819-830. PubMed ID: 26340424
Summary:
In Drosophila ovarian germ cells, PIWI-interacting RNAs (piRNAs) direct Aubergine and Argonaute3 to cleave transposon transcripts and instruct Piwi to repress transposon transcription, thereby safeguarding the germline genome. This study reports that RNA cleavage by Argonaute3 initiates production of most Piwi-bound piRNAs. The cardinal function of Argonaute3, whose piRNA guides predominantly correspond to sense transposon sequences, is to produce antisense piRNAs that direct transcriptional silencing by Piwi, rather than to make piRNAs that guide post-transcriptional silencing by Aubergine. It was also found that the Tudor domain protein Qin prevents Aubergine's cleavage products from becoming Piwi-bound piRNAs, ensuring that antisense piRNAs guide Piwi. Although Argonaute3 slicing is required to efficiently trigger phased piRNA production, an alternative, slicing-independent pathway suffices to generate Piwi-bound piRNAs that repress transcription of a subset of transposon families. This alternative pathway may help flies silence newly acquired transposons for which they lack extensively complementary piRNAs.

Bertin, B., Renaud, Y., Aradhya, R., Jagla, K. and Junion, G. (2015). TRAP-rc, translating ribosome affinity purification from rare cell populations of Drosophila embryos. J Vis Exp [Epub ahead of print]. PubMed ID: 26381166
Summary:
Measuring levels of mRNAs in the process of translation in individual cells provides information on the proteins involved in cellular functions at a given point in time. The protocol dubbed Translating Ribosome Affinity Purification (TRAP) is able to capture this mRNA translation process in a cell-type-specific manner. Based on the affinity purification of polysomes carrying a tagged ribosomal subunit, TRAP can be applied to translatome analyses in individual cells, making it possible to compare cell types during the course of developmental processes or to track disease development progress and the impact of potential therapies at molecular level. This study reports an optimized version of the TRAP protocol, called TRAP-rc (rare cells), dedicated to identifying engaged-in-translation RNAs from rare cell populations. TRAP-rc was validated using the Gal4/UAS targeting system in a restricted population of muscle cells in Drosophila embryos. This novel protocol allows the recovery of cell-type-specific RNA in sufficient quantities for global gene expression analytics such as microarrays or RNA-seq. The robustness of the protocol and the large collections of Gal4 drivers make TRAP-rc a highly versatile approach with potential applications in cell-specific genome-wide studies.

Saturday, October 3rd

Heidari, R., Monnier, V., Martin, E. and Tricoire, H. (2015). Methylene blue partially rescues heart defects in a Drosophila model of Huntington's disease. J Huntingtons Dis 4: 173-186. PubMed ID: 26397898
Summary:
Huntington's disease (HD) is a Polyglutamine disease caused by the presence of CAG repeats in the first exon of Huntingtin (Htt), a large protein with multiple functions. This study reports the construction of inducible Drosophila HD heart models, expressing two Nter fragments of the protein encompassing either exon 1 or the first 171 amino acids and the characterization of heart phenotypes in vivo. Both mHtt fragments were shown to be able to impair fly cardiac function with different characteristics. Additionally, expression of mHtt, which was limited to adulthood only, leads to mild heart impairment, as opposed to a strong and age-dependent phenotype observed when mHtt expression was driven during both developmental and adult stages. Also, treatment with methylene blue (MB), a protective compound in mitochondria-related diseases, partially protects the fly's heart against mHtt-induced toxicity, but does not rescue neuronal or glial phenotypes in other fly models of HD. This may be linked to its low penetration through the fly's blood-brain barrier. These data suggest that improvement of mitochondrial function by MB, or related compounds, could be an efficient therapeutic strategy to prevent cardiac failure in HD patients.

Babcock, D. T. and Ganetzky, B. (2015). Transcellular spreading of huntingtin aggregates in the Drosophila brain. Proc Natl Acad Sci U S A. 112(39):E5427-33. PubMed ID: 26351672
Summary:
A key feature of many neurodegenerative diseases is the accumulation and subsequent aggregation of misfolded proteins. Recent studies have highlighted the transcellular propagation of protein aggregates in several major neurodegenerative diseases, although the precise mechanisms underlying this spreading and how it relates to disease pathology remain unclear. This study used a polyglutamine-expanded form of human huntingtin (Htt; see Drosophila huntingtin) with a fluorescent tag to monitor the spreading of aggregates in the Drosophila brain in a model of Huntington's disease. Upon expression of this construct in a defined subset of neurons, it was demonstrated that protein aggregates accumulate at synaptic terminals and progressively spread throughout the brain. These aggregates are internalized and accumulate within other neurons. Htt aggregates cause non-cell-autonomous pathology, including loss of vulnerable neurons that can be prevented by inhibiting endocytosis in these neurons. Finally it was shown that the release of aggregates requires N-ethylmalemide-sensitive fusion protein 1, demonstrating that active release and uptake of Htt aggregates are important elements of spreading and disease progression.

Clark, R. I., Salazar, A., Yamada, R., Fitz-Gibbon, S., Morselli, M., Alcaraz, J., Rana, A., Rera, M., Pellegrini, M., Ja, W. W. and Walker, D. W. (2015). Distinct shifts in microbiota composition during Drosophila aging impair intestinal function and drive mortality. Cell Rep 12: 1656-1667. PubMed ID: 26321641
Summary:
Alterations in the composition of the intestinal microbiota have been correlated with aging and measures of frailty in the elderly. However, the relationships between microbial dynamics, age-related changes in intestinal physiology, and organismal health remain poorly understood. This study shows that dysbiosis of the intestinal microbiota, characterized by an expansion of the Gammaproteobacteria, is tightly linked to age-onset intestinal barrier dysfunction in Drosophila. Indeed, alterations in the microbiota precede and predict the onset of intestinal barrier dysfunction in aged flies. Changes in microbial composition occurring prior to intestinal barrier dysfunction contribute to changes in excretory function and immune gene activation in the aging intestine. In addition, a distinct shift in microbiota composition was shown to follow intestinal barrier dysfunction, leading to systemic immune activation and organismal death. These results indicate that alterations in microbiota dynamics could contribute to and also predict varying rates of health decline during aging in mammals.

Obata, F. and Miura, M. (2015). Enhancing S-adenosyl-methionine catabolism extends Drosophila lifespan. Nat Commun 6: 8332. PubMed ID: 26383889
Summary:
Methionine restriction extends the lifespan of various model organisms. Limiting S-adenosyl-methionine (SAM) synthesis, the first metabolic reaction of dietary methionine, extends longevity in Caenorhabditis elegans but accelerates pathology in mammals. This study shows that, as an alternative to inhibiting SAM synthesis, enhancement of SAM catabolism by Glycine N-methyltransferase (Gnmt) extends the lifespan in Drosophila. Gnmt strongly buffers systemic SAM levels by producing sarcosine in either high-methionine or low-sams conditions. During ageing, systemic SAM levels in flies are increased. Gnmt is transcriptionally induced in a dFoxO-dependent manner; however, this is insufficient to suppress SAM elevation completely in old flies. Overexpression of gnmt suppresses this age-dependent SAM increase and extends longevity. Pro-longevity regimens, such as dietary restriction or reduced insulin signalling, attenuate the age-dependent SAM increase, and rely at least partially on Gnmt function to exert their lifespan-extending effect in Drosophila. This study suggests that regulation of SAM levels by Gnmt is a key component of lifespan extension.

Friday, October 2nd

Breuer, M. and Ohkura, H. (2015). A negative loop within the nuclear pore complex controls global chromatin organization. Genes Dev 29: 1789-1794. PubMed ID: 26341556
Summary:
The nuclear pore complex (NPC) tethers chromatin to create an environment for gene regulation, but little is known about how this activity is regulated to avoid excessive tethering of the genome. Tethering specific genomic loci to the NPC appears to contribute to transcriptional activation. Also, the NPC has been further implicated in creating a repressive environment or retaining genes at the periphery after repression, possibly contributing to epigenetic transcriptional memory. This paper proposes a negative regulatory loop within the NPC controlling the chromatin attachment state, in which Nup155 and Nup93 recruit Nup62 to suppress chromatin tethering by Nup155. Depletion of Nup62 severely disrupts chromatin distribution in the nuclei of female germlines and somatic cells, which can be reversed by codepleting Nup155. See a model for the chromatin attachment state controlled by an internal regulatory circuit in the NPC. Thus, this universal regulatory system within the NPC is crucial to control large-scale chromatin organization in the nucleus.

Li, M., Ma, Z., Liu, J. K., Roy, S., Patel, S. K., Lane, D. C. and Cai, H. N. (2015). An organizational hub of developmentally regulated chromatin loops in the Drosophila Antennapedia complex. Mol Cell Biol 35(23):4018-29. PubMed ID: 26391952
Summary:
The complex expression pattern of the Drosophila homeotic gene Sex combs reduced (Scr) is directed by an unusually long regulatory sequence harboring diverse cis elements and an intervening neighbor gene fushi tarazu (ftz). This study reports the presence of a multitude of Chromatin boundary elements (CBEs) in the Scr regulatory region. Selective and dynamic pairing among these CBEs mediates developmentally regulated chromatin loops. In particular, the SF1 boundary plays a central role in organizing two subsets of chromatin loops: one subset encloses ftz, limiting its access by the surrounding Scr enhancers and compartmentalizing distinct histone modifications; and the other subset subdivides the Scr regulatory sequences into independent enhancer access domains. Tandem pairing of SF1 and SF2, two strong CBEs that flank the ftz domain, providing a mechanism for the endogenous Scr enhancer to circumvent the ftz domain. This study demonstrates how an endogenous CBE network, centrally orchestrated by SF1, could remodel the genomic environment to facilitate gene regulation during development.

Singh, A.K. and Lakhotia, S.C. (2015). The hnRNP A1 homolog Hrb87F/Hrp36 is important for telomere maintenance in Drosophila melanogaster. Chromosoma [Epub ahead of print]. PubMed ID: 26373285
Summary:
Unlike the telomerase-dependent mammalian telomeres, HeT-A, TART, and TAHRE (HTT) retroposon arrays regulate Drosophila telomere length. Cap prevents telomeric associations (TAs) and telomeric fusions (TFs). Results from this study suggest important roles of Hrb87F in telomeric HTT array and cap maintenance in Drosophila. All chromosome arms, except 2L, in Df(3R)Hrb87F homozygotes (Hrb87F-null) display significantly elongated telomeres with amplified HTT arrays and high TAs, all of which resolve without damage. Presence of FLAG-tagged Hrb87F (FLAG-Hrb87F) on cap and subtelomeric regions following hsFLAG-Hrb87F transgene expression in Df(3R)Hrb87F homozygotes suppresses TAs without affecting telomere length. A normal X-chromosome telomere expands within five generations in Hrb87F-null background and displays high TAs, but not when hsFLAG-Hrb87F is co-expressed. Tel 1 /Gaiano line or HP1 loss-of-function mutant-derived expanded telomeres carry Hrb87F on cap and HTT arrays while Hrb87F-null telomeres have HP1 and HOAP on caps and expanded HTT arrays. ISWI, seen only on cap on normal telomeres, is abundant on Hrb87F-null expanded HTT arrays. Together, these suggest complex interactions between members of the proteome of telomeres so that absence of any key member leads to telomere expansion and/or enhanced TAs/TFs. HTT expansion in Hrb87F-null condition is not developmental but a germline event presumably because absence of Hrb87F in germline may deregulate HTT retroposition/replication leading to telomere elongation.

Shimaji, K., Konishi, T., Tanaka, S., Yoshida, H., Kato, Y., Ohkawa, Y., Sato, T., Suyama, M., Kimura, H. and Yamaguchi, M. (2015). Genomewide identification of target genes of histone methyltransferase dG9a during Drosophila embryogenesis. Genes Cells 20(11):902-14. PubMed ID: 26334932
Summary:
Post-translational modification of the histone plays important roles in epigenetic regulation of various biological processes. Among the identified histone methyltransferases (HMTases), G9a is a histone H3 Lys 9 (H3K9)-specific example active in euchromatic regions. Drosophila G9a (dG9a) has been reported to feature H3K9 dimethylation activity in vivo. This study shows that the time required for hatching of a homozygous dG9a null mutant and heteroallelic combination of dG9a null mutants is delayed, suggesting that dG9a is at least partially responsible for progression of embryogenesis. Immunocytochemical analyses of the wild-type and the dG9a null mutant flies indicated that dG9a localizes in cytoplasm up to nuclear division cycle 7 where it is likely responsible for di-methylation of nucleosome-free H3K9. From cycles 8-11, dG9a moves into the nucleus and is responsible for di-methylating H3K9 in nucleosomes. RNA-sequence analysis utilizing early wild-type and dG9a mutant embryos showed that dG9a down-regulates expression of genes responsible for embryogenesis. RNA fluorescent in situ hybridization analysis further showed temporal and spatial expression patterns of these mRNAs did not significantly change in the dG9a mutant. These results indicate that dG9a controls transcription levels of some zygotic genes without changing temporal and spatial expression patterns of the transcripts of these genes.

Thursday, October 1st

Isabella, A. J. and Horne-Badovinac, S. (2015). Dynamic regulation of basement membrane protein levels promotes egg chamber elongation in Drosophila. Dev Biol [Epub ahead of print]. PubMed ID: 26348027
Summary:
Basement membranes (BMs) are sheet-like extracellular matrices that provide essential support to epithelial tissues. Recent evidence suggests that regulated changes in BM architecture can direct tissue morphogenesis. The Drosophila egg chamber transforms from a spherical to an ellipsoidal shape as it matures. This elongation coincides with a stage-specific increase in Type IV Collagen (Col IV) levels in the BM surrounding the egg chamber. This study identified the Collagen-binding protein SPARC as a negative regulator of egg chamber elongation and shows that SPARC down-regulation is necessary for the increase in Col IV levels to occur. SPARC was found to interact with Col IV prior to secretion and it is proposed that, through this interaction, SPARC blocks the incorporation of newly synthesized Col IV into the BM. A decrease was observed in Perlecan levels during elongation, and Perlecan was shown to be a negative regulator of this process. These data provide mechanistic insight into SPARC's conserved role in matrix dynamics and demonstrate that regulated changes in BM composition influence organ morphogenesis.

Ng, W.C., Chin, J.S., Tan, K.J. and Yew, J.Y. (2015). The fatty acid elongase Bond is essential for Drosophila sex pheromone synthesis and male fertility. Nat Commun 6: 8263. PubMed ID: 26369287
Summary:
Insects use a spectacular variety of chemical signals to guide their social behaviours. How such chemical diversity arises is a long-standing problem in evolutionary biology. This study describes the contribution of the fatty acid elongase Bond to both pheromone diversity and male fertility in Drosophila. Genetic manipulation and mass spectrometry analysis reveal that the loss of bond eliminates the male sex pheromone (3R,11Z,19Z)-3-acetoxy-11,19-octacosadien-1-ol (CH503). Unexpectedly, silencing bond expression severely suppresses male fertility and the fertility of conspecific rivals. These deficits are rescued on ectopic expression of bond in the male reproductive system. A comparative analysis across six Drosophila species shows that the gain of a novel transcription initiation site is correlated with bond expression in the ejaculatory bulb, a primary site of male pheromone production. Taken together, these results indicate that modification of cis-regulatory elements and subsequent changes in gene expression pattern is one mechanism by which pheromone diversity arises

Reubens, M.C., Biller, M.D., Bedsole, S.E., Hopkins, L.T., Ables, E.T. and Christensen, T.W. (2015). Mcm10 is required for oogenesis and early embryogenesis in Drosophila. Mech Dev [Epub ahead of print]. PubMed ID: 26369283
Summary:
Efficient replication of the genome and the establishment of endogenous chromatin states are processes that are essential to eukaryotic life. It is well documented that Mcm10 is intimately linked to both of these important biological processes; therefore, it is not surprising that Mcm10 is commonly misregulated in many human cancers. Most of the research regarding the biological roles of Mcm10 has been performed in single-cell or cell-free in-vitro systems. Though these systems are informative, they are unable to provide information on the cell-specific function of Mcm10 in the context of the tissue and organ systems that comprise multicellular eukaryotes. This study sought to identify the potential biological functions of Mcm10 in the context of a complex multicellular organism by analysis in Drosophila using three novel hypomorphic alleles. Observation of embryonic nuclear morphology and quantification of embryo hatch rates reveal that maternal loading of Mcm10 is required for embryonic nuclear stability and suggest a role for Mcm10 post zygotic transition. Contrary to the essential nature of Mcm10 depicted in the literature, it does not appear to be required for adult viability in Drosophila if embryonic requirements are met. Although not required for adult somatic viability, analysis of fecundity and ovarian morphology in mutant females suggest that Mcm10 plays a role in maintenance of the female germline. Taken together, these results demonstrate critical roles for Mcm10 during early embryogenesis, and mark the first data linking Mcm10 to female specific reproduction in multicellular eukaryotes.

Liu, G., Sanghavi, P., Bollinger, K. E., Perry, L., Marshall, B., Roon, P., Tanaka, T., Nakamura, A. and Gonsalvez, G. B. (2015). Efficient endocytic uptake and maturation in Drosophila oocytes requires Dynamitin/p50. Genetics 201(2):631-49. PubMed ID: 26265702
Summary:
Dynactin is a multi-subunit complex that functions as a regulator of the Dynein motor. A central component of this complex is Dynamitin/p50 (Dmn). Dmn is required for endosome motility in mammalian cell lines. However, the extent to which Dmn participates in the sorting of cargo via the endosomal system is unknown. This study examined the endocytic role of Dmn using the Drosophila melanogaster oocyte as a model. Yolk proteins are internalized into the oocyte via clathrin-mediated endocytosis, trafficked through the endocytic pathway, and stored in condensed yolk granules. Oocytes that were depleted of Dmn contained fewer yolk granules than controls. In addition, these oocytes accumulated numerous endocytic intermediate structures. Particularly prominent were enlarged endosomes that were relatively devoid of yolk proteins. Ultrastructural and genetic analyses indicate that the endocytic intermediates are produced downstream of Rab5. Similar phenotypes were observed upon depleting Dynein heavy chain (Dhc) or Lis1. Dhc is the motor subunit of the Dynein complex and Lis1 is a regulator of Dynein activity. It is therefore proposed that Dmn performs its function in endocytosis via the Dynein motor. Consistent with a role for Dynein in endocytosis, the motor co-localized with the endocytic machinery at the oocyte cortex in an endocytosis-dependent manner. These results suggest a model whereby endocytic activity recruits Dynein to the oocyte cortex. The motor along with its regulators, Dynactin and Lis1, functions to ensure efficient endocytic uptake and maturation.

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