What's hot today:
Current papers in developmental biology and gene function
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Sunday, January 31st, 2016

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December 2015 		David-Morrison, G., Xu, Z., Rui, Y.N., Charng, W.L., Jaiswal, M., Yamamoto, S., Xiong, B., Zhang, K., Sandoval, H., Duraine, L., Zuo, Z., Zhang, S. and Bellen, H.J. (2016). WAC regulates mTOR activity by acting as an adaptor for the TTT and Pontin/Reptin complexes. Dev Cell 36: 139-151. PubMed ID: 26812014
Summary:
The ability to sense energy status is crucial in the regulation of metabolism via the mechanistic Target of Rapamycin Complex 1 (mTORC1). The assembly of the TTT-Pontin/Reptin complex is responsive to changes in energy status. Under energy-sufficient conditions, the TTT-Pontin/Reptin complex promotes mTORC1 dimerization and mTORC1-Rag interaction, which are critical for mTORC1 activation. This study shows that WAC is a regulator of energy-mediated mTORC1 activity. In a Drosophila screen designed to isolate mutations that cause neuronal dysfunction, wacky, the homolog of WAC, was identified. Loss of Wacky leads to neurodegeneration, defective mTOR activity, and increased autophagy. Wacky and WAC have conserved physical interactions with mTOR and its regulators, including Pontin and Reptin, which bind to the TTT complex to regulate energy-dependent activation of mTORC1. WAC promotes the interaction between TTT and Pontin/Reptin in an energy-dependent manner, thereby promoting mTORC1 activity by facilitating mTORC1 dimerization and mTORC1-Rag interaction.

Casas-Tinto, S., Lolo, F. N. and Moreno, E. (2015). Active JNK-dependent secretion of Drosophila Tyrosyl-tRNA synthetase by loser cells recruits haemocytes during cell competition. Nat Commun 6: 10022. PubMed ID: 26658841
Summary:
Cell competition is a process by which the slow dividing cells (losers) are recognized and eliminated from growing tissues. Loser cells are extruded from the epithelium and engulfed by the haemocytes, the Drosophila macrophages. However, how macrophages identify the dying loser cells is unclear. This study shows that apoptotic loser cells secrete Tyrosyl-tRNA synthetase (TyrRS), which is best known as a core component of the translational machinery. Secreted TyrRS is cleaved by matrix metalloproteinases generating MiniTyr and EMAP fragments. EMAP acts as a guiding cue for macrophage migration in the Drosophila larvae, as it attracts the haemocytes to the apoptotic loser cells. JNK signalling and Kish, a component of the secretory pathway, are autonomously required for the active secretion of TyrRS by the loser cells. Altogether, this mechanism guarantees effective removal of unfit cells from the growing tissue.

Fisher, K. H., Stec, W., Brown, S. and Zeidler, M. P. (2015). Mechanisms of JAK/STAT pathway negative regulation by the short coreceptor Eye Transformer / Latran. Mol Biol Cell. PubMed ID: 26658615
Summary:
Transmembrane receptors interact with extracellular ligands to transduce intracellular signaling cascades, modulate target gene expression and regulate processes such as proliferation, apoptosis, differentiation and homeostasis. As a consequence, aberrant signaling events often underlie human disease. While the vertebrate JAK/STAT signaling cascade is transduced via multiple receptor combinations, the Drosophila pathway has only one full-length signaling receptor, Domeless (Dome) and a single negatively acting receptor, Eye Transformer/Latran (Et/Lat). This study investigated the molecular mechanisms underlying Et/Lat activity. Et/Lat was shown to negatively regulates JAK/STAT pathway activity and can bind to Dome so reducing Dome:Dome homo-dimerisation by creating signaling-incompetent Dome:Et/Lat heterodimers. Surprisingly, Et/Lat was found to be able to bind to both JAK and STAT92E, but despite the presence of putative cytokine binding motifs, does not detectably interact with pathway ligands. Et/Lat is trafficked through the endocytic machinery for lysosomal degradation, but at a much slower rate than Dome - a difference that may enhance its ability to sequester Dome into signaling incompetent complexes. These data offer new insights into the molecular mechanism and regulation of Et/Lat in Drosophila that may inform understanding of how short receptors function in other organisms.

Li, T., Cao, C., Yang, T., Zhang, L., He, L., Xi, Z., Bian, G. and Liu, N. (2015). A G-protein-coupled receptor regulation pathway in cytochrome P450-mediated permethrin-resistance in mosquitoes, Culex quinquefasciatus. Sci Rep 5: 17772. PubMed ID: 26656663
Summary:
Rhodopsin-like G protein-coupled receptors (GPCRs) are known to be involved in the GPCR signal transduction system and regulate many essential physiological processes in organisms. This study revealed that knockdown of the rhodopsin-like GPCR gene, showing 57% identity to Drosophila NinaE) in resistant mosquitoes resulted in a reduction of mosquitoes' resistance to permethrin, simultaneously reducing the expression of two cAMP-dependent protein kinase A genes (PKAs) and four resistance related cytochrome P450 genes. The function of rhodopsin-like GPCR was further confirmed using transgenic lines of Drosophila, in which the tolerance to permethrin and the expression of Drosophila resistance P450 genes were both increased. The roles of GPCR signaling pathway second messenger cyclic adenosine monophosphate (cAMP) and downstream effectors PKAs in resistance were investigated using cAMP production inhibitor Bupivacaine HCl and the RNAi technique. Inhibition of cAMP production led to significant decreases in both the expression of four resistance P450 genes and two PKA genes and mosquito resistance to permethrin. Knockdown of the PKA genes had shown the similar effects on permethrin resistance and P450 gene expression. Taken together, these studies revealed the role of the GPCR/cAMP/PKA-mediated regulatory pathway governing P450 gene expression and P450-mediated resistance in Culex mosquitoes.

Saturday, January 30th

Unckless, R.L., Howick, V.M. and Lazzaro, B.P. (2016). Convergent balancing selection on an antimicrobial peptide in Drosophila. Curr Biol [Epub ahead of print]. PubMed ID: 26776733
Summary:
Genes of the immune system often evolve rapidly and adaptively, presumably driven by antagonistic interactions with pathogens. Those genes encoding secreted antimicrobial peptides (AMPs), however, have failed to exhibit conventional signatures of strong adaptive evolution, especially in arthropods and often segregate for null alleles and gene deletions. Furthermore, quantitative genetic studies have failed to associate naturally occurring polymorphism in AMP genes with variation in resistance to infection. Both the lack of signatures of positive selection in AMPs and lack of association between genotype and immune phenotypes have yielded an interpretation that AMP genes evolve under relaxed evolutionary constraint, with enough functional redundancy that variation in, or even loss of, any particular peptide would have little effect on overall resistance. In stark contrast to the current paradigm, this study identified a naturally occurring amino acid polymorphism in the AMP Diptericin that is highly predictive of resistance to bacterial infection in Drosophila melanogaster. The identical amino acid polymorphism arose in parallel in the sister species D. simulans, by independent mutation with equivalent phenotypic effect. Convergent substitutions at the same amino acid residue have evolved at least five times across the Drosophila genus. The study hypothesizes that the alternative alleles are maintained by balancing selection through context-dependent or fluctuating selection. This pattern of evolution appears to be common in AMPs but is invisible to conventional screens for adaptive evolution that are predicated on elevated rates of amino acid divergence.

Lack, J. B., Monette, M. J., Johanning, E. J., Sprengelmeyer, Q. D. and Pool, J. E. (2016). Decanalization of wing development accompanied the evolution of large wings in high-altitude Drosophila. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 26755605
Summary:
In higher organisms, the phenotypic impacts of potentially harmful or beneficial mutations are often modulated by complex developmental networks. Stabilizing selection may favor the evolution of developmental canalization-that is, robustness despite perturbation-to insulate development against environmental and genetic variability. In contrast, directional selection acts to alter the developmental process, possibly undermining the molecular mechanisms that buffer a trait's development, but this scenario has not been shown in nature. This study examined the developmental consequences of size increase in highland Ethiopian Drosophila melanogaster. Ethiopian inbred strains exhibited much higher frequencies of wing abnormalities than lowland populations, consistent with an elevated susceptibility to the genetic perturbation of inbreeding. Mutagenesis was then used to test whether Ethiopian wing development is, indeed, decanalized. Ethiopian strains were far more susceptible to this genetic disruption of development, yielding 26 times more novel wing abnormalities than lowland strains in F2 males. Wing size and developmental perturbability cosegregated in the offspring of between-population crosses, suggesting that genes conferring size differences had undermined developmental buffering mechanisms. These findings represent the first observation of morphological evolution associated with decanalization in the same tissue, underscoring the sensitivity of development to adaptive change.

Craddock, E. M., Gall, J. G. and Jonas, M. (2016). Hawaiian Drosophila genomes: size variation and evolutionary expansions. Genetica [Epub ahead of print]. PubMed ID: 26790663
Summary:
This paper reports genome sizes of one Hawaiian Scaptomyza and 16 endemic Hawaiian Drosophila species that include five members of the antopocerus species group, one member of the modified mouthpart group, and ten members of the picture wing clade. Genome size expansions have occurred independently multiple times among Hawaiian Drosophila lineages, and have resulted in an over 2.3-fold range of genome sizes among species, with the largest observed in Drosophila cyrtoloma (1C = 0.41 pg). Evidence was found that these repeated genome size expansions were likely driven by the addition of significant amounts of heterochromatin and satellite DNA. For example, the data reveal that the addition of seven heterochromatic chromosome arms to the ancestral haploid karyotype, and a remarkable proportion of ~70 % satellite DNA, account for the greatly expanded size of the D. cyrtoloma genome. Moreover, the genomes of 13/17 Hawaiian picture wing species are composed of substantial proportions (22-70 %) of detectable satellites (all but one of which are AT-rich). These results suggest that in this tightly knit group of recently evolved species, genomes have expanded, in large part, via evolutionary amplifications of satellite DNA sequences in centric and pericentric domains (especially of the X and dot chromosomes), which have resulted in longer acrocentric chromosomes or metacentrics with an added heterochromatic chromosome arm. Possible evolutionary mechanisms are discussed that may have shaped these patterns, including rapid fixation of novel expanded genomes during founder-effect speciation.

Kapun, M., Fabian, D. K., Goudet, J. and Flatt, T. (2016). Genomic evidence for adaptive inversion clines in Drosophila melanogaster. Mol Biol Evol [Epub ahead of print]. PubMed ID: 26796550
Summary:
Clines in chromosomal inversion polymorphisms - presumably driven by climatic gradients - are common but there is surprisingly little evidence for selection acting on them. This long-standing issue was addressed in Drosophila melanogaster by using diagnostic SNP markers to estimate inversion frequencies from 28 whole-genome Pool-seq samples collected from 10 populations along the North American east coast. Inversions In(3L)P, In(3R)Mo and In(3R)Payne showed clear latitudinal clines, and for In(2L)t, In(2R)NS, and In(3R)Payne the steepness of the clinal slopes changed between summer and fall. Consistent with an effect of seasonality on inversion frequencies, small but stable seasonal fluctuations of In(2R)NS and In(3R)Payne were detected in a temperate Pennsylvanian population over 4 years. In support of spatially varying selection, it was observed that the cline in In(3R)Payne has remained stable for >40 years and that the frequencies of In(2L)t and In(3R)Payne are strongly correlated with climatic factors that vary latitudinally, independent of population structure. To test whether these patterns are adaptive, the amount of genetic differentiation of inversions versus neutral SNPs was compared, and the clines in In(2L)t and In(3R)Payne were found to be maintained non-neutrally and independent of admixture. Numerous clinal inversion-associated SNPs were also identified, many of which exhibit parallel differentiation along the Australian cline and reside in genes known to affect fitness-related traits. Together, these results provide strong evidence that inversion clines are maintained by spatially - and perhaps also temporally - varying selection. These data are interpreted in light of current hypotheses about how inversions are established and maintained.

Crombach, A., Wotton, K. R., Jimenez-Guri, E. and Jaeger, J. (2016). Gap gene regulatory dynamics evolve along a genotype network. Mol Biol Evol [Epub ahead of print]. PubMed ID: 26796549
Summary:
Developmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as "system drift". System drift is illustrated by the gap gene network-involved in segmental patterning-in dipteran insects. In the classic model organism Drosophila melanogaster and the non-model scuttle fly Megaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is essentially identical in both species. In this detailed modeling analysis of system drift, gene circuits were used that are fit to quantitative gap gene expression data in M. abdita, and they were compared to an equivalent set of models from D. melanogaster. The results of this comparative analysis show precisely how compensatory regulatory mechanisms achieve equivalent final patterns in both species. The larger implications of the work are discussed in terms of "genotype networks" and the ways in which the structure of regulatory networks can influence patterns of evolutionary change (evolvability).

Nguyen, A. D., Gotelli, N. J. and Cahan, S. H. (2016). The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evol Biol 16: 15. PubMed ID: 26787420
Summary:
This study reconstructed the evolutionary history of three families of Heat Shock Proteins (Hsp90, Hsp70, Hsp40) across 12 eusocial Hymenopteran species and four other insect orders. Thermal inducibility of eight Hsps was predicted and tested from the presence of cis-regulatory heat shock elements (HSEs). Evidence was found for duplications, losses, and cis-regulatory changes in two of the three gene families. One member of the Hsp90 gene family, hsp83, duplicated basally in the Hymenoptera, with shifts in HSE motifs in the novel copy. Both copies were retained in bees, but ants retained only the novel HSE copy. For Hsp70, Hymenoptera lack the primary heat-inducible orthologue from Drosophila melanogaster and instead induce the cognate form, hsc70-4, which also underwent an early duplication. Episodic diversifying selection was detected along the branch predating the duplication of hsc70-4 and continued along one of the paralogue branches after duplication. Four out of eight Hsp genes were heat-inducible and matched the predictions based on presence of conserved HSEs. It is concluded that ants utilize lineage-specific heat inducible Hsps, whose expression patterns are associated with adaptive variation in thermal tolerance between two ant species. Collectively, these analyses suggest that Hsp sequence and expression patterns may reflect the forces of selection acting on thermal tolerance in ants and other social Hymenoptera.

Friday, January 29th

Kučerová, L., Kubrak, O.I., Bengtsson, J.M., Strnad, H., Nylin, S., Theopold, U. and Nässel, D.R. (2016). Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster. BMC Genomics 17: 50. PubMed ID: 26758761
Summary:
This study conducted a genome wide analysis of transcript changes in diapausing Drosophila and found a differential regulation of more than 4600 genes. Gene ontology (GO) and KEGG pathway analysis reveal that many of these genes are part of signaling pathways that regulate metabolism, stress responses, detoxification, immunity, protein synthesis and processes during aging. More specifically, gene readouts and detailed mapping of the pathways indicate downregulation of insulin-IGF (IIS), target of rapamycin (TOR) and MAP kinase signaling, whereas Toll-dependent immune signaling, JNK and JAK/STAT pathways are upregulated during diapause. Furthermore, transcriptional regulation of a large number of genes specifically associated with aging and longevity was detected. Many affected genes and signal pathways are shared between dormancy, aging and lifespan extension, including IIS, TOR, JAK/STAT and JNK. A substantial fraction of the genes affected by diapause have also been found to alter their expression in response to starvation and cold exposure in Drosophila, and the pathways overlap those reported in GO analysis of other invertebrates in dormancy or even hibernating mammals. This study, thus, shows that Drosophila is a genetically tractable model for dormancy in other organisms and effects of dormancy on aging and lifespan.

Galenza, A., Hutchinson, J., Campbell, S.D., Hazes, B. and Foley, E. (2016). Glucose modulates Drosophila longevity and immunity independent of the microbiota. Biol Open [Epub ahead of print]. PubMed ID: 26794610
Summary:
The acquisition of nutrients is essential for maintenance of metabolic processes in all organisms. Nutritional imbalance contributes to myriad metabolic disorders that include malnutrition, diabetes and even cancer. Recently, the importance of macronutrient ratio of food has emerged as a critical factor to determine health outcomes. This study shows that individual modifications to a completely defined diet markedly impact multiple aspects of organism wellbeing in Drosophila melanogaster. Through a longitudinal survey of several diets it was demonstrated that increased levels of dietary glucose significantly improve longevity and immunity in adult Drosophila. Metagenomic studies show that relative macronutrient levels not only influence the host, but also have a profound impact on microbiota composition. However, it was found that elevated dietary glucose extends the lifespan of adult flies even when raised in a germ-free environment. Furthermore, when challenged with a chronic enteric infection, flies fed a diet with added glucose have increased survival times even in the absence of an intact microbiota. Thus, in contrast to known links between the microbiota and animal health, these findings uncover a novel microbiota-independent response to diet that impacts host wellbeing. As dietary responses are highly conserved in animals, these results offer a general understanding of the association between glucose metabolism and animal health.

Bousquet, F., Chauvel, I., Flaven-Pouchon, J., Farine, J. P. and Ferveur, J. F. (2016). Dietary rescue of altered metabolism gene reveals unexpected Drosophila mating cues. J Lipid Res [Epub ahead of print]. PubMed ID: 26759364
Summary:
To develop and reproduce, animals need long-chain Mono and PolyUnsaturated Fatty Acids (MUFAs; PUFAs). Although some UFAs can be synthesized by the organism, others must be provided by the diet. The gene desat1, involved in Drosophila UFA metabolism, is necessary for both larval development and for adult sex pheromone communication. Larvae in which desat1 expression was knocked down throughout development were found to die during the larval stages when raised on standard food. By contrast pure MUFAs or PUFAs, but not saturated FAs, added to the larval diet, rescued animals to adulthood with the best effect being obtained with oleic acid (C18:1). Male and female mating behavior and fertility were affected very differently by preimaginal UFA-rich diet. Adult diet also strongly influenced several aspects of reproduction: flies raised on C18:1 rich diet showed increased mating performance compared to flies raised on standard adult diet. Therefore, both larval and adult desat1 expression control sex-specific mating signals.

Reis, T. (2016). Effects of synthetic diets enriched in specific nutrients on Drosophila development, body fat, and lifespan. PLoS One 11: e0146758. PubMed ID: 26741692
Summary:
Gene-diet interactions playa crucial but poorly understood role in susceptibility to obesity. Accordingly, the development of genetically tractable model systems to study the influence of diets in obesity-prone genetic backgrounds is a focus of current research. This paper presents a modified synthetic Drosophila diet optimized for timely larval development, a stage dedicated to energy storage. Specifically increasing the levels of individual macronutrients-carbohydrate, lipid, or protein-resulted in markedly different organismal effects. A high-carbohydrate diet adversely affected the timing of development, size, early lifespan and body fat. Strikingly, quadrupling the amount of dietary lipids had none of these effects. Diets rich in protein appeared to be the most beneficial, as larvae developed faster, with no change in size, into long-lived adults. This synthetic diet will significantly facilitate the study of gene-diet interactions in organismal energy balance.

Thursday, January 28th

Amoyel, M., Anderson, J., Suisse, A., Glasner, J. and Bach, E.A. (2016). Socs36E controls niche competition by repressing MAPK signaling in the Drosophila testis. PLoS Genet 12: e1005815. PubMed ID: 26807580
Summary:
Socs36E, which encodes a negative feedback inhibitor of the JAK/STAT pathway, is the first identified regulator of niche competition in the Drosophila testis. The competitive behavior of Socs36E mutant cyst stem cells (CySCs) has been attributed to increased JAK/STAT signaling. This study shows that competitive behavior of Socs36E mutant CySCs is due in large part to unbridled Mitogen-Activated Protein Kinase (MAPK) signaling. In Socs36E mutant clones, MAPK activity is elevated. Furthermore, it was found that clonal upregulation of MAPK in CySCs leads to their outcompetition of wild type CySCs and of germ line stem cells, recapitulating the Socs36E mutant phenotype. Indeed, when MAPK activity is removed from Socs36E mutant clones, they lose their competitiveness but maintain self-renewal, presumably due to increased JAK/STAT signaling in these cells. Consistently, loss of JAK/STAT activity in Socs36E mutant clones severely impairs their self-renewal. Thus, these results enable the genetic separation of two essential processes that occur in stem cells. While some niche signals specify the intrinsic property of self-renewal, which is absolutely required in all stem cells for niche residence, additional signals control the ability of stem cells to compete with their neighbors. Socs36E is node through which these processes are linked, demonstrating that negative feedback inhibition integrates multiple aspects of stem cell behavior. 

Levings, D. C., Arashiro, T. and Nakato, H. (2016). Heparan sulfate regulates the number and centrosome positioning of Drosophila male germline stem cells. Mol Biol Cell [Epub ahead of print]. PubMed ID: 26792837
Summary:
Stem cell division is tightly controlled via secreted signaling factors and cell adhesion molecules provided from local niche structures. Molecular mechanisms by which each niche component regulates stem cell behaviors remain to be elucidated. This study shows that heparan sulfate (HS), a class of glycosaminoglycan chains, regulates the number and asymmetric division of germline stem cells (GSCs) in the Drosophila testis. GSC number is sensitive to the levels of 6-O sulfate groups on HS. Loss of 6-O sulfation also disrupted normal positioning of centrosomes, a process required for asymmetric division of GSCs. Blocking HS sulfation specifically in the hub led to increased GSC numbers and mispositioning of centrosomes. The same treatment also perturbed the enrichment of Apc2, a component of the centrosome anchoring machinery, at the hub-GSC interface. This perturbation of the centrosome anchoring process ultimately led to an increase in the rate of spindle misorientation and symmetric GSC division. This study shows that specific HS modifications provide a novel regulatory mechanism for stem cell asymmetric division. The results also suggest that HS-mediated niche signaling acts upstream of GSC division orientation control.

Singh, S. R., Liu, Y., Zhao, J., Zeng, X. and Hou, S. X. (2016). The novel tumour suppressor Madm regulates stem cell competition in the Drosophila testis. Nat Commun 7: 10473. PubMed ID: 26792023
Summary:
Stem cell competition has emerged as a mechanism for selecting fit stem cells/progenitors and controlling tumourigenesis. However, little is known about the underlying molecular mechanism. This study identified Mlf1-adaptor molecule (Madm), a novel tumour suppressor that regulates the competition between germline stem cells (GSCs) and somatic cyst stem cells (CySCs) for niche occupancy. Madm knockdown results in overexpression of the EGF receptor ligand vein (vn), which further activates EGF receptor signalling and integrin expression non-cell autonomously in CySCs to promote their overproliferation and ability to outcompete GSCs for niche occupancy. Conversely, expressing a constitutively activated form of the Drosophila JAK kinase (hop(Tum-l)) promotes Madm nuclear translocation, and suppresses vn and integrin expression in CySCs that allows GSCs to outcompete CySCs for niche occupancy and promotes GSC tumour formation. Tumour suppressor-mediated stem cell competition presented in this study could be a mechanism of tumour initiation in mammals.

Laurinyecz, B., Peter, M., Vedelek, V., Kovacs, A. L., Juhasz, G., Maroy, P., Vigh, L., Balogh, G. and Sinka, R. (2016). Reduced expression of CDP-DAG synthase changes lipid composition and leads to male sterility in Drosophila. Open Biol 6 [Epub ahead of print]. PubMed ID: 26791243
Summary:
Drosophila spermatogenesis is an ideal system to study the effects of changes in lipid composition, because spermatid elongation and individualization requires extensive membrane biosynthesis and remodelling. The bulk of transcriptional activity is completed with the entry of cysts into meiotic division, which makes post-meiotic stages of spermatogenesis very sensitive to even a small reduction in gene products. In this study, the effect of are described changes in lipid composition during spermatogenesis using a hypomorphic male sterile allele of the Drosophila CDP-DAG synthase (CdsA) gene. The CdsA mutant shows defects in spermatid individualization and enlargement of mitochondria and the axonemal sheath of the spermatids. Furthermore, it was possible to genetically rescue the male sterile phenotype by overexpressing Phosphatidylinositol synthase (dPIS) in a CdsA mutant background. The results of lipidomic and genetic analyses of the CdsA mutant highlight the importance of correct lipid composition during sperm development and show that phosphatidic acid levels are crucial in late stages of spermatogenesis.

Wednesday, January 27th

Saras, A. and Tanouye, M. A. (2016). Mutations of the calcium channel gene cacophony suppress seizures in Drosophila. PLoS Genet 12: e1005784. PubMed ID: 26771829
Summary:
Bang sensitive (BS) Drosophila mutants display characteristic seizure-like phenotypes resembling, in some aspects, those of human seizure disorders such as epilepsy. The BS mutant parabss1, caused by a gain-of-function mutation of the voltage-gated Na+ channel gene, is extremely seizure-sensitive with phenotypes that have proven difficult to ameliorate by anti-epileptic drug feeding or by seizure-suppressor mutation. It has been presented as a model for intractable human epilepsy. This study show that cacophony (cacTS2), a mutation of the Drosophila presynaptic Ca++ channel α1 subunit gene, is a particularly potent seizure-suppressor mutation, reverting seizure-like phenotypes for parebss1 and other BS mutants. Seizure-like phenotypes for parabss1 may be suppressed by as much as 90% in double mutant combinations with cacTS2. Unexpectedly, it was found that parebss1 also reciprocally suppresses cacTS2 seizure-like phenotypes. The cacTS2 mutant displays these seizure-like behaviors and spontaneous high-frequency action potential firing transiently after exposure to high temperature. This seizure-like behavior in cacTS2 is ameliorated by 85% in double mutant combinations with parebss1.

Muraro, N. I. and Ceriani, M. F. (2015). Acetylcholine from visual circuits modulates the activity of arousal neurons in Drosophila. J Neurosci 35: 16315-16327. PubMed ID: 26674859
Summary:
Drosophila melanogaster's large lateral ventral neurons (lLNvs) are part of both the circadian and sleep-arousal neuronal circuits. In the past, electrophysiological analysis revealed that lLNvs fire action potentials (APs) in bursting or tonic modes and that the proportion of neurons firing in those specific patterns varies circadianly. This study provides evidence that lLNvs fire in bursts both during the day and at night and that the frequency of bursting is what is modulated in a circadian fashion. Moreover, lLNvs AP firing is not only under cell autonomous control, but is also modulated by the network, and in the process a novel preparation was developed to assess this. lLNv bursting mode was shown to rely on a cholinergic input because application of nicotinic acetylcholine receptor antagonists impairs this firing pattern. Finally, bursting of lLNvs depends was found to depend on an input from visual circuits that includes the cholinergic L2 monopolar neurons from the lamina. This work sheds light on the physiological properties of lLNvs and on a neuronal circuit that may provide visual information to these important arousal neurons.

Pitmon, E., Stephens, G., Parkhurst, S. J., Wolf, F. W., Kehne, G., Taylor, M. and Lebestky, T. (2016). The D1 Family Dopamine Receptor, DopR, potentiates hindleg grooming behavior in Drosophila. Genes Brain Behav [Epub ahead of print]. PubMed ID: 26749475
Summary:
Drosophila groom away debris and pathogens from the body using their legs in a stereotyped sequence of innate motor behaviors. This study investigated one aspect of the grooming repertoire by characterizing the D1 family dopamine receptor DopR. Removal of DopR results in decreased hindleg grooming, as substantiated by quantitation of dye remaining on mutant and RNAi animals versus controls and direct scoring of behavioral events. These data are also supported by pharmacological results that D1 receptor agonists fail to potentiate grooming behaviors in headless DopR flies. DopR protein is broadly expressed in the neuropil of the thoracic ganglion and overlaps with TH-positive dopaminergic neurons. Broad neuronal expression of Dopamine Receptor in mutant animals restored normal grooming behaviors. These data provide evidence for the role of DopR in potentiating hindleg grooming behaviors in the thoracic ganglion of adult Drosophila. This is a remarkable juxtaposition to the considerable role of D1 family dopamine receptors in rodent grooming, and future investigations of evolutionary relationships of circuitry may be warranted.

Ebrahim, S. A., Dweck, H. K., Stokl, J., Hofferberth, J. E., Trona, F., Weniger, K., Rybak, J., Seki, Y., Stensmyr, M. C., Sachse, S., Hansson, B. S. and Knaden, M. (2015). Drosophila avoids parasitoids by sensing their semiochemicals via a dedicated olfactory circuit. PLoS Biol 13: e1002318. PubMed ID: 26674493
Summary:
Detecting danger is one of the foremost tasks for a neural system. Larval parasitoids constitute clear danger to Drosophila, as up to 80% of fly larvae become parasitized in nature. Drosophila melanogaster larvae and adults avoid sites smelling of the main parasitoid enemies, Leptopilina wasps. This avoidance is mediated via a highly specific olfactory sensory neuron (OSN) type. While the larval OSN expresses the olfactory receptor Or49a and is tuned to the Leptopilina odor iridomyrmecin, the adult expresses both Or49a and Or85f and in addition detects the wasp odors actinidine and nepetalactol. The information is transferred via projection neurons to a specific part of the lateral horn known to be involved in mediating avoidance. Drosophila has thus developed a dedicated circuit to detect a life-threatening enemy based on the smell of its semiochemicals. Such an enemy-detecting olfactory circuit has earlier only been characterized in mice and nematodes.

Tuesday, January 26th

Chiu, J. C. and Edery, I. (2015). Identification of light-sensitive phosphorylation sites on PERIOD that regulate the pace of circadian rhythms in Drosophila. Mol Cell Biol [Epub ahead of print]. PubMed ID: 26711257
Summary:
The main components regulating the pace of circadian clocks in animals are Period (Per) proteins, transcriptional regulators that by means of complex multi-site phosphorylation programs undergo daily changes in levels and nuclear accumulation. This study investigated the function of two phosphorylation sites at Ser826 and Ser828 located in a putative nuclear localization signal (NLS) on the Drosophila melanogaster Per protein. These sites are phosphorylated by Doubletime (Dbt; Drosophila homolog of CK1delta/), the key circadian kinase regulating the daily changes in Per stability and phosphorylation. Mutant flies where phosphorylation at Ser826/Ser828 is blocked manifest behavioral rhythms with periods slightly longer then 1 hour and altered temperature compensation properties. Intriguingly, although phosphorylation at these sites does not influence Per stability, timing of nuclear entry or transcriptional autoinhibition, the phospho-occupancy at Ser826/Ser828 is rapidly stimulated by light and blocked by Timeless (Tim), the major photosensitive clock component in Drosophila and a crucial binding partner of Per. These findings identify the first phosphorylation sites on core clock proteins that are acutely regulated by photic cues and suggest that some phospho-sites on Per proteins can modulate the pace of downstream behavioral rhythms without altering central aspects of the clock mechanism.

Fischer, R., Helfrich-Forster, C. and Peschel, N. (2016). GSK-3 β does not stabilize Cryptochrome in the circadian clock of Drosophila. PLoS One 11: e0146571. PubMed ID: 26741981
Summary:
Cryptochrome (CRY) is the primary photoreceptor of Drosophila's circadian clock. It resets the circadian clock by promoting light-induced degradation of the clock protein Timeless (TIM) in the proteasome. Under constant light, the clock stops because TIM is absent, and the flies become arrhythmic. In addition to TIM degradation, light also induces CRY degradation. This depends on the interaction of CRY with several proteins such as the E3 ubiquitin ligases Jetlag (JET) and Ramshackle (BRWD3). However, CRY can seemingly also be stabilized by interaction with the kinase Shaggy (SGG), the GSK-3 beta fly orthologue. Consequently, flies with SGG overexpression in certain dorsal clock neurons are reported to remain rhythmic under constant light. This study investigated the interaction between CRY, Ramshackle and SGG and started to perform protein interaction studies in S2 cells. Surprisingly, it was not possible to replicate the results that SGG overexpression does stabilize CRY, neither in S2 cells nor in the relevant clock neurons. SGG rather does the contrary. Furthermore, flies with SGG overexpression in the dorsal clock neurons became arrhythmic as did wild-type flies. Nevertheless, the published interaction of SGG with TIM was reproducible, since flies with SGG overexpression in the lateral clock neurons shortened their free-running period. It is concluded that SGG does not directly interact with CRY but rather with TIM. Furthermore, it was demonstrated that an unspecific antibody explains the observed stabilization effects on CRY.

Afschar, S., et al. (2016). Nuclear hormone receptor DHR96 mediates the resistance to xenobiotics but not the increased lifespan of insulin-mutant Drosophila. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 26787908
Summary:
Lifespan of laboratory animals can be increased by genetic, pharmacological, and dietary interventions. Increased expression of genes involved in xenobiotic metabolism, together with resistance to xenobiotics, are frequent correlates of lifespan extension. This study examined this correlation by experimentally increasing resistance of Drosophila to the DDT, by artificial selection or by transgenic expression of a gene encoding a cytochrome P450. Although both interventions increase DDT resistance, neither increase lifespan. Furthermore, dietary restriction increases lifespan without increasing xenobiotic resistance, confirming that the two traits can be uncoupled. Reduced activity of the insulin/Igf signaling (IIS) pathway increases resistance to xenobiotics and extends lifespan in Drosophila, and can also increase longevity in C. elegans, mice, and possibly humans. A nuclear hormone receptor, DHR96, was identified as an essential mediator of the increased xenobiotic resistance of IIS mutant flies. However, the IIS mutants remain long-lived in the absence of DHR96 and the xenobiotic resistance that it confers. Thus, in Drosophila IIS mutants, increased xenobiotic resistance and enhanced longevity are not causally connected.

Aradhya, R., Zmojdzian, M., Da Ponte, J. P. and Jagla, K. (2015). Muscle niche-driven Insulin-Notch-Myc cascade reactivates dormant adult muscle precursors in Drosophila. Elife 4 [Epub ahead of print]. PubMed ID: 26650355
Summary:
How stem cells specified during development keep their non-differentiated quiescent state, and how they are reactivated, remain poorly understood. This study applied a Drosophila model to follow in vivo behavior of Adult Muscle Precursors (AMPs), the transient fruit fly muscle stem cells. Emerging AMPs send out thin filopodia that make contact with neighboring muscles. AMPs keep their filopodia-based association with muscles throughout their dormant state but also when they start to proliferate, suggesting that muscles could play a role in AMP reactivation. Indeed, genetic analyses indicate that muscles send inductive dIlp6 signals that switch the Insulin pathway ON in closely associated AMPs. This leads to the activation of Notch, which regulates AMP proliferation via dMyc. Altogether, this study reports that Drosophila AMPs display homing behavior to muscle niche and that the niche-driven Insulin-Notch-dMyc cascade plays a key role in setting the activated state of AMPs.

Monday, January 25th

Huisinga, K. L., Riddle, N. C., Leung, W., Shimonovich, S., McDaniel, S., Figueroa-Clarevega, A. and Elgin, S. C. (2015). Targeting of P element reporters to heterochromatic domains by transposable element 1360 in Drosophila melanogaster. Genetics [Epub ahead of print]. PubMed ID: 26680659
Summary:
Heterochromatin is a common DNA packaging form employed by eukaryotes to constitutively silence transposable elements. Determining which sequences to package as heterochromatin is vital for an organism. This study used Drosophila to study heterochromatin formation, exploiting position effect variegation, a process whereby a transgene is silenced stochastically if inserted in proximity to heterochromatin, leading to a variegating phenotype. Previous studies identified the transposable element 1360 as a target for heterochromatin formation. This study used transgene reporters with either one or four copies of 1360 to determine if increasing local repeat density can alter the fraction of the genome supporting heterochromatin formation. Including 1360 in the reporter increases the frequency with which variegating phenotypes are observed. This increase is due to a greater recovery of insertions at the telomere-associated sequences (~50% of variegating inserts). In contrast to variegating insertions elsewhere, the phenotype of telomere-associated sequence insertions is largely independent of the presence of 1360 in the reporter. Variegating and fully expressed transgenes were found to be located in different types of chromatin, and variegating reporters in the telomere-associated sequences differ from those in pericentric heterochromatin. Indeed, chromatin marks at the transgene insertion site can be used to predict the eye phenotype. This analysis reveals that increasing the local repeat density (via the transgene reporter) does not enlarge the fraction of the genome supporting heterochromatin formation. Rather, additional copies of 1360 appear to target the reporter to the telomere-associated sequences with greater efficiency, thus leading to an increased recovery of variegating insertions.

Boettiger, A. N., Bintu, B., Moffitt, J. R., Wang, S., Beliveau, B. J., Fudenberg, G., Imakaev, M., Mirny, L. A., Wu, C. T. and Zhuang, X. (2016). Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature [Epub ahead of print]. PubMed ID: 26760202
Summary:
At the intermediate scale of genomic spatial organization of kilobases to megabases, which encompasses the sizes of genes, gene clusters and regulatory domains, the three-dimensional (3D) organization of DNA is implicated in multiple gene regulatory mechanisms. At this scale, the genome is partitioned into domains of different epigenetic states that are essential for regulating gene expression. This study investigated the 3D organization of chromatin in different epigenetic states using super-resolution imaging. Genomic domains were classified in Drosophila cells into transcriptionally active, inactive or Polycomb-repressed states, and distinct chromatin organizations were observed for each state. All three types of chromatin domains exhibit power-law scaling between their physical sizes in 3D and their domain lengths, but each type has a distinct scaling exponent. Polycomb-repressed domains show the densest packing and most intriguing chromatin folding behaviour, in which chromatin packing density increases with domain length. Distinct from the self-similar organization displayed by transcriptionally active and inactive chromatin, the Polycomb-repressed domains are characterized by a high degree of chromatin intermixing within the domain. Moreover, compared to inactive domains, Polycomb-repressed domains spatially exclude neighbouring active chromatin to a much stronger degree. Computational modelling and knockdown experiments suggest that reversible chromatin interactions mediated by Polycomb-group proteins play an important role in these unique packaging properties of the repressed chromatin. Taken together, these super-resolution images reveal distinct chromatin packaging for different epigenetic states at the kilobase-to-megabase scale, a length scale that is directly relevant to genome regulation.

Eren-Ghiani, Z., Rathke, C., Theofel, I. and Renkawitz-Pohl, R. (2015). Prtl99C acts together with protamines and safeguards male fertility in Drosophila. Cell Rep 13: 2327-2335. PubMed ID: 26673329
Summary:
The formation of motile spermatozoa involves the highly conserved formation of protamine-rich, tightly packed chromatin. However, genetic loss of protamine function in Drosophila and mice does not lead to significant decompaction of sperm chromatin. This indicates that other proteins act redundantly or together with protamines. This study identifies Prtl99C as a Drosophila sperm chromatin-associated protein that is essential for male fertility. Whereas the loss of protamines results in modest elongation of sperm nuclei, knockdown of Prtl99C has a much stronger effect on sperm nuclei. Loss of protamines and Prtl99C indicates an additive effect of these proteins on chromatin compaction, in agreement with independent loading of these factors into sperm chromatin. These data reveal that at least three chromatin-binding proteins act together in chromatin reorganization to compact the paternal chromatin.

Liu, X. and Secombe, J. (2015). The Histone demethylase KDM5 activates gene expression by recognizing chromatin context through its PHD reader motif. Cell Rep 13: 2219-2231. PubMed ID: 26673323
Summary:
KDM5 family proteins are critically important transcriptional regulators whose physiological functions in the context of a whole animal remain largely unknown. Using genome-wide gene expression and binding analyses in Drosophila adults, this study demonstrates that KDM5 (Lid) is a direct regulator of genes required for mitochondrial structure and function. Significantly, this occurs independently of KDM5's well-described JmjC domain-encoded histone demethylase activity. Instead, it requires the PHD motif of KDM5 that binds to histone H3 that is di- or trimethylated on lysine 4 (H3K4me2/3). Genome-wide, KDM5 binding overlaps with the active chromatin mark H3K4me3, and a fly strain specifically lacking H3K4me2/3 binding shows defective KDM5 promoter recruitment and gene activation. KDM5 therefore plays a central role in regulating mitochondrial function by utilizing its ability to recognize specific chromatin contexts. Importantly, KDM5-mediated regulation of mitochondrial activity is likely to be key in human diseases caused by dysfunction of this family of proteins.

Sunday, January 24th

Bharadwaj, R., Cunningham, K. M., Zhang, K. and Lloyd, T. E. (2015). FIG4 regulates lysosome membrane homeostasis independent of phosphatase function. Hum Mol Genet [Epub ahead of print]. PubMed ID: 26662798
Summary:
FIG4 is a phosphoinositide phosphatase that is mutated in several diseases including Charcot-Marie-Tooth Disease 4J (CMT4J) and Yunis-Varon syndrome (YVS). To investigate the mechanism of disease pathogenesis, Drosophila models were generated of FIG4-related diseases. Fig4 null mutant flies are viable but exhibit marked enlargement of the lysosomal compartment in muscle cells and neurons, accompanied by an age-related decline in flight ability. Transgenic animals expressing Drosophila Fig4 missense mutations corresponding to human pathogenic mutations can partially rescue lysosomal expansion phenotypes, consistent with these mutations causing decreased FIG4 function. Interestingly, Fig4 mutations predicted to inactivate FIG4 phosphatase activity rescue lysosome expansion phenotypes, and mutations in the phosphoinositide (3) phosphate kinase Fab1 that performs the reverse enzymatic reaction also causes a lysosome expansion phenotype. Since FIG4 and FAB1 are present together in the same biochemical complex, these data are consistent with a model in which FIG4 serves a phosphatase-independent biosynthetic function that is essential for lysosomal membrane homeostasis. Lysosomal phenotypes are suppressed by genetic inhibition of Rab7 or the HOPS complex, demonstrating that FIG4 functions after endosome-to-lysosome fusion. Furthermore, disruption of the retromer complex, implicated in recycling from the lysosome to Golgi, does not lead to similar phenotypes as Fig4, suggesting that the lysosomal defects are not due to compromised retromer-mediated recycling of endolysosomal membranes. These data show that FIG4 plays a critical noncatalytic function in maintaining lysosomal membrane homeostasis, and that this function is disrupted by mutations that cause CMT4J and YVS.

Chow, C. Y., Kelsey, K. J., Wolfner, M. F. and Clark, A. G. (2015). Candidate genetic modifiers of retinitis pigmentosa identified by exploiting natural variation in Drosophila. Hum Mol Genet [Epub ahead of print]. PubMed ID: 26662796
Summary:
Individuals carrying the same pathogenic mutation can present with a broad range of disease outcomes. While some of this variation arises from environmental factors, it is increasingly recognized that the background genetic variation of each individual can have a profound effect on the expressivity of a pathogenic mutation. In order to understand this background effect on disease-causing mutations, studies need to be performed across a wide range of backgrounds. Recent advancements in model organism biology allow testing of mutations across genetically diverse backgrounds and identification of the genes that influence the expressivity of a mutation. This study used the Drosophila Genetic Reference Panel, a collection of approximately 200 wild-derived strains, to test the variability of the retinal phenotype of the Rh1G69D Drosophila model of retinitis pigmentosa (RP). The Rh1G69D retinal phenotype is quite a variable quantitative phenotype. To identify the genes driving this extensive phenotypic variation, a genome-wide association study was performed. One hundred and six candidate genes were identified, including 14 high-priority candidates. Functional testing by RNAi indicates that 10/13 top candidates tested influence the expressivity of Rh1G69D. The human orthologs of the candidate genes have not previously been implicated as RP modifiers and their functions are diverse, including roles in endoplasmic reticulum stress, apoptosis and retinal degeneration and development. This study demonstrates the utility of studying a pathogenic mutation across a wide range of genetic backgrounds. These candidate modifiers provide new avenues of inquiry that may reveal new RP disease mechanisms and therapies.

Zhu, Z. J., Wu, K. C., Yung, W. H., Qian, Z. M. and Ke, Y. (2016). Differential interaction between iron and mutant alpha-synuclein causes distinctive Parkinsonian phenotypes in Drosophila. Biochim Biophys Acta [Epub ahead of print]. PubMed ID: 26769358
Summary:
α-synuclein aggregation is the central hallmark of both sporadic and familial Parkinson's disease (PD). Patients with different PD-causing genetic defects of α-synuclein usually show distinctive clinical features that are atypical to sporadic PD. Iron accumulation is invariably found in PD. Recent studies showed that mutant and wild-type α-synuclein may have differential interaction with iron and mutant α-synuclein toxicity could be preferentially exacerbated by iron. It was thus hypothesized that iron overload could selectively influence mutant α-synuclein toxicity and disease phenotypes. To test the hypothesis, whether Drosophila melanogaster over-expressing A53T, A30P, and wild-type (WT) α-synuclein have different responses to iron treatment was tested. Jron treatment was shown to induced similar reduction of survival rate in all flies but induced a more severe motor decline in A53T and A30P mutant α-synuclein expressing flies, suggesting interaction between mutant α-synuclein and iron. Although no significant difference in total head iron content was found among these flies, it was demonstrated that iron treatment induced selective DA neuron loss in motor-related PPM3 cluster only in the flies that express A53T and A30P mutant α-synuclein. This study provides the first in vivo evidence that iron overload could induce distinctive neuropathology and disease phenotypes in mutant but not WT alpha-synuclein expressing flies, providing insights to the cause of clinical features selectively exhibited by mutant alpha-synuclein carriers.

Lugtenberg, D., et al. (2016). De novo loss-of-function mutations in WAC cause a recognizable intellectual disability syndrome and learning deficits in Drosophila. Eur J Hum Genet [Epub ahead of print]. PubMed ID: 26757981
Summary:
Recently WAC was reported as a candidate gene for intellectual disability (ID) based on the identification of a de novo mutation in an individual with severe ID. WAC regulates transcription-coupled histone H2B ubiquitination and has previously been implicated in the 10p12p11 contiguous gene deletion syndrome. This study reports on 10 individuals with de novo WAC mutations which were identified through routine (diagnostic) exome sequencing and targeted resequencing of WAC in 2326 individuals with unexplained ID. All but one mutation was expected to lead to a loss-of-function of WAC. Clinical evaluation of all individuals revealed phenotypic overlap for mild ID, hypotonia, behavioral problems and distinctive facial dysmorphisms, including a square-shaped face, deep set eyes, long palpebral fissures, and a broad mouth and chin. These clinical features were also previously reported in individuals with 10p12p11 microdeletion syndrome. To investigate the role of WAC in ID, the importance of the Drosophila WAC orthologue (CG8949) was studied in habituation, a non-associative learning paradigm. Neuronal knockdown of Drosophila CG8949 resulted in impaired learning, suggesting that WAC is required in neurons for normal cognitive performance. In conclusion, this study has defined a clinically recognizable ID syndrome, caused by de novo loss-of-function mutations in WAC. Independent functional evidence in Drosophila further supported the role of WAC in ID. On the basis of these data WAC can be added to the list of ID genes with a role in transcription regulation through histone modification.

Pouly, D., Chenaux, S., Martin, V., Babis, M., Koch, R., Nagoshi, E., Katanaev, V. L., Gachon, F. and Staub, O. (2016). USP2-45 is a circadian clock output effector regulating calcium absorption at the post-translational level. PLoS One 11: e0145155. PubMed ID: 26756164
Summary:
The mammalian circadian clock influences most aspects of physiology and behavior through the transcriptional control of a wide variety of genes, mostly in a tissue-specific manner. About 20 clock-controlled genes (CCGs) oscillate in virtually all mammalian tissues and are generally considered as core clock components. One of them is Ubiquitin-Specific Protease 2 (Usp2), whose status remains controversial, as it may be a cogwheel regulating the stability or activity of core cogwheels or an output effector. This study reports that Usp2 is a clock output effector related to bodily Ca2+ homeostasis, a feature that is conserved across evolution. Drosophila with a whole-body knockdown of the orthologue of Usp2, (Ubiquitin specific protease 2) predominantly die during pupation but are rescued by dietary Ca2+ supplementation. Usp2-KO mice show hyperabsorption of dietary Ca2+ in small intestine, likely due to strong overexpression of the membrane scaffold protein NHERF4, a regulator of the Ca2+ channel TRPV6 mediating dietary Ca2+ uptake. In this tissue, USP2-45 is found in membrane fractions and negatively regulates NHERF4 protein abundance in a rhythmic manner at the protein level. In clock mutant animals (Cry1/Cry2-dKO; see Drosophila Cryptochrome), rhythmic USP2-45 expression is lost, as well as the one of NHERF4, confirming the inverse relationship between USP2-45 and NHERF4 protein levels. Finally, USP2-45 interacts in vitro with NHERF4 and endogenous Clathrin Heavy Chain (see Drosophila Clathrin Heavy Chain). Taken together these data has led the authors to define USP2-45 as the first clock output effector acting at the post-translational level at cell membranes and possibly regulating membrane permeability of Ca2+.

Fu, W., Sun, J., Huang, G., Liu, J. C., Kaufman, A., Ryan, R. J., Ramanathan, S. Y., Venkatesh, T. and Singh, B. (2016). Squamous cell carcinoma related oncogene (SCCRO) family members regulate cell growth and proliferation through their cooperative and antagonistic effects on Cullin neddylation. J Biol Chem [Epub ahead of print]. PubMed ID: 26792857
Summary:
SCCRO (squamous cell carcinoma related oncogene; a.k.a. DCUN1D1) is a highly conserved gene that functions as an E3 in neddylation. Although inactivation of SCCRO in yeast results in lethality, SCCRO-/- mice are viable. The exclusive presence of highly conserved paralogues in higher organisms led to an assessment of whether compensation by SCCRO's paralogues rescues lethality in SCCRO-/- mice. Using murine and Drosophila models, the in vivo activities of SCCRO and its paralogues were assessed in cullin neddylation (see Drosophila Cullin1). SCCRO family members were found to have overlapping and antagonistic activity that regulates neddylation and cell proliferation activities in vivo. In flies, both dSCCRO (CG7427) and dSCCRO3 (CG13322) promote neddylation and cell proliferation, whereas dSCCRO4 (CG6597) negatively regulates these processes. Analysis of somatic clones showed that the effects that these paralogues have on proliferation serve to promote cell competition, leading to apoptosis in clones, with a net decrease in neddylation activity. dSCCRO and, to a lesser extent, dSCCRO3 rescue the neddylation and proliferation defects promoted by expression of SCCRO4. dSCCRO and dSCCRO3 functioned cooperatively, with their coexpression resulting in an increase in both the neddylated cullin fraction and proliferation activity. In contrast, human SCCRO and SCCRO4 promotes and human SCCRO3 inhibits neddylation and proliferation when expressed in flies. These findings provide the first insights into the mechanisms through which SCCRO family members cooperatively regulate neddylation and cell proliferation.

Saturday, January 23rd

Guo, Z., Batiha, O., Bourouh, M., Fifield, E. and Swan, A. (2015). Role of Securin, Separase and Cohesins in female meiosis, and polar body formation in Drosophila. J Cell Sci [Epub ahead of print]. PubMed ID: 26675236
Summary:
Chromosome segregation in meiosis is controlled by a conserved pathway that culminates in Separase-mediated cleavage of the alpha-kleisin, Rec8, leading to dissolution of cohesin rings. Drosophila has no rec8 gene and the absence of a known Separase target raises the question of whether Separase and its regulator Securin are important in Drosophila meiosis. This study investigated the role of Securin, Separase and the cohesin complex in female meiosis using FISH against centromeric and chromosome arm-specific sequences to monitor cohesion. Securin destruction and Separase activity are required for timely release of arm cohesion in anaphase I and centromere-proximal cohesion in anaphase II. They are also required for release of arm cohesion on polar body chromosomes. Cohesion on polar body chromosomes depends on the cohesin components SMC3 and Rad21, the mitotic alpha-kleisin. This study provides cytological evidence that SMC3 is required for arm cohesion in female meiosis, but Rad21, in agreement with recent findings, is not. It is concluded that in Drosophila meiosis, cohesion is regulated by a conserved Securin/Separase pathway that targets a diverged Separase target possibly within the cohesin complex.

Fu, J., Lipinszki, Z., Rangone, H., Min, M., Mykura, C., Chao-Chu, J., Schneider, S., Dzhindzhev, N. S., Gottardo, M., Riparbelli, M. G., Callaini, G. and Glover, D. M. (2016). Conserved molecular interactions in centriole-to-centrosome conversion. Nat Cell Biol 18: 87-99. PubMed ID: 26595382
Summary:
Centrioles are required to assemble centrosomes for cell division and cilia for motility and signalling. New centrioles assemble perpendicularly to pre-existing ones in G1-S and elongate throughout S and G2. Fully elongated daughter centrioles are converted into centrosomes during mitosis to be able to duplicate and organize pericentriolar material in the next cell cycle. This study shows that centriole-to-centrosome conversion requires sequential loading of Cep135, Ana1 (Cep295) and Asterless (Cep152) onto daughter centrioles during mitotic progression in both Drosophila and human. This generates a molecular network spanning from the inner- to outermost parts of the centriole. Ana1 forms a molecular strut within the network, and its essential role can be substituted by an engineered fragment providing an alternative linkage between Asterless and Cep135. This conserved architectural framework is essential for loading Asterless or Cep152, the partner of the master regulator of centriole duplication, Plk4. This study thus uncovers the molecular basis for centriole-to-centrosome conversion that renders daughter centrioles competent for motherhood.

Caous, R., Pascal, A., Rome, P., Richard-Parpaillon, L., Karess, R. and Giet, R. (2015). Spindle assembly checkpoint inactivation fails to suppress neuroblast tumour formation in aurA mutant Drosophila. Nat Commun 6: 8879. PubMed ID: 26568519
Summary:
Tissue homeostasis requires accurate control of cell proliferation, differentiation and chromosome segregation. Drosophila sas-4 and aurA mutants present brain tumours with extra neuroblasts (NBs), defective mitotic spindle assembly and delayed mitosis due to activation of the spindle assembly checkpoint (SAC). This study inactivated the SAC in aurA and sas-4 mutants to determine whether the generation of aneuploidy compromises NB proliferation. Inactivation of the SAC in the sas-4 mutant impairs NB proliferation and disrupts euploidy. By contrast, disrupting the SAC in the aurA mutant does not prevent NB amplification, tumour formation or chromosome segregation. The monitoring of Mad2 and cyclin B dynamics in live aurA NBs reveals that SAC satisfaction is not coupled to cyclin B degradation. Thus, the NBs of aurA mutants present delayed mitosis, with accurate chromosome segregation occurring in a SAC-independent manner. This study reports the existence of an Aurora A-dependent mechanism promoting efficient, timed cyclin B degradation.

Phadnis, N., Baker, E. P., Cooper, J. C., Frizzell, K. A., Hsieh, E., de la Cruz, A. F., Shendure, J., Kitzman, J. O. and Malik, H. S. (2015). An essential cell cycle regulation gene causes hybrid inviability in Drosophila. Science 350: 1552-1555. PubMed ID: 26680200
Summary:
Speciation, the process by which new biological species arise, involves the evolution of reproductive barriers, such as hybrid sterility or inviability between populations. However, identifying hybrid incompatibility genes remains a key obstacle in understanding the molecular basis of reproductive isolation. This study devised a genomic screen, which identified a cell cycle-regulation gene, GST-containing FLYWCH zinc-finger protein (gfzf) as the cause of male inviability in hybrids resulting from a cross between Drosophila melanogaster and D. simulans. Ablation of the D. simulans allele of this gene is sufficient to rescue the adult viability of hybrid males. This dominantly acting cell cycle regulator causes mitotic arrest and, thereby, inviability of male hybrid larvae. Evidence is provided that the same checkpoints that normally ensure the correction of mitotic errors may be also responsible for the inviability of hybrid males in the D. melanogaster x D. simulans interspecies cross. This genomic method provides a facile means to accelerate the identification of hybrid incompatibility genes in other model and nonmodel systems.

Friday, January 22nd

Peleg, S., Feller, C., Forne, I., Schiller, E., Sévin, D.C., Schauer, T., Regnard, C., Straub, T., Prestel, M., Klima, C., Schmitt Nogueira, M., Becker, L., Klopstock, T., Sauer, U., Becker, P.B., Imhof, A. and Ladurner, A.G. (2016). Life span extension by targeting a link between metabolism and histone acetylation in Drosophila. EMBO Rep [Epub ahead of print]. PubMed ID: 26781291
Summary:
Old age is associated with a progressive decline of mitochondrial function and changes in nuclear chromatin. However, little is known about how metabolic activity and epigenetic modifications change as organisms reach their midlife. This study assessed how cellular metabolism and protein acetylation change during early aging in Drosophila melanogaster. Contrary to common assumptions, it was found that flies increase oxygen consumption and become less sensitive to histone deacetylase inhibitors as they reach midlife. Further, midlife flies show changes in the metabolome, elevated acetyl-CoA levels, alterations in protein-notably histone-acetylation, as well as associated transcriptome changes. Based on these observations, the activity of the acetyl-CoA-synthesizing enzyme ATP citrate lyase (ATPCL) or the levels of the histone H4 K12-specific acetyltransferase Chameau were decreased. It was found that these targeted interventions both alleviate the observed aging-associated changes and promote longevity. These findings reveal a pathway that couples changes of intermediate metabolism during aging with the chromatin-mediated regulation of transcription and changes in the activity of associated enzymes that modulate organismal life span.

Lopez-Panades, E. and Casacuberta, E. (2015). NAP-1, Nucleosome assembly protein 1, a histone chaperone involved in Drosophila telomeres. Insect Biochem Mol Biol [Epub ahead of print]. PubMed ID: 26742602
Summary:
Telomere elongation is a function that all eukaryote cells must accomplish in order to guarantee, first, the stability of the end of the chromosomes and second, to protect the genetic information from the inevitable terminal erosion. The targeted transposition of the telomere transposons HeT-A, TART and TAHRE perform this function in Drosophila, while the telomerase mechanism elongates the telomeres in most eukaryotes. In order to integrate telomere maintenance together with cell cycle and metabolism, different components of the cell interact, regulate, and control the proteins involved in telomere elongation. Different partners of the telomerase mechanism have already been described, but in contrast, very few proteins have been related with assisting the telomere transposons of Drosophila. This study describes the implication of NAP-1 (Nucleosome assembly protein 1), a histone chaperone that has been involved in nuclear transport, transcription regulation, and chromatin remodeling, in telomere biology. Nap-1 and HeT-A Gag, one of the major components of the Drosophila telomeres, are part of the same protein complex. It was also demonstrated that their close interaction is necessary to guarantee telomere stability in dividing cells. NAP-1 was further shown to regulates the transcription of the HeT-A retrotransposon, pointing to a positive regulatory role of NAP-1 in telomere expression. All these results facilitate the understanding of the transposon telomere maintenance mechanism, as well as the integration of telomere biology with the rest of the cell metabolism.

Marzullo, M. and Gatti, M. (2016). Telomere fusion in Drosophila: The role of subtelomeric chromatin. Fly (Austin) [Epub ahead of print]. PubMed ID: 26786804
Summary:
Drosophila telomeres are maintained by transposition to chromosome ends of the HeT-A, TART and TAHRE retrotransposons, collectively designated as HTT. Although all Drosophila telomeres terminate with HTT arrays and are capped by the terminin complex, they differ in the type of subtelomeric chromatin. The HTT sequences of YS, YL, XR, and 4L are juxtaposed to constitutive heterochromatin, while the HTTs of the other telomeres are linked to either the TAS repeat-associated chromatin (XL, 2L, 2R, 3L, 3R) or to the specialized 4R chromatin. It was found that mutations in pendolino (peo) cause telomeric fusions (telomeric fusions) that preferentially involve the heterochromatin-associated telomeres (Ha-telomeres), a telomeric fusion pattern never observed in the other 10 telomere-capping mutants characterized so far. Peo, is homologous to the E2 variant ubiquitin-conjugating enzymes and is required for DNA replication. These analyses lead to the hypothesis that DNA replication in Peo-depleted cells results in specific fusigenic lesions concentrated in Ha-telomeres. These data provide the first demonstration that subtelomeres can affect telomere fusion.

Peng, J.C., Valouev, A., Liu, N. and Lin, H. (2016). Piwi maintains germline stem cells and oogenesis in Drosophila through negative regulation of Polycomb group proteins. Nat Genet [Epub ahead of print]. PubMed ID: 26780607
Summary:
The Drosophila melanogaster Piwi protein regulates both niche and intrinsic mechanisms to maintain germline stem cells, but its underlying mechanism remains unclear. This study reports that Piwi interacts with Polycomb group complexes PRC1 and PRC2 in niche and germline cells to regulate ovarian germline stem cells and oogenesis. Piwi physically interacts with the PRC2 subunits Su(z)12 and Esc in the ovary and in vitro. Chromatin coimmunoprecipitation of Piwi, the PRC2 enzymatic subunit E(z), histone H3 trimethylated at lysine 27 (H3K27me3) and RNA polymerase II in wild-type and piwi mutant ovaries demonstrates that Piwi binds a conserved DNA motif at ∼72 genomic sites and inhibits PRC2 binding to many non-Piwi-binding genomic targets and H3K27 trimethylation. Moreover, Piwi influences RNA polymerase II activities in Drosophila ovaries, likely via inhibiting PRC2. The study hypothesizes that Piwi negatively regulates PRC2 binding by sequestering PRC2 in the nucleoplasm, thus reducing PRC2 binding to many targets and influencing transcription during oogenesis.

Thursday, January 21st

Kuckwa, J., Fritzen, K., Buttgereit, D., Rothenbusch-Fender, S. and Renkawitz-Pohl, R. (2015). A new level of plasticity: Drosophila smooth-like testes muscles compensate failure of myoblast fusion. Development [Epub ahead of print]. PubMed ID: 26657767
Summary:
The testis of Drosophila resembles an individual testis tubule of mammals. Both are surrounded by a sheath of smooth muscles, which in Drosophila are multinuclear and originate from a pool of myoblasts that are set aside in the embryo and accumulate on the genital disc later in development. These muscle stem cells start to differentiate early during metamorphosis and give rise to all muscles of the inner male reproductive system. Shortly before the genital disc and the developing testes connect to each other, multinuclear nascent myotubes appear on the anterior tips of the seminal vesicles. This study shows that adhesion molecules were distinctly localized on the seminal vesicles; founder cell-like myoblasts (FC-like) expressed Dumbfounded (Duf) and Roughest (Rst), and fusion-competent myoblast-like cells (FCM-like) mainly expressed Sticks and stones (Sns). The smooth but multinuclear myotubes of the testes arose by myoblast fusion. RNAi-mediated attenuation of Sns or both Duf and Rst severely reduced the number of nuclei in the testes muscles. Duf and Rst likely acted independently in this context. Despite reduced fusion, myotubes migrated onto the testes, testes were shaped and coiled, muscle filaments arranged as in the wild-type, and spermatogenesis proceeded normally. Hence, the testes muscles compensated for fusion defects so that the myofibres encircling the adult testes are indistinguishable from those of the wild- type and male fertility is guaranteed.

Vonesch, S.C., Lamparter, D., Mackay, T.F., Bergmann, S. and Hafen, E. (2016). Genome-wide analysis reveals novel regulators of growth in Drosophila melanogaster. PLoS Genet 12: e1005616. PubMed ID: 26751788
Summary:
Organismal size depends on the interplay between genetic and environmental factors. Genome-wide association (GWA) analyses in humans have implied many genes in the control of height but suffer from the inability to control the environment. Genetic analyses in Drosophila have identified conserved signaling pathways controlling size; however, how these pathways control phenotypic diversity is unclear. This study performed GWA of size traits using the Drosophila Genetic Reference Panel of inbred, sequenced lines. It was found that the top associated variants differ between traits and sexes; do not map to canonical growth pathway genes, but can be linked to these by epistasis analysis; and are enriched for genes and putative enhancers. A cluster of associations close to the kek1 locus, a well-characterized growth regulator, was identified but otherwise most variants are located in or close to genes that do not belong to the conserved pathways but may interact with these in a biological network. 33 novel growth regulatory genes that participate in diverse cellular processes were validated, most notably cellular metabolism and cell polarity. Performing GWA on well-studied developmental traits under controlled conditions expands the understanding of developmental processes underlying phenotypic diversity. 

Mariappa, D., Zheng, X., Schimpl, M., Raimi, O., Ferenbach, A. T., Muller, H. A. and van Aalten, D. M. (2015). Dual functionality of O-GlcNAc transferase is required for Drosophila development. Open Biol 5. PubMed ID: 26674417
Summary:
Post-translational modification of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc) catalysed by O-GlcNAc transferase (OGT) has been linked to regulation of diverse cellular functions. OGT possesses a C-terminal glycosyltransferase catalytic domain and N-terminal tetratricopeptide repeats that are implicated in protein-protein interactions. Drosophila OGT (DmOGT) is encoded by super sex combs (sxc), mutants of which are pupal lethal. This study used a genetic approach to demonstrate that post-pupal Drosophila development can proceed with negligible OGT catalysis. Structural and enzymatic comparison between human OGT (hOGT) and DmOGT informed the rational design of DmOGT point mutants with a range of reduced catalytic activities. Strikingly, a severely hypomorphic OGT mutant complements sxc pupal lethality. However, the hypomorphic OGT mutant-rescued progeny do not produce F2 adults, because a set of Hox genes is de-repressed in F2 embryos, resulting in homeotic phenotypes. Thus, OGT catalytic activity is required up to late pupal stages, while further development proceeds with severely reduced OGT activity.

Vissers, J.H., Manning, S.A., Kulkarni, A. and Harvey, K.F. (2016). A Drosophila RNAi library modulates Hippo pathway-dependent tissue growth. Nat Commun 7: 10368. PubMed ID: 26766446
Summary:
Libraries of transgenic Drosophila melanogaster carrying RNA interference (RNAi) constructs have been used extensively to perform large-scale functional genetic screens in vivo. For example, RNAi screens have facilitated the discovery of multiple components of the Hippo pathway, an evolutionarily conserved growth-regulatory network. This study investigates an important technical limitation with the widely used VDRC KK RNAi collection. It was found that approximately 25% of VDRC KK RNAi lines cause false-positive enhancement of the Hippo pathway, owing to ectopic expression of the Tiptop transcription factor. Of relevance to the broader Drosophila community, ectopic tiptop (tio) expression can also cause organ malformations and mask phenotypes such as organ overgrowth. To enhance the use of the VDRC KK RNAi library, this study generated a D. melanogaster strain that will allow researchers to test, in a single cross, whether their genetic screen of interest will be affected by ectopic tio expression.

Wednesday, January 20th

Rabinovich, D., Yaniv, S.P., Alyagor, I. and Schuldiner, O. (2016). Nitric oxide as a switching mechanism between axon degeneration and regrowth during developmental remodeling. Cell 164: 170-182. PubMed ID: 26771490
Summary:
During development, neurons switch among growth states, such as initial axon outgrowth, axon pruning, and regrowth. By studying the stereotypic remodeling of the Drosophila mushroom body (MB), this study found that the heme-binding nuclear receptor E75 is dispensable for initial axon outgrowth of MB γ neurons but is required for their developmental regrowth. Genetic experiments and pharmacological manipulations on ex-vivo-cultured brains indicate that neuronally generated nitric oxide (NO) promotes pruning but inhibits regrowth. It was found that high NO levels inhibit the physical interaction between the E75 and UNF nuclear receptors, likely accounting for its repression of regrowth. Additionally, NO synthase (NOS) activity is downregulated at the onset of regrowth, at least partially, by short inhibitory NOS isoforms encoded within the NOS locus, indicating how NO production could be developmentally regulated. Taken together, these results suggest that NO signaling provides a switching mechanism between the degenerative and regenerative states of neuronal remodeling.

Friedrich, J., Sorge, S., Bujupi, F., Eichenlaub, M.P., Schulz, N.G., Wittbrodt, J. and Lohmann, I. (2016). Hox function is required for the development and maintenance of the Drosophila feeding motor unit. Cell Rep [Epub ahead of print]. PubMed ID: 26776518
Summary:
Feeding is an evolutionarily conserved and integral behavior that depends on the rhythmic activity of feeding muscles stimulated by specific motoneurons. However, critical molecular determinants underlying the development of the neuromuscular feeding unit are largely unknown. This study identifies the Hox transcription factor Deformed (Dfd) as essential for feeding unit formation, from initial specification to the establishment of active synapses, by controlling stage-specific sets of target genes. Importantly, Dfd was found to control the expression of functional components of synapses, such as Ankyrin2-XL, a protein known to be critical for synaptic stability and connectivity. Furthermore, Dfd also acts as a potential regulator of synaptic specificity, as it represses expression of the synaptic cell adhesion molecule Connectin (Con). These results demonstrate that Dfd is critical for the establishment and maintenance of the neuromuscular unit required for feeding behavior, which might be shared by other group 4 Hox genes.

Yu, Y., Lee, H.C., Chen, K.C., Suhan, J., Qiu, M., Ba, Q. and Yang, G. (2016). Inner membrane fusion mediates spatial distribution of axonal mitochondria. Sci Rep 6: 18981. PubMed ID: 26742817
Summary:
In eukaryotic cells, mitochondria form a dynamic interconnected network to respond to changing needs at different subcellular locations. A fundamental yet unanswered question regarding this network is whether, and if so how, local fusion and fission of individual mitochondria affect their global distribution. To address this question, this study developed high-resolution computational image analysis techniques to examine the relations between mitochondrial fusion/fission and spatial distribution within the axon of Drosophila larval neurons. It was found that stationary and moving mitochondria undergo fusion and fission regularly but follow different spatial distribution patterns and exhibit different morphology. Disruption of inner membrane fusion by knockdown of dOpa1, Drosophila Optic Atrophy 1, not only increases the spatial density of stationary and moving mitochondria but also changes their spatial distributions and morphology differentially. Knockdown of dOpa1 also impairs axonal transport of mitochondria. But the changed spatial distributions of mitochondria results primarily from disruption of inner membrane fusion because knockdown of Milton, a mitochondrial kinesin-1 adapter, causes similar transport velocity impairment but different spatial distributions. Together, these data reveal that stationary mitochondria within the axon interconnect with moving mitochondria through fusion and fission and that local inner membrane fusion between individual mitochondria mediates their global distribution.

Beck, C., Singh, T., Farooqi, A., Venkatesh, T. and Vazquez, M. (2015). Controlled microfluidics to examine growth-factor induced migration of neural Progenitors in the Drosophila visual system. J Neurosci Methods [Epub ahead of print]. PubMed ID: 26738658
Summary:
Exogenous signaling from ligands such as Fibroblast Growth Factor (FGF) control glia differentiation, cell migration, and axonal wrapping central to vision. This study employs a microfluidic device to examine how controlled concentration gradient fields of FGF are able to regulate the migration of vision-critical glia cells with and without cellular contact with neuronal progenitors. The findings quantitatively illustrate a concentration-gradient dependent chemotaxis toward FGF, and further demonstrate that glia require collective and coordinated neuronal locomotion to achieve directionality, sustain motility, and propagate long cell distances in the visual system. Conventional assays are unable to examine concentration- and gradient-dependent migration. The current data illustrate quantitative correlations between ligand concentration/gradient and glial cell distance traveled, independent or in contact with neurons. It is concluded that microfluidic systems in combination with a genetically-amenable experimental system empowers researchers to dissect the signaling pathways that underlie cellular migration during nervous system development. The findings illustrate the need for coordinated neuron-glia migration in the Drosophila visual system, as only glia within heterogeneous populations exhibited increasing motility along distances that increased with increasing FGF concentration. Such coordinated migration and chemotactic dependence can be manipulated for potential therapeutic avenues for NS repair and/or disease treatment.

Tuesday, January 19th

Kuntz, S. G. and Eisen, M. B. (2015). Oxygen changes drive non-uniform scaling in Drosophila melanogaster embryogenesis. F1000Res 4: 1102. PubMed ID: 26673611
Summary:
It has been demonstrated that while changes in temperature produce dramatic shifts in the time elapsed during Drosophila embryogenesis, the relative timing of events within embryogenesis does not change. However, it was unclear if this uniform scaling is an intrinsic property of developing embryos, or if it is specific to thermal fluctuations. To investigate this, this study characterized the embryonic response to changes in oxygen concentration, which also impact developmental rate, using time-lapse imaging, and found it fundamentally different from the temperature response. Most notably, changes in oxygen levels drive developmental heterochrony, with the timing of several morphological processes showing distinct scaling behaviors. Gut formation is severely slowed by decreases in oxygen, while head involution and syncytial development are less impacted than the rest of development, and the order of several developmental landmarks is inverted at different oxygen levels. These data reveal that the uniform scaling seen with changes in temperature is not a trivial consequence of adjusting developmental rate. The developmental rate changes produced by changing oxygen concentrations dwarf those induced by temperature, and greatly impact survival. While extreme temperatures increase early embryo mortality, mild hypoxia increases arrest and death during mid-embryogenesis and mild hyperoxia increases survival over normoxia.

Machado, P. F., Duque, J., Etienne, J., Martinez-Arias, A., Blanchard, G. B. and Gorfinkiel, N. (2015). Emergent material properties of developing epithelial tissues. BMC Biol 13: 98. PubMed ID: 26596771
Summary:
This study measures the mechanical properties of epithelial cells during dorsal closure. The relationship between apicomedial myosin fluorescence intensity and strain during fluctuations is shown to be consistent with a linear behaviour. Myosin fluorescence intensity was used as a proxy for active force generation. This study established relative changes in separate effective mechanical properties in vivo. Over the course of dorsal closure, the tissue solidifies and effective stiffness doubles as net contraction of the tissue commences. Combining these findings with those from previous laser ablation experiments, it was shown that both apicomedial and junctional stress also increase over time, with the relative increase in apicomedial stress approximately twice that of other obtained measures. These results show that in an epithelial tissue undergoing net contraction, stiffness and stress are coupled. Dorsal closure cell apical contraction is driven by the medial region where the relative increase in stress is greater than that of stiffness. At junctions, by contrast, the relative increase in the mechanical properties is the same, so the junctional contribution to tissue deformation is constant over time. An increase in myosin activity is likely to underlie, at least in part, the change in medioapical properties and it is suggested that its greater effect on stress relative to stiffness is fundamental to actomyosin systems and confers on tissues the ability to regulate contraction rates in response to changes in external mechanics.

Wu, H., Manu, Jiao, R. and Ma, J. (2015). Temporal and spatial dynamics of scaling-specific features of a gene regulatory network in Drosophila. Nat Commun 6: 10031. PubMed ID: 26644070
Summary:
A widely appreciated aspect of developmental robustness is pattern formation in proportion to size. But how such scaling features emerge dynamically remains poorly understood. This study generated a data set of the expression profiles of six gap genes in Drosophila melanogaster embryos that differ significantly in size. Expression patterns exhibit size-dependent dynamics both spatially and temporally. A dynamic emergence of under-scaling in the posterior was uncovered, accompanied by reduced expression levels of gap genes near the middle of large embryos. Simulation results show that a size-dependent Bicoid gradient input can lead to reduced Kruppel expression that can have long-range and dynamic effects on gap gene expression in the posterior. Thus, for emergence of scaled patterns, the entire embryo may be viewed as a single unified dynamic system where maternally derived size-dependent information interpreted locally can be propagated in space and time as governed by the dynamics of a gene regulatory network.

Yu, J.C. and Fernandez-Gonzalez, R. (2016). Local mechanical forces promote polarized junctional assembly and axis elongation in Drosophila. Elife [Epub ahead of print]. PubMed ID: 26747941
Summary:
Axis elongation is a conserved process in which the head-to-tail or anterior-posterior (AP) axis of an embryo extends. In Drosophila, cellular rearrangements drive axis elongation. Cells exchange neighbours by converging into transient multicellular vertices which resolve through the assembly of new cell interfaces parallel to the AP axis. This study found that new interfaces elongate in pulses correlating with periodic contractions of the surrounding cells. Inhibiting actomyosin contractility globally, or specifically in the cells around multicellular vertices, disrupts the rate and directionality of new interface assembly. Laser ablation indicates that new interfaces sustain greater tension than non-elongating ones. A method to apply ectopic tension was developed, and increasing AP tension locally was found to increase the elongation rate of new edges by 2.1-fold. Increasing dorsal-ventral tension results in vertex resolution perpendicular to the AP direction. The study proposes that local, periodic contractile forces polarize vertex resolution to drive Drosophila axis elongation.

Monday, January 18th

Cugusi, S., Li, Y., Jin, P. and Lucchesi, J.C. (2016). The Drosophila helicase MLE targets hairpin structures in genomic transcripts. PLoS Genet 12: e1005761. PubMed ID: 26752049
Summary:
RNA hairpins are a common type of secondary structure that play a role in every aspect of RNA biochemistry including RNA editing, mRNA stability, localization and translation of transcripts, and in the activation of the RNA interference (RNAi) and microRNA (miRNA) pathways. Participation in these functions often requires restructuring the RNA molecules by the association of single-strand (ss) RNA-binding proteins or by the action of helicases. The Drosophila MLE helicase has long been identified as a member of the MSL complex responsible for dosage compensation. The complex includes one of two long non-coding RNAs and MLE has been shown to remodel the roX RNA hairpin structures in order to initiate assembly of the complex. This study reports that this function of MLE may apply to the hairpins present in the primary RNA transcripts that generate the small molecules responsible for RNA interference. Using stocks from the Transgenic RNAi Project and the Vienna Drosophila Research Center, it was shown that MLE specifically targets hairpin RNAs at their site of transcription. The association of MLE at these sites is independent of sequence and chromosome location. The study uses two functional assays to test the biological relevance of this association and determine that MLE participates in the RNAi pathway.

Rideout, E. J., Narsaiya, M. S. and Grewal, S. S. (2015). The Sex determination gene transformer regulates male-female differences in Drosophila body size. PLoS Genet 11: e1005683. PubMed ID: 26710087
Summary:
Almost all animals show sex differences in body size. For example, in Drosophila, females are larger than males. Although Drosophila is widely used as a model to study growth, the mechanisms underlying this male-female difference in size remain unclear. This study describes a novel role for the sex determination gene transformer (tra) in promoting female body growth. Normally, Tra is expressed only in females. Loss of Tra in female larvae decreases body size, while ectopic Tra expression in males increases body size. Although Tra was found to exerts autonomous effects on cell size, it was also discovered that Tra expression in the fat body augments female body size in a non cell-autonomous manner. These effects of Tra do not require its only known targets doublesex and fruitless. Instead, Tra expression in the female fat body promotes growth by stimulating the secretion of insulin-like peptides from insulin producing cells in the brain. These data suggest a model of sex-specific growth in which body size is regulated by a previously unrecognized branch of the sex determination pathway, and identify Tra as a novel link between sex and the conserved insulin signaling pathway.

Valzania, L., Ono, H., Ignesti, M., Cavaliere, V., Bernardi, F., Gamberi, C., Lasko, P. and Gargiulo, G. (2015). Drosophila 4EHP is essential for the larval-pupal transition and required in the prothoracic gland for ecdysone biosynthesis. Dev Biol. PubMed ID: 26721418
Summary:
Maternal expression of the translational regulator 4EHP (eIF4E-Homologous Protein) has an established role in generating protein gradients essential for specifying the Drosophila embryonic pattern. This study generated a null mutation of 4EHP, which revealed for the first time that it is essential for viability and for completion of development. In fact, 4EHP null larvae, and larvae ubiquitously expressing RNAi targeting 4EHP, are developmentally delayed, fail to grow and eventually die. In addition, expressing RNAi that targets 4EHP specifically in the prothoracic gland disrupted ecdysone biosynthesis, causing a block of the transition from the larval to pupal stages. This phenotype can be rescued by dietary administration of ecdysone. Consistent with this, 4EHP is highly expressed in the prothoracic gland and it is required for wild type expression levels of steroidogenic enzymes. Taken together, these results uncover a novel essential function for 4EHP in regulating ecdysone biosynthesis.

Wang, H., Ma, Z., Niu, K., Xiao, Y., Wu, X., Pan, C., Zhao, Y., Wang, K., Zhang, Y. and Liu, N. (2015). Antagonistic roles between Nibbler and Hen1 modulate piRNA 3' ends in Drosophila. Development [Epub ahead of print]. PubMed ID: 26718004
Summary:
In eukaryotes, aberrant expression of transposable elements is detrimental to the host genome. Piwi-interacting RNAs of approximately 23 to 30 nucleotides (nt) bound to PIWI-clade Argonaute proteins silence transposons strictly dependent on their sequence complementarity. Hence, a key question in understanding piRNA pathways is to determine mechanisms that modulate piRNA sequences. This study identified a protein-protein interaction between Nibbler (Nbr), a 3'-to-5' exoribonuclease and Piwi, linking Nbr activity with piRNA pathways. A delicate interplay occurs between Nbr and Hen1, a methyltransferase involved in 2'-O-methylation at 3' terminal nucleotides of piRNAs, connecting two genes with opposing activities in biogenesis of piRNA 3' ends. With age, piRNAs become shorter and less, coupled with de-repression of select TEs. Activities of nbr and hen1 inherently contribute to TE silencing and age-dependent profiles of piRNAs. It is proposed that antagonistic roles between nbr and hen1 define a mechanism to modulate piRNA 3'ends.

Jakob, L., Treiber, T., Treiber, N., Gust, A., Kramm, K., Hansen, K., Stotz, M., Wankerl, L., Herzog, F., Hannus, S., Grohmann, D. and Meister, G. (2016). Structural and functional insights into the fly microRNA biogenesis factor Loquacious. RNA [Epub ahead of print]. PubMed ID: 26769856
Summary:
In the microRNA (miRNA) pathway, Dicer processes precursors to mature miRNAs. For efficient processing, double-stranded RNA-binding proteins support Dicer proteins. In flies, Loquacious (Loqs) interacts with Dicer1 (Dcr1) to facilitate miRNA processing. The structure of the third double-stranded RNA-binding domain (dsRBD) of Loqs has been solved, and specific structural elements have been defined that interact with Dcr1. In addition, the linker preceding dsRBD3 was shown to contribute significantly to Dcr1 binding. Furthermore, this structural work demonstrates that the third dsRBD of Loqs forms homodimers. Mutations in the dimerization interface abrogate Dcr1 interaction. Loqs, however, binds to Dcr1 as a monomer using the identified dimerization surface, suggesting that Loqs might form dimers under conditions where Dcr1 is absent or not accessible. Since critical sequence elements are conserved, it is suggested that dimerization might be a general feature of dsRBD proteins in gene silencing.

Weber, J., Bao, H., Hartlmuller, C., Wang, Z., Windhager, A., Janowski, R., Madl, T., Jin, P. and Niessing, D. (2016). Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha. Elife 5. PubMed ID: 26744780
Summary:
The neuronal DNA-/RNA-binding protein Pur-alpha is a transcription regulator and core factor for mRNA-localization. Pur-alpha deficient mice die after birth with pleiotropic neuronal defects. This study reports the crystal structure of the DNA-/RNA-binding domain of Pur-alpha in complex with ssDNA. It reveals base-specific recognition and offers a molecular explanation for the effect of point mutations in the 5q31.3 microdeletion syndrome. Consistent with the crystal structure, biochemical and NMR data indicate that Pur-alpha binds DNA and RNA in the same way, suggesting binding modes for tri- and hexanucleotide repeat RNAs in two neurodegenerative RNAopathies. Additionally, structure-based in vitro experiments resolved the molecular mechanism of Pur-alpha's unwindase activity. Complementing in vivo analyses in Drosophila demonstrated the importance of a highly conserved phenylalanine for Pur-alpha's unwinding and neuroprotective function. By uncovering the molecular mechanisms of nucleic-acid binding, this study contributes to understanding the cellular role of Pur-alpha and its implications in neurodegenerative diseases.

Sunday, January 17th

Wang, Z., Wu, D., Liu, Y., Xia, X., Gong, W., Qiu, Y., Yang, J., Zheng, Y., Li, J., Wang, Y. F., Xiang, Y., Hu, Y. and Zhou, X. (2015). Drosophila Dicer-2 has an RNA interference-independent function that modulates Toll immune signaling. Sci Adv 1: e1500228. PubMed ID: 26601278
Summary:
Dicer-2 is the central player for small interfering RNA biogenesis in the Drosophila RNA interference (RNAi) pathway. Intriguingly, Dicer-2 has an unconventional RNAi-independent function that positively modulates Toll immune signaling, which defends against Gram-positive bacteria, fungi, and some viruses, in both cells and adult flies. The loss of Dicer-2 expression makes fruit flies more susceptible to fungal infection. Dicer-2 posttranscriptionally modulates Toll signaling because Dicer-2 is required for the proper expression of Toll protein but not for Toll protein stability or Toll mRNA transcription. Moreover, Dicer-2 directly binds to the 3' untranslated region (3'UTR) of Toll mRNA via its PAZ (Piwi/Argonaute/Zwille) domain and is required for protein translation mediated by Toll 3'UTR. The loss of Toll 3'UTR binding activity makes Dicer-2 incapable of promoting Toll signaling. These data indicate that the interaction between Dicer-2 and Toll mRNA plays a pivotal role in Toll immune signaling. In addition, Dicer-2 is also required for the Toll signaling induced by two different RNA viruses in Drosophila cells. Consequently, these findings uncover a novel RNAi-independent function of Dicer-2 in the posttranscriptional regulation of Toll protein expression and signaling, indicate an unexpected intersection of the RNAi pathway and the Toll pathway, and provide new insights into Toll immune signaling, Drosophila Dicer-2, and probably Dicer and Dicer-related proteins in other organisms.

Allen, V.W., O'Connor, R.M., Ulgherait, M., Zhou, C.G., Stone, E.F., Hill, V.M., Murphy, K.R., Canman, J.C., Ja, W.W. and Shirasu-Hiza, M.M. (2015). period-regulated feeding behavior and TOR signaling modulate survival of infection. Curr Biol [Epub ahead of print]. PubMed ID: 26748856
Summary:
Most metazoans undergo dynamic, circadian-regulated changes in behavior and physiology. Currently, it is unknown how circadian-regulated behavior impacts immunity against infection. This study of behaviorally arrhythmic Drosophila circadian period mutants identifies a novel link between nutrient intake and tolerance of infection with B. cepacia, a bacterial pathogen of rising importance in hospital-acquired infections. Infection tolerance in wild-type animals was found to be stimulated by acute exposure to dietary glucose and amino acids. Glucose-stimulated tolerance was induced by feeding or direct injection; injections reveal a narrow window for glucose-stimulated tolerance. In contrast, amino acids stimulate tolerance only when ingested. The role of a known amino-acid-sensing pathway, the TOR (Target of Rapamycin) pathway, was investigated in immunity. TORC1 is circadian regulated and inhibition of TORC1 decreases resistance, as in vertebrates. Surprisingly, inhibition of the less well-characterized TOR complex 2 (TORC2) dramatically increases survival, through both resistance and tolerance mechanisms. This work suggests that dietary intake on the day of infection by B. cepacia can make a significant difference in long-term survival. TOR signaling mediates both resistance and tolerance of infection, and TORC2 was identified as a novel potential therapeutic target for increasing survival of infection.

Park, E. S., Elangovan, M., Kim, Y. J. and Yoo, Y. J. (2015). UbcD4, an ortholog of E2-25K/Ube2K, is essential for activation of the immune deficiency pathway in Drosophila. Biochem Biophys Res Commun [Epub ahead of print]. PubMed ID: 26707646
Summary:
Ubiquitination is a key regulatory mechanism in the immune deficiency (IMD) pathway in Drosophila. This study developed a simple immunoblot method to identify components involved in this pathway. Considering the emerging roles of ubiquitin-conjugating enzymes (E2s) in determining ubiquitin chain types and ubiquitination speed, a screen was performed for E2s required for IMD activation. UbcD4, in addition to the previously reported E2s Effete and Bendless, was shown to be required for activation of the IMD pathway. RNAi-mediated knockdown of the UbcD4 ortholog, E2-25K/Ube2K, inhibited TNFα- and LPS-mediated activation of the NF-κB pathway, implying that UbcD4 and E2-25K/Ube2K play a conserved role as positive regulators in both pathways.

Lamiable, O., et al. (2016). Cytokine Diedel and a viral homologue suppress the IMD pathway in Drosophila. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 26739560
Summary:
Insect viruses express suppressors of RNA interference or apoptosis, highlighting the importance of these cell intrinsic antiviral mechanisms in invertebrates. This study reports the identification and characterization of a family of proteins encoded by insect DNA viruses that are homologous to a 12-kDa circulating protein encoded by the virus-induced Drosophila gene diedel (die). die mutant flies were shown to have shortened lifespan and succumb more rapidly than controls when infected with Sindbis virus. This reduced viability is associated with deregulated activation of the immune deficiency (IMD) pathway of host defense and can be rescued by mutations in the genes encoding the homolog of IKKγ or IMD itself. These results reveal an endogenous pathway that is exploited by insect viruses to modulate NF-κB signaling and promote fly survival during the antiviral response.

Saturday, January 16th

Stanley, C.E. Jr. and Kulathinal, R.J. (2016). Genomic signatures of domestication on neurogenetic genes in Drosophila melanogaster. BMC Evol Biol 16: 6. PubMed ID: 26728183
Summary:
Domesticated animals quickly evolve docile and submissive behaviors after isolation from their wild conspecifics. Model organisms reared for prolonged periods in the laboratory also exhibit similar shifts towards these domesticated behaviors. Yet whether this divergence is due to inadvertent selection in the lab or the fixation of deleterious mutations remains unknown. This study compares the genomes of lab-reared and wild-caught Drosophila melanogaster to understand the genetic basis of these recently endowed behaviors common to laboratory models. From reassembled genomes of common lab strains, unique, derived variants not present in global populations (lab-specific SNPs) were identified. Decreased selective constraints across low frequency SNPs (unique to one or two lab strains) are different from patterns found in the wild and more similar to neutral expectations, suggesting an overall accumulation of deleterious mutations. However, high-frequency lab SNPs found in most or all lab strains reveal an enrichment of X-linked loci and neuro-sensory genes across large extended haplotypes. Among shared polymorphisms, highly differentiated SNPs were also found, in which the derived allele is higher in frequency in the wild (Fst*wild>lab), enriched for similar neurogenetic ontologies, indicative of relaxed selection on more active wild alleles in the lab. Among random mutations that continuously accumulate in the laboratory, common adaptive signatures in domesticated lab strains of fruit flies were detected. These results demonstrate that lab animals can quickly evolve domesticated behaviors via unconscious selection by humans early on a broad pool of disproportionately large neurogenetic targets followed by the fixation of accumulated deleterious mutations on functionally similar targets.

Chakraborty, M. and Fry, J.D. (2015). Evidence that environmental heterogeneity maintains a detoxifying enzyme polymorphism in Drosophila melanogaster. Curr Biol [Epub ahead of print]. PubMed ID: 26748852
Summary:
Environmental heterogeneity is thought to be an important process maintaining genetic variation in populations: if alternative alleles are favored in different environments, a stable polymorphism can be maintained. This situation has been hypothesized to occur in genes encoding multi-substrate enzymes, in which changes that increase activity with one substrate typically decrease activity with others, but examples of polymorphisms maintained by this mechanism are rare. This study presents evidence that a polymorphism in an enzyme gene in Drosophila melanogaster is maintained by such a trade-off. The mitochondrially localized aldehyde dehydrogenase in D. melanogaster has two important functions: detoxifying acetaldehyde derived from dietary ethanol and detoxifying larger aldehydes produced as byproducts of oxidative phosphorylation. A derived variant of the enzyme, Leu479Phe, is present in moderate frequencies in most temperate populations but is rare in more ethanol-averse tropical populations. Using purified recombinant protein, the Leu-Phe substitution was shown to increase turnover rate of acetaldehyde but decrease turnover rate of larger aldehydes. Furthermore, using transgenic fly lines, the substitution was shown to increase lifetime fitness on medium supplemented with an ecologically relevant ethanol concentration but decreases fitness on medium lacking ethanol. The strong, opposing selection pressures, coupled with documented highly variable ethanol concentrations in breeding sites of temperate populations, implicate an essential role for environmental heterogeneity in maintaining the polymorphism.

Wolff, J. N., Pichaud, N., Camus, M. F., Cote, G., Blier, P. U. and Dowling, D. K. (2016).. Evolutionary implications of mitochondrial genetic variation: Mitochondrial genetic effects on OXPHOS respiration and mitochondrial quantity change with age and sex in fruit flies. J Evol Biol [Epub ahead of print]. PubMed ID: 26728607
Summary:
The ancient acquisition of the mitochondrion into the ancestor of modern-day eukaryotes is thought to have been pivotal in facilitating the evolution of complex life. Mitochondria retain their own diminutive genome, with mitochondrial genes encoding core subunits involved in oxidative phosphorylation. Traditionally, it was assumed there was little scope for genetic variation to accumulate and be maintained within the mitochondrial genome. However, in the past decade, mitochondrial genetic variation has been routinely tied to the expression of life-history traits such as fertility, development, and longevity. To examine whether these broad-scale effects on life-history trait expression might ultimately find their root in mitochondrially-mediated effects on core bioenergetic function, this study measured the effects of genetic variation across twelve different mitochondrial haplotypes on respiratory capacity and mitochondrial quantity in Drosophila. Strains of flies were used that differed only in their mitochondrial haplotype, and each sex was tested separately at two different adult ages. Mitochondrial haplotypes affected both respiratory capacity and mitochondrial quantity. However, these effects were highly context-dependent, with the genetic effects contingent on both the sex and the age of the flies. These sex- and age-specific genetic effects are likely to resonate across the entire organismal life-history, providing insights into how mitochondrial genetic variation may contribute to sex-specific trajectories of life-history evolution.

Frazee, S. R. and Masly, J. P. (2015). Multiple sexual selection pressures drive the rapid evolution of complex morphology in a male secondary genital structure. Ecol Evol 5: 4437-4450. PubMed ID: 26664690
Summary:
The genitalia of internally fertilizing taxa represent a striking example of rapid morphological evolution. Although sexual selection can shape variation in genital morphology, it has been difficult to test whether multiple sexual selection pressures combine to drive the rapid evolution of individual genital structures. This study tested the hypothesis that both pre- and postcopulatory sexual selection can act in concert to shape complex structural variation in secondary genital morphology. The size and shape of the posterior lobes of Drosophila melanogaster males were genetically modified, and the consequences of morphological variation was tested on several reproductive measures. The posterior lobes were found to be necessary for genital coupling, and they are also the targets of multiple postcopulatory processes that shape quantitative variation in morphology, even though these structures make no direct contact with the external female genitalia or internal reproductive organs during mating. Males with smaller and less structurally complex posterior lobes were found to suffer substantial fitness costs in competitive fertilization experiments. These results show that sexual selection mechanisms can combine to shape the morphology of a single genital structure and that the posterior lobes of D. melanogaster are the targets of multiple postcopulatory selection pressures.

Friday, January 15th

Luu, P., Zaki, S.A., Tran, D.H. and French, R.L. (2015). A novel gene controlling the timing of courtship initiation in Drosophila melanogaster. Genetics [Epub ahead of print]. PubMed ID: 26721856
Summary:
Over the past 35 years, developmental geneticists have made impressive progress towards an understanding of how genes specify morphology and function, particularly as relates to the specification of each physical component of an organism. In the last 20 years, male courtship behavior in Drosophila melanogaster has emerged as a robust model system for the study of genetic specification of behavior. Courtship behavior is both complex and innate, and a single gene, fruitless (fru), is both necessary and sufficient for all aspects of the courtship ritual. Typically, loss of male-specific Fruitless proteins function results in male flies that perform the courtship ritual incorrectly, slowly, or not at all. This study describes a novel requirement for fru: a group of cells in which male Fru proteins are required to reduce the speed of courtship initiation. In addition, the study identified a gene, Trapped in endoderm 1 (Tre1), which is required in these cells for normal courtship and mating behavior. Tre1 encodes a G-protein-coupled receptor required for establishment of cell polarity and cell migration, and has previously not been shown to be involved in courtship behavior. The results of feminization of the Tre1-expressing neurons, as well as the effects on courtship behavior of mutation of Tre1 were described. In addition, it was shown that Tre1 is expressed in a sexually dimorphic pattern in the central and peripheral nervous systems, and the role of the Tre1 cells in mate identification was investigated.

Jagadeeshan, S., Shah, U., Chakrabarti, D. and Singh, R. S. (2015). Female choice or male sex drive? The advantages of male body size during mating in Drosophila melanogaster. PLoS One 10: e0144672. PubMed ID: 26658421
Summary:
The mating success of larger male Drosophila has been traditionally been explained by female choice. Female choice can explain this success by virtue of females taking less time to mate with preferred males, but so can the more aggressive or persistent courtships efforts of large males. Since mating is a negotiation between the two sexes, the behaviors of both are likely to interact and influence mating outcomes. This study explored these negotiations by testing for the relative influence of male behaviors and its effect on influencing female courtship arousal threshold, the time taken for females to accept copulation. The results show that large males indeed have higher copulation success compared to smaller males. Competition between two males or an increasing number of males had no influence on female sexual arousal threshold;-females therefore may have a relatively fixed 'arousal threshold' that must be reached before they are ready to mate, and larger males appear to be able to manipulate this threshold sooner. On the other hand, the females' physiological and behavioral state drastically influences mating; once females have crossed the courtship arousal threshold they take less time to mate and mate indiscriminately with large and small males. Mating quicker with larger males may be misconstrued to be due to female choice; the results suggest that the mating advantage of larger males may be more a result of heightened male activity and relatively less of female choice. Body size per se may not be a trait under selection by female choice, but size likely amplifies male activity and signal outputs in courtship, allowing them to influence female arousal threshold faster.

Hoopfer, E.D., Jung, Y., Inagaki, H.K., Rubin, G.M. and Anderson, D.J. (2015). P1 interneurons promote a persistent internal state that enhances inter-male aggression in Drosophila. Elife [Epub ahead of print]. PubMed ID: 26714106
Summary:
How brains are hardwired to produce aggressive behavior, and how aggression circuits are related to those that mediate courtship, is not well understood. This large-scale screen for aggression-promoting neurons in Drosophila identifies several independent hits that enhance both inter-male aggression and courtship. Genetic intersections reveal that P1 interneurons, previously thought to exclusively control male courtship, are responsible for both phenotypes. The aggression phenotype is fly-intrinsic, and requires male-specific chemosensory cues on the opponent. Optogenetic experiments indicate that P1 activation promotes aggression vs. wing extension at low vs. high thresholds, respectively. High frequency photostimulation promotes wing extension and aggression in an inverse manner, during light ON and OFF, respectively. P1 activation enhances aggression by promoting a persistent internal state, which could endure for minutes prior to social contact. Thus P1 neurons promote an internal state that facilitates both aggression and courtship, and can control these social behaviors in a threshold-dependent manner. 		Jeong, K., Lee, S., Seo, H., Oh, Y., Jang, D., Choe, J., Kim, D., Lee, J. H. and Jones, W. D. (2015). Ca-alpha1T, a fly T-type Ca(2+) channel, negatively modulates sleep. Sci Rep 5: 17893. PubMed ID: 26647714
Summary:
Mammalian T-type Ca(2+) channels are encoded by three separate genes (Cav3.1, 3.2, 3.3). These channels are reported to be sleep stabilizers important in the generation of the delta rhythms of deep sleep, but controversy remains. The identification of precise physiological functions for the T-type channels has been hindered, at least in part, by the potential for compensation between the products of these three genes and a lack of specific pharmacological inhibitors. Invertebrates have only one T-type channel gene, but its functions are even less well-studied. Ca-alpha1T, the only Cav3 channel gene in Drosophila melanogaster, was cloned and expressed in Xenopus oocytes and HEK-293 cells and was confirmed to pass typical T-type currents. Voltage-clamp analysis revealed the biophysical properties of Ca-alpha1T show mixed similarity, sometimes falling closer to Cav3.1, sometimes to Cav3.2, and sometimes to Cav3.3. Ca-alpha1T was found to be broadly expressed across the adult fly brain in a pattern vaguely reminiscent of mammalian T-type channels. In addition, flies lacking Ca-alpha1T show an abnormal increase in sleep duration most pronounced during subjective day under continuous dark conditions despite normal oscillations of the circadian clock. Thus, this study suggests invertebrate T-type Ca(2+) channels promote wakefulness rather than stabilizing sleep.

Thursday, January 14th

Derivery, E., Seum, C., Daeden, A., Loubery, S., Holtzer, L., Julicher, F. and Gonzalez-Gaitan, M. (2015). Polarized endosome dynamics by spindle asymmetry during asymmetric cell division. Nature 528: 280-285. PubMed ID: 26659188
Summary:
During asymmetric division, fate determinants at the cell cortex segregate unequally into the two daughter cells. It has recently been shown that Sara (Smad anchor for receptor activation) signalling endosomes in the cytoplasm also segregate asymmetrically during asymmetric division. Biased dispatch of Sara endosomes mediates asymmetric Notch/Delta signalling during the asymmetric division of sensory organ precursors in Drosophila. In flies, this has been generalized to stem cells in the gut and the central nervous system, and, in zebrafish, to neural precursors of the spinal cord. However, the mechanism of asymmetric endosome segregation is not understood. This study shows that the plus-end kinesin motor Klp98A targets Sara endosomes to the central spindle, where they move bidirectionally on an antiparallel array of microtubules. The microtubule depolymerizing kinesin Klp10A and its antagonist Patronin generate central spindle asymmetry. This asymmetric spindle, in turn, polarizes endosome motility, ultimately causing asymmetric endosome dispatch into one daughter cell. This mechanism was demonstrated by inverting the polarity of the central spindle by polar targeting of Patronin using nanobodies (single-domain antibodies). This spindle inversion targets the endosomes to the wrong cell. These data uncover the molecular and physical mechanism by which organelles localized away from the cellular cortex can be dispatched asymmetrically during asymmetric division.

Xu, Y., An, F., Borycz, J. A., Borycz, J., Meinertzhagen, I. A. and Wang, T. (2015). Histamine Recycling Is Mediated by CarT, a Carcinine Transporter in Drosophila Photoreceptors. PLoS Genet 11: e1005764. PubMed ID: 26713872
Summary:
Histamine is an important chemical messenger that regulates multiple physiological processes in both vertebrate and invertebrate animals. Even so, how glial cells and neurons recycle histamine remains to be elucidated. Drosophila photoreceptor neurons use histamine as a neurotransmitter, and the released histamine is recycled through neighboring glia, where it is conjugated to beta-alanine to form carcinine. However, how carcinine is then returned to the photoreceptor remains unclear. In an mRNA-seq screen for photoreceptor cell-enriched transporters, CG9317, an SLC22 transporter family protein, was identified and named CarT (Carcinine Transporter). S2 cells that express CarT are able to take up carcinine in vitro. In the compound eye, CarT is exclusively localized to photoreceptor terminals. Null mutations of cart alter the content of histamine and its metabolites. Moreover, null cart mutants are defective in photoreceptor synaptic transmission and lack phototaxis. These findings reveal that CarT is required for histamine recycling at histaminergic photoreceptors and provide evidence for a CarT-dependent neurotransmitter trafficking pathway between glial cells and photoreceptor terminals.

Tognon, E., Kobia, F., Busi, I., Fumagalli, A., De Masi, F. and Vaccari, T. (2016). Control of lysosomal biogenesis and Notch-dependent tissue patterning by components of the TFEB-V-ATPase axis in Drosophila melanogaster. Autophagy [Epub ahead of print]. PubMed ID: 26727288
Summary:
In vertebrates, TFEB (transcription factor EB) and MITF (microphthalmia-associated transcription factor; see Drosophila Mitf) family of basic Helix-Loop-Helix (bHLH) transcription factors regulate both lysosomal function and organ development. However, it is not clear whether these 2 processes are interconnected. This study shows that Mitf, the single TFEB and MITF ortholog in Drosophila, controls expression of vacuolar-type H+-ATPase pump (V-ATPase) subunits. Remarkably, it was also found that expression of Vha16-1 and Vha13, encoding 2 key components of V-ATPase, is patterned in the wing imaginal disc. In particular, Vha16-1 expression follows differentiation of proneural regions of the disc. These regions, that will form sensory organs in the adult, appear to possess a distinctive endo-lysosomal compartment and Notch (N) localization. Modulation of Mitf activity in the disc in vivo alters endo-lysosomal function and disrupts proneural patterning. Similar to these findings in Drosophila, in human breast epithelial cells, it was observed that the impairment of the Vha16-1 human ortholog ATP6V0C changes the size and function of the endo-lysosomal compartment and depletion of TFEB reduces ligand-independent N signaling activity. These data suggest that lysosomal-associated functions regulated by the TFEB-V-ATPase axis might play a conserved role in shaping cell fate.

Yu, Y., Lee, H. C., Chen, K. C., Suhan, J., Qiu, M., Ba, Q. and Yang, G. (2016). Inner membrane fusion mediates spatial distribution of axonal mitochondria. Sci Rep 6: 18981. PubMed ID: 26742817
Summary:
In eukaryotic cells, mitochondria form a dynamic interconnected network to respond to changing needs at different subcellular locations. A fundamental yet unanswered question regarding this network is whether, and if so how, local fusion and fission of individual mitochondria affect their global distribution. To address this question, high-resolution computational image analysis techniques were developed to examine the relations between mitochondrial fusion/fission and spatial distribution within the axon of Drosophila larval neurons. Stationary and moving mitochondria underwent fusion and fission regularly but followed different spatial distribution patterns and exhibited different morphology. Disruption of inner membrane fusion by knockdown of dOpa1, Drosophila Optic Atrophy 1, not only increased the spatial density of stationary and moving mitochondria but also changed their spatial distributions and morphology differentially. Knockdown of dOpa1 also impaired axonal transport of mitochondria. But the changed spatial distributions of mitochondria resulted primarily from disruption of inner membrane fusion because knockdown of Milton, a mitochondrial kinesin-1 adapter, caused similar transport velocity impairment but different spatial distributions. Together, these data reveals that stationary mitochondria within the axon interconnect with moving mitochondria through fusion and fission and that local inner membrane fusion between individual mitochondria mediates their global distribution.

Wednesday, February 13th

Komura-Kawa, T., Hirota, K., Shimada-Niwa, Y., Yamauchi, R., Shimell, M., Shinoda, T., Fukamizu, A., O'Connor, M. B. and Niwa, R. (2015). The Drosophila zinc finger transcription factor Ouija board controls ecdysteroid biosynthesis through specific regulation of spookier. PLoS Genet 11: e1005712. PubMed ID: 26658797
Summary:
During larval and pupal development, ecdysteroids are synthesized in the prothoracic gland (PG) from dietary cholesterol via a series of hydroxylation and oxidation steps. This study reports identification and characterization of the C2H2-type zinc finger transcription factor Ouija board (Ouib) necessary for ecdysteroid production in the PG in Drosophila. Expression of ouib is predominantly limited to the PG, and genetic null mutants of ouib result in larval developmental arrest that can be rescued by administrating an active ecdysteroid. Interestingly, ouib mutant animals exhibit a strong reduction in the expression of one ecdysteroid biosynthetic enzyme, Spookier. Using a cell culture-based luciferase reporter assay, Ouib protein stimulates transcription of spok by binding to a specific ~15 bp response element in the spok PG enhancer element. Most remarkable, the developmental arrest phenotype of ouib mutants is rescued by over-expression of a functionally-equivalent paralog of spookier. These observations imply that the main biological function of Ouib is to specifically regulate spookier transcription during Drosophila development.

Han, H., Fan, J., Xiong, Y., Wu, W., Lu, Y., Zhang, L. and Zhao, Y. (2016). Chi and dLMO function antagonistically on Notch signaling through directly regulation of fng transcription. Sci Rep 6: 18937. PubMed ID: 26738424
Summary:
Genes apterous (ap), chip (chi) and beadex (bx) play important roles in the dorsal-ventral compartmentalization in Drosophila wing discs. Meanwhile, Notch signaling is essential to the same process. It has been reported that Ap and Chi function as a tetramer to regulate Notch signaling. At the same time, dLMO (the protein product of gene bx) regulates the activity of Ap by competing its binding with Chi. However, the detailed functions of Chi and dLMO on Notch signaling and the relevant mechanisms remain largely unknown. This study reports the detailed functions of Chi and dLMO on Notch signaling. It was found that different Chi protein levels in adjacent cells activate Notch signaling mainly in the cells with higher level of Chi. Also, dLMO induces antagonistical phenotypes on Notch signaling compared to that induced by Chi. These processes depend on their direct regulation of fringe (fng) transcription. 

Ferraro, T., Esposito, E., Mancini, L., Ng, S., Lucas, T., Coppey, M., Dostatni, N., Walczak, A.M., Levine, M. and Lagha, M. (2015). Transcriptional memory in the Drosophila embryo. Curr Biol [Epub ahead of print]. PubMed ID: 26748851
Summary:
Transmission of active transcriptional states from mother to daughter cells has the potential to foster precision in the gene expression programs underlying development. Such transcriptional memory has been specifically proposed to promote rapid reactivation of complex gene expression profiles after successive mitoses in Drosophila development. By monitoring transcription in living Drosophila embryos, this study provides the first evidence for transcriptional memory in animal development. The activities of stochastically expressed transgenes were measured in order to distinguish active and inactive mother cells and the behaviors of their daughter nuclei after mitosis. Quantitative analyses reveal that there is a 4-fold higher probability for rapid reactivation after mitosis when the mother experiences transcription. Moreover, memory nuclei activate transcription twice as fast as neighboring inactive mothers, thus leading to augmented levels of gene expression. The study proposes that transcriptional memory is a mechanism of precision, which helps coordinate gene activity during embryogenesis.

Akbari, O. S., Papathanos, P. A., Sandler, J. E., Kennedy, K. and Hay, B. A. (2014). Identification of germline transcriptional regulatory elements in Aedes aegypti. Sci Rep 4: 3954. PubMed ID: 24492376
Summary:
The mosquito Aedes aegypti is the principal vector for the yellow fever and dengue viruses, and is also responsible for recent outbreaks of the alphavirus chikungunya. Vector control strategies utilizing engineered gene drive systems are being developed as a means of replacing wild, pathogen transmitting mosquitoes with individuals refractory to disease transmission, or bringing about population suppression. Several of these systems, including Medea, UDMEL, and site-specific nucleases, which can be used to drive genes into populations or bring about population suppression, utilize transcriptional regulatory elements that drive germline-specific expression. This study report the identification of multiple regulatory elements able to drive gene expression specifically in the female germline, or in the male and female germline, in the mosquito Aedes aegypti. These elements can also be used as tools with which to probe the roles of specific genes in germline function and in the early embryo, through overexpression or RNA interference.

Tuesday, January 12th

Sitnik, J.L., Gligorov, D., Maeda, R.K., Karch, F. and Wolfner, M.F. (2016). Secondary cell expressed genes in the male accessory gland are needed for the female post-mating response in Drosophila melanogaster. Genetics [Epub ahead of print]. PubMed ID: 26746709
Summary:
Seminal proteins from the Drosophila male accessory gland induce post-mating responses (PMR) in females. The PMR comprises behavioral and physiological changes that include increased egg-laying, decreased receptivity to courting males, and changes in the storage and use of sperm. Many of these changes are induced by a "sex peptide" (SP), and are maintained by SP's binding to, and slow-release from, sperm. The accessory gland contains two secretory cell types whose morphology and development differs. Products of these "main" and "secondary" cells work interdependently to induce and maintain the PMR. To identify individual genes needed for the morphology and function of secondary cells, this study analyzed iab6cocu males, whose secondary cells have abnormal morphology and fail to provide products to maintain the PMR. By RNA-seq, 77 genes were identified whose expression is down-regulated by a factor of >5x in iab6cocu males. By functional assays and microscopy, 20 candidate genes were tested and it was found that at least 9 are required for normal storage and release of SP in mated females. Knockdown of each of these 9 genes consequently leads to a reduction in egg-laying and an increase in receptivity over time, confirming a role for the secondary cells in maintaining the long-term PMR. Interestingly, only 1 of the 9 genes, CG3349, encodes a previously reported seminal fluid protein (Sfp), suggesting that secondary cells may perform essential functions beyond the production and modification of known Sfps. At least 3 of the 9 genes also regulate the size and/or abundance of secondary cell vacuoles, suggesting that the vacuoles' contents may be important for the machinery used to maintain the PMR.

Mendes, C. C. and Mirth, C. K. (2015). Stage-specific plasticity in ovary size is regulated by Insulin/Insulin-Like growth factor and Ecdysone signalling in Drosophila. Genetics [Epub ahead of print]. PubMed ID: 26715667
Summary:
Animals from flies to humans adjust their development in response to environmental conditions through a series of developmental checkpoints, which alter the sensitivity of organs to environmental perturbation. Despite their importance, little is known about the molecular mechanisms through which this change in sensitivity occurs. This study has identified two phases of sensitivity to larval nutrition that contribute to plasticity in ovariole number, an important determinant of fecundity, in Drosophila melanogaster. These two phases of sensitivity are separated by the developmental checkpoint called critical weight; poor nutrition has greater effects on ovariole number in larvae before critical weight than afterwards. This switch in sensitivity results from distinct developmental processes. In pre-critical weight larvae, poor nutrition delays the onset of terminal filament cell differentiation, the starting point for ovariole development, and strongly suppresses the rate of terminal filament addition and the rate of increase in ovary volume. Conversely, in post-critical weight larvae, poor nutrition only affects the rate of increase in ovary volume. These results further indicate that two hormonal pathways, the insulin/insulin-like growth factor and the ecdysone signalling pathways, modulate the timing and rates of all three developmental processes. The change in sensitivity in the ovary results from changes in the relative contribution of each pathway to the rates of TF addition and increase in ovary volume before and after critical weight. This work deepens the understanding of how hormones act to modify the sensitivity of organs to environmental conditions, thereby affecting their plasticity.

Peters, N. C. and Berg, C. A. (2015). Dynamin-mediated endocytosis is required for tube closure, cell intercalation, and biased apical expansion during epithelial tubulogenesis in the Drosophila ovary. Dev Biol [Epub ahead of print]. PubMed ID: 26542010
Summary:
Most metazoans are able to grow beyond a few hundred cells and to support differentiated tissues because they elaborate multicellular, epithelial tubes that are indispensable for nutrient and gas exchange. To identify and characterize the cellular behaviors and molecular mechanisms required for the morphogenesis of epithelial tubes (i.e., tubulogenesis), the D. melanogaster ovary was analyzed. In the ovary, epithelia surrounding the developing egg chambers first pattern, then form and extend a set of simple, paired, epithelial tubes, the dorsal appendage (DA) tubes, and they create these structures in the absence of cell division or cell death. This genetically tractable system allows the assessment of the relative contributions that coordinated changes in cell shape, adhesion, orientation, and migration make to basic epithelial tubulogenesis. Dynamin, a conserved regulator of endocytosis and the cytoskeleton, serves a key role in DA tubulogenesis. Dynamin is require for distinct aspects of DA tubulogenesis: DA-tube closure, DA-tube-cell intercalation, and biased apical-luminal cell expansion. Evidence is provided that Dynamin promotes these processes by facilitating endocytosis of cell-cell and cell-matrix adhesion complexes; precise levels and sub-cellular distribution of E-Cadherin and specific Integrin subunits impact DA tubulogenesis. Thus, these studies identify novel morphogenetic roles (i.e., tube closure and biased apical expansion), and expand upon established roles (i.e., cell intercalation and adhesion remodeling), for Dynamin in tubulogenesis.

Das, A., Shah, S. J., Fan, B., Paik, D., DiSanto, D. J., Hinman, A. M., Cesario, J. M., Battaglia, R. A., Demos, N. and McKim, K. S. (2015). Spindle assembly and chromosome segregation requires central spindle proteins in Drosophila oocytes. Genetics [Epub ahead of print]. PubMed ID: 26564158
Summary:
Oocytes segregate chromosomes in the absence of centrosomes. In this situation, the chromosomes direct spindle assembly. It is still unclear in this system, what factors are required for homologous chromosome bi-orientation and spindle assembly. The Drosophila kinesin-6 protein Subito, though non-essential for mitotic spindle assembly, is required to organize a bipolar meiotic spindle and chromosome bi-orientation in oocytes. Along with the chromosomal passenger complex (CPC), Subito is an important part of the metaphase I central spindle. This study consisted of genetic screens to identify genes that interact with subito or the CPC component Incenp. In addition, the meiotic mutant phenotype for some of the genes identified in these screens were characterized. Use of a heat shock inducible system showed that the Centralspindlin component RacGAP50C and downstream regulators of cytokinesis Rho1, Sticky and RhoGEF2, are required for homologous chromosome bi-orientation in metaphase I oocytes. This suggests a novel function for proteins normally involved in mitotic cell division, in the regulation of microtubule-chromosome interactions. The kinetochore protein, Polo kinase, was also shown to be required for maintaining chromosome alignment and spindle organization in metaphase I oocytes. In combination these results support a model where the meiotic central spindle and associated proteins are essential for acentrosomal chromosome segregation.

Monday, January 11th

Svendsen, P. C., Ryu, J. R. and Brook, W. J. (2015). The expression of the T-box selector gene midline in the leg imaginal disc is controlled by both transcriptional regulation and cell lineage. Biol Open [Epub ahead of print]. PubMed ID: 26581591
Summary:
The Drosophila Tbx20 homologs midline and H15 act as selector genes for ventral fate in Drosophila legs. midline and H15 expression defines the ventral domain of the leg and the two genes are necessary and sufficient for the development of ventral fate. Ventral-specific expression of midline and H15 is activated by Wingless (Wg) and repressed by Decapentaplegic (Dpp). This study identifed VLE, a 5 kb enhancer that drives ventral specific expression in the leg disc that is very similar to midline expression. Subdivision of VLE identifies two regions that mediate both activation and repression and third region that only mediates repression. Loss- and gain-of-function genetic mosaic analysis shows that the activating and repressing regions respond to Wg and Dpp signaling respectively. All three repression regions depend on the activity of Mothers-against-decapentaplegic, a Drosophila r-Smad that mediates Dpp signaling, and respond to ectopic expression of the Dpp target genes optomoter-blind and Dorsocross 3. However, only one repression region is responsive to loss of schnurri, a co-repressor required for direct repression by Dpp-signaling. Thus, Dpp signaling restricts midline expression through both direct repression and through the activation of downstream repressors. midline and H15 expression are both subject to cross-repression and feedback inhibition. Finally, a lineage analysis indicates that ventral midline-expressing cells and dorsal omb-expressing cells do not mix during development. Together this data indicates that the ventral-specific expression of midline results from both transcriptional regulation and from a lack of cell-mixing between dorsal and ventral cells.

Fernandez-Nicolas, A. and Belles, X. (2015). CREB-binding protein contributes to the regulation of endocrine and developmental pathways in insect hemimetabolan pre-metamorphosis. Biochim Biophys Acta. PubMed ID: 26706852
Summary:
CREB-binding protein (CBP) is a promiscuous transcriptional co-regulator. In insects, CBP has been studied in the fly Drosophila melanogaster, where it is known as Nejire. Studies in D. melanogaster have revealed that Nejire is involved in the regulation of many pathways during embryo development, especially in anterior/posterior polarity, through Hedgehog and Wingless signaling, and in dorsal/ventral patterning, through TGF-β signaling. Regarding post-embryonic development, Nejire influences histone acetyl transferase activity on the ecdysone signaling pathway. Functional genomics studies using RNAi have shown that CBP contributes to the regulation of feeding and ecdysis during the pre-metamorphic nymphal instar of the cockroach Blattella germanica and is involved in TGF-β, ecdysone, and MEKRE93 pathways, contributing to the activation of Kr-h1 and E93 expression. In D. melanogaster, Nejire's involvement in the ecdysone pathway in pre-metamorphic stages is conserved, whereas the TGF-β pathway has only been described in the embryo. CBP role in ecdysis pathway and in the activation of Kr-h1 and E93 expression is described in this study for the first time. It is concluded that studies in D. melanogaster may have been suggestive that CBP functions in insects are concentrated in the embryo. Results obtained in B. germanica indicate, however, that CBP have diverse and important functions in post-embryonic development and metamorphosis, especially regarding endocrine signaling. Further research into a higher diversity of models will probably reveal that the multiple post-embryonic roles of CBP observed in B. germanica are general in insects.

Fried, P. and Iber, D. (2015). Read-out of dynamic morphogen gradients on growing domains. PLoS One 10: e0143226. PubMed ID: 26599604
Summary:
Quantitative data from the Drosophila wing imaginal disc reveals that the amplitude of the Decapentaplegic (Dpp) morphogen gradient increases continuously. It is an open question how cells can determine their relative position within a domain based on a continuously increasing gradient. This study shows that pre-steady state diffusion-based dispersal of morphogens results in a zone within the growing domain where the concentration remains constant over the patterning period. The position of the zone that is predicted based on quantitative data for the Dpp morphogen corresponds to where the Dpp-dependent gene expression boundaries of spalt (sal) and daughters against dpp (dad) emerge. The model also suggests that genes that are scaling and are expressed at lateral positions are either under the control of a different read-out mechanism or under the control of a different morphogen. The patterning mechanism explains the extraordinary robustness that is observed for variations in Dpp production, and offers an explanation for the dual role of Dpp in controlling patterning and growth. Pre-steady-state dynamics are pervasive in morphogen-controlled systems, thus making this a probable general mechanism for the scaled read-out of morphogen gradients in growing developmental systems.

Seeds, A. M., Tsui, M. M., Sunu, C., Spana, E. P. and York, J. D. (2015). Inositol phosphate kinase 2 is required for imaginal disc development in Drosophila. Proc Natl Acad Sci U S A 112: 15660-15665. PubMed ID: 26647185
Summary:
Inositol phosphate kinase 2 (Ipk2), also known as IP multikinase IPMK, is an evolutionarily conserved protein that initiates production of inositol phosphate intracellular messengers (IPs), which are critical for regulating nuclear and cytoplasmic processes. This study reports that Ipk2 kinase activity is required for the development of the adult fruit fly epidermis. Ipk2 mutants show impaired development of their imaginal discs, the primordial tissues that form the adult epidermis. Although disk tissue seems to specify normally during early embryogenesis, loss of Ipk2 activity results in increased apoptosis and impairment of proliferation during larval and pupal development. The proliferation defect is in part attributed to a reduction in JAK/STAT signaling, possibly by controlling production or secretion of the pathway's activating ligand, Unpaired. Constitutive activation of the JAK/STAT pathway downstream of Unpaired partially rescues the disk growth defects in Ipk2 mutants. Thus, IP production is essential for proliferation of the imaginal discs, in part, by regulating JAK/STAT signaling. This work demonstrates an essential role for Ipk2 in producing inositide messengers required for imaginal disk tissue maturation and subsequent formation of adult body structures and provides molecular insights to signaling pathways involved in tissue growth and stability during development.

Sunday, January 10th

Burguete, A. S., Almeida, S., Gao, F. B., Kalb, R., Akins, M. R. and Bonini, N. M. (2015). GGGGCC microsatellite RNA is neuritically localized, induces branching defects, and perturbs transport granule function. Elife 4. PubMed ID: 26650351
Summary:
Microsatellite expansions are the leading cause of numerous neurodegenerative disorders. This study demonstrates that GGGGCC and CAG microsatellite repeat RNAs associated with C9orf72 in ALS/FTD and with polyglutamine diseases, respectively, localize to neuritic granules that undergo active transport into distal neuritic segments. In cultured mammalian spinal cord neurons, the presence of neuritic GGGGCC repeat RNA correlates with neuronal branching defects and the repeat RNA localizes to granules that label with FMRP, a transport granule component. Using a Drosophila GGGGCC expansion disease model, this study characterized dendritic branching defects that are modulated by FMRP and Orb2. The human orthologues of these modifiers are misregulated in induced pluripotent stem cell-differentiated neurons from GGGGCC expansion carriers. These data suggest that expanded repeat RNAs interact with the mRNA transport and translation machinery, causing transport granule dysfunction. This could be a novel mechanism contributing to the neuronal defects associated with C9orf72 and other microsatellite expansion diseases.

Frankel, S., Woods, J., Ziafazeli, T. and Rogina, B. (2015). RPD3 histone deacetylase and nutrition have distinct but interacting effects on Drosophila longevity. Aging (Albany NY) [Epub ahead of print]. PubMed ID: 26647291
Summary:
Single-gene mutations that extend longevity have revealed regulatory pathways related to aging and longevity. RPD3 is a conserved histone deacetylase (Class I HDAC). Previous studies have shown that Drosophila Rpd3 mutations increase longevity. This study tested the longevity effects of RPD3 on multiple nutrient levels. Dietary restriction (DR) has additive effects on RPD3-mediated longevity extension, but the effect may be modestly attenuated relative to controls. RPD3 and DR therefore appear to operate by distinct but interacting mechanisms. Since RPD3 regulates transcription, the mRNA levels for two proteins involved in nutrient signaling, 4E-BP and Tor, were examined in rpd3 mutant flies. 4E-BP mRNA was reduced under longevity-increasing conditions. Epistasis between RPD3 and 4E-BP with regard to longevity was then tested. Flies only heterozygous for a mutation in Thor, the 4E-BP gene, have modestly decreased life spans. Flies mutant for both rpd3 and Thor show a superposition of a large RPD3-mediated increase and a small Thor-mediated decrease in longevity at all food levels, consistent with each gene product having distinct effects on life span. However, DR-mediated extension was absent in males carrying both mutations and lessened in females. These results support the view that multiple discrete but interacting mechanisms regulate longevity.

Julien, C., et al. (2016). Conserved pharmacological rescue of hereditary spastic paraplegia-related phenotypes across model organisms. Hum Mol Genet [Epub ahead of print]. PubMed ID: 26744324
Summary:
Hereditary spastic paraplegias (HSPs) are a group of neurodegenerative diseases causing progressive gait dysfunction. Over 50 genes have now been associated with HSP. Despite the recent explosion in genetic knowledge, HSP remains without pharmacological treatment. Loss-of-function mutation of the SPAST gene, also known as SPG4, is the most common cause of HSP in patients. SPAST (see Drosophila Spastin) is conserved across animal species and regulates microtubule dynamics. Recent studies have shown that it also modulates endoplasmic reticulum (ER) stress. This study utilized null SPAST homologues in C. elegans, Drosophila, and zebrafish to tested FDA approved compounds known to modulate ER stress in order to ameliorate locomotor phenotypes associated with HSP. Locomotor defects found in all of the spastin models could be partially rescued by phenazine, methylene blue, N-acetyl-cysteine, guanabenz and salubrinal. In addition, established biomarkers of ER stress levels correlated with improved locomotor activity upon treatment across model organisms. These results provide insights into biomarkers and novel therapeutic avenues for HSP.

Chongtham, A. and Agrawal, N. (2016). Curcumin modulates cell death and is protective in Huntington's disease model. Sci Rep 6: 18736. PubMed ID: 26728250
Summary:
Huntington's disease (HD) is a progressive, dominantly inherited neurological disorder caused by an abnormal expansion of polyglutamine (polyQ) repeat within the Huntingtin (Htt) protein with no disease modifying treatments. In a Drosophila model of HD, expression of mutant Huntingtin (Htt) protein with expanded polyQ leads to formation of inclusion bodies (IBs), increase in cellular toxicity, progression of motor disabilities and reduced viability. Multiple cellular events such as oxidative stress, mitochondrial dysfunction, inflammation and transcriptional dysregulation are reported to contribute to pathology, however, to date there are no disease-modifying treatments with least side effects. Therefore, this study investigated effect of the phytochemical curcumin on HD pathogenesis. Curcumin, a phytochemical and commonly used ingredient in Asian food has a wide spectrum of anti-oxidant, anti-inflammatory and anti-fibrilogenic properties. This study provides evidence that curcumin significantly ameliorates disease symptoms in a Drosophila model of HD by suppressing cell death and can be a key to halting the progression of Huntington's disease with least side effects.

Liu, J., Li, T., Thomas, J. M., Pei, Z., Jiang, H., Engelender, S., Ross, C. A. and Smith, W. W. (2016). Synphilin-1 attenuates mutant LRRK2-induced neurodegeneration in Parkinson's disease models. Hum Mol Genet. PubMed ID: 26744328
Summary:
Mutations in leucine-rich repeat kinase 2 (LRRK2) cause autosomal-dominant Parkinsonism with pleomorphic pathology including deposits of aggregated protein and neuronal degeneration. The pathogenesis of LRRK2-linked PD is not fully understood. Using co-immunoprecipitation, this study found that LRRK2 interacted with synphilin-1, a cytoplasmic protein that interacts with α-synuclein and has implications in PD pathogenesis. LRRK2 interacted with the N-terminus of synphilin-1 whereas synphilin-1 predominantly interacted with the C-terminus of LRRK2, including kinase domain. Co-expression of synphilin-1 with LRRK2 increased LRRK2-induced cytoplasmic aggregation in cultured cells. Moreover, synphilin-1 also attenuated mutant LRRK2-induced toxicity and reduced LRRK2 kinase activity in cultured cells. Knockdown of synphilin-1 by siRNA enhanced LRRK2 neuronal toxicity. In vivo Drosophila studies, coexpression of synphilin-1 and mutant G2019S-LRRK2 in double transgenic Drosophila increased survival and improved locomotor activity. Expression of synphilin-1 protects against G2019S-LRRK2-induced dopamine neuron loss and reduced LRRK2 phosphorylation in double transgenic fly brains. These findings demonstrate that synphilin-1 attenuates mutant LRRK2-induced PD-like phenotypes and plays a neural protective role.

Li, S., et al. (2016). Genetic interaction of hnRNPA2B1 and DNAJB6 in a Drosophila model of multisystem proteinopathy. Hum Mol Genet [Epub ahead of print]. PubMed ID: 26744327
Summary:
This study sought to establish a mechanistic link between diseases caused by mutations in two genes associated with adult-onset inherited myopathies, hnRNPA2B1 and DNAJB6. Hrb98DE and mrj are the Drosophila homologs of human hnRNPA2B1 and DNAJB6, respectively. Disease-homologous mutations were introduced to Hrb98DE. Ectopic expression of the disease-associated mutant form of hnRNPA2B1 or Hrb98DE in fly muscle resulted in progressive, age-dependent cytoplasmic inclusion pathology, as observed in humans with hnRNPA2B1-related myopathy. Cytoplasmic inclusions consisted of hnRNPA2B1 or Hrb98DE protein in association with the stress granule marker ROX8 and additional endogenous RNA-binding proteins, suggesting that these pathological inclusions are related to stress granules. Notably, TDP-43 was also recruited to these cytoplasmic inclusions. Remarkably, overexpression of MRJ rescued this phenotype and suppressed the formation of cytoplasmic inclusions, whereas reduction of endogenous MRJ by a classical loss of function allele enhanced it. Moreover wild-type, but not disease-associated mutant forms of MRJ, interacted with RNA-binding proteins after heat shock and prevented their accumulation in aggregates. These results indicate both genetic and physical interaction between disease-linked RNA-binding proteins and DNAJB6/mrj, suggesting etiologic overlap between the pathogenesis of hIBM and LGMD initiated by mutations in hnRNPA2B1 and DNAJB6.

Saturday, January 9th

Telonis-Scott, M., Sgrò, C.M., Hoffmann, A.A. and Griffin, P.C. (2016). Cross-study comparison reveals common genomic, network and functional signatures of desiccation resistance in Drosophila melanogaster. Mol Biol Evol [Epub ahead of print]. PubMed ID: 26733490
Summary:
Repeated attempts to map the genomic basis of complex traits often yield different outcomes because of the influence of genetic background, gene-by-environment interactions and/or statistical limitations. However, where repeatability is low at the level of individual genes, overlap often occurs in gene ontology categories, genetic pathways, and interaction networks. This study reports on the genomic overlap for natural desiccation resistance from a Pool-GWAS experiment and a selection experiment in flies collected from the same region in southeastern Australia in different years. Over 600 SNPs associated with desiccation resistance in flies derived from almost 1000 wild-caught genotypes were identified, a similar number of loci to that observed in a previous genomic study of selected lines, demonstrating the genetic complexity of this ecologically important trait. By harnessing the power of cross-study comparison, the candidates from almost 400 genes in each study were narrowed to a core set of 45 genes, enriched for stimulus, stress and defense responses. In addition to gene-level overlap, there was higher-order congruence at the network and functional levels, suggesting genetic redundancy in key stress sensing, stress response, immunity, signaling, and gene expression pathways. Variants linked to different molecular aspects of desiccation physiology previously verified from functional experiments were also identified. This approach provides insight into the genomic basis of a complex and ecologically important trait and predicts candidate genetic pathways to explore in multiple genetic backgrounds and related species within a functional framework.

Chertemps, T., Younus, F., Steiner, C., Durand, N., Coppin, C. W., Pandey, G., Oakeshott, J. G. and Maibeche, M. (2015). An antennal carboxylesterase from Drosophila melanogaster, Esterase 6, is a candidate odorant-degrading enzyme toward food odorants. Front Physiol 6: 315. PubMed ID: 26594178
Summary:
Reception of odorant molecules within insect olfactory organs involves several sequential steps, including their transport through the sensillar lymph, interaction with the respective sensory receptors, and subsequent inactivation. Odorant-degrading enzymes (ODEs) putatively play a role in signal dynamics by rapid degradation of odorants in the vicinity of the receptors. Recently work has shown that an extracellular carboxylesterase, Esterase-6 (EST-6), is involved in the physiological and behavioral dynamics of the response of Drosophila to its volatile pheromone ester, cis-vaccenyl acetate. However, as the expression pattern of the Est-6 gene in the antennae is not restricted to the pheromone responding sensilla, tests were performed to see EST-6 could play a broader function in the antennae. Recombinant EST-6 was found to be able to efficiently hydrolyse several volatile esters that would be emitted by its natural food in vitro. Electrophysiological comparisons of mutant Est-6 null flies and a control strain showed that the dynamics of the antennal response to these compounds is influenced by EST-6, with the antennae of the null mutants showing prolonged activity in response to them. Antennal responses to the strongest odorant, pentyl acetate showed that the repolarization dynamics were modified even at low doses but without modification of the detection threshold. Behavioral choice experiments with pentyl acetate also showed differences between genotypes; attraction to this compound was observed at a lower dose among the null than control flies. As EST-6 is able to degrade various bioactive odorants emitted by food and plays a role in the response to these compounds, a role as an ODE is hypothesized for this enzyme toward food volatiles.

Wu, K., Zhang, J., Zhang, Q., Zhu, S., Shao, Q., Clark, K. D., Liu, Y. and Ling, E. (2015). Plant phenolics are detoxified by prophenoloxidase in the insect gut. Sci Rep 5: 16823. PubMed ID: 26592948
Summary:
Plant phenolics are a group of important secondary metabolites that are toxic to many animals and insects if ingested at high concentrations. This study used Drosophila, Bombyx and Helicoverpa armigera as models to study the metabolism of plant phenolics by prophenoloxidases. Insect foreguts were found to release prophenoloxidases into the lumen, and the survival of prophenoloxidase-deletion mutants was impaired when animals were fed several plant phenolics and tea extracts. Using l-DOPA as a model substrate, biochemical assays in large Lepidopteran insects demonstrated that low levels of l-DOPA are rapidly metabolized into intermediates by phenoloxidases. Feeding with excess l-DOPA showed that the metabolic intermediate 5,6-dihydroxyindole reached the hindgut either by passing directly through the midgut, or by transport through the hemolymph. In the hindgut, 5,6-dihydroxyindole was further oxidized by prophenoloxidases. These results show that plant phenolics are not toxic to insects unless prophenoloxidase genes are lost or the levels of phenolics exceed the catalytic activity of the gut prophenoloxidases.

Kawano, T., Ryuda, M., Matsumoto, H., Ochiai, M., Oda, Y., Tanimura, T., Csikos, G., Moriya, M. and Hayakawa, Y. (2015). Function of desiccate in gustatory sensilla of Drosophila melanogaster. Sci Rep 5: 17195. PubMed ID: 26610608
Summary:
Desiccate (Desi), initially discovered as a gene expressing in the epidermis of Drosophila larvae for protection from desiccation stress, was recently found to be robustly expressed in the adult labellum; however, the function, as well as precise expression sites, was unknown. This study found that Desi is expressed in two different types of non-neuronal cells of the labellum, the epidermis and thecogen accessory cells. Labellar Desi expression was significantly elevated under arid conditions, accompanied by an increase in water ingestion by adults. Desi overexpression also promoted water ingestion. In contrast, a knockdown of Desi expression reduced feeding as well as water ingestion due to a drastic decrease in the gustatory sensillar sensitivity for all tested tastants. These results indicate that Desi helps protect insects from desiccation damage by not only preventing dehydration through the integument but also accelerating water ingestion via elevated taste sensitivities of the sensilla.

Friday, January 8th

Lin, W.Y., Williams, C.R., Yan, C. and Parrish, J.Z. (2016). Functions of the SLC36 transporter Pathetic in growth control. Fly (Austin) [Epub ahead of print]. PubMed ID: 26735916
Summary:
Neurons exhibit extreme diversity in size, but whether large neurons have specialized mechanisms to support their growth is largely unknown. The SLC36 amino acid transporter Pathetic (Path) has been identified as a factor required for extreme dendrite growth in neurons. Path is broadly expressed, but only neurons with large dendrite arbors or small neurons that are forced to grow large require path for their growth. To gain insight into the basis of growth control by path, this study generated additional alleles of path and further examined the apparent specificity of growth defects in path mutants. Prior finding that loss of path function imposes an upper limit on neuron growth was conformed, and additionally it was found that path likely limits overall neurite length rather than dendrite length alone. Using a GFP knock-in allele of path, additional tissues were identified where path likely functions in nutrient sensing and possibly growth control. Finally, it was demonstrated that path regulates translational capacity in a cell type that does not normally require path for growth, suggesting that path may confer robustness on growth programs by buffering translational output. Altogether, these studies suggest that Path is a nutrient sensor with widespread function in Drosophila.

Wang, P., Chen, Y., Li, C., Zhao, R., Wang, F., Lin, X., Cao, L., Li, S., Hu, L., Gao, Y., Li, Y. and Wu, S. (2015). Drosophila eye developmental defect caused by elevated Lmx1a activity is reliant on chip expression. Biochem Biophys Res Commun. PubMed ID: 26718403
Summary:
The LIM-homeodomain (LIM-HD) family member Lmx1a has been successfully used to induce dopaminergic neurons from other cell types, thus showing significant implications in replacement therapies of Parkinson's disease, but the underlying mechanism remains elusive. This study used Drosophila eye as a model system to investigate how forced expression of dLmx1a (CG4328) and dLmx1a (CG32105), the fly homologs of human Lmx1a, alters cell identify. Ectopic expression of dLmx1a suppresses the formation of Drosophila eye tissue; the LIM and HD were found to be two essential domains. dLmx1a requires and physically binds to Chip, a well-known cofactor of LIM-HD proteins. Chip connects two dLmx1a proteins to form a functional tetrameric complex. In addition, evidence is provided showing that dLmx1a expression results in the suppression of two retina determination gene eyes absent (eya) and string (stg). Taken together, these findings identified Chip as a novel partner of dLmx1a to alter cell differentiation in Drosophila eye through repressing eya and stg expression, and provide an animal model for further understanding the molecular mechanism whereby Lmx1a determines cell fate.

Hige, T., Aso, Y., Modi, M. N., Rubin, G. M. and Turner, G. C. (2015). Heterosynaptic plasticity underlies aversive olfactory learning in Drosophila. Neuron 88: 985-998. PubMed ID: 26637800
Summary:
Although associative learning has been localized to specific brain areas in many animals, identifying the underlying synaptic processes in vivo has been difficult. This study provides the first demonstration of long-term synaptic plasticity at the output site of the Drosophila mushroom body. Pairing an odor with activation of specific dopamine neurons induces both learning and odor-specific synaptic depression. The plasticity induction strictly depends on the temporal order of the two stimuli, replicating the logical requirement for associative learning. Furthermore, dopamine action was shown to be confined to and distinct across different anatomical compartments of the mushroom body lobes. Finally, overlap between sparse representations of different odors defines both stimulus specificity of the plasticity and generalizability of associative memories across odors. Thus, the plasticity found in this study not only manifests important features of associative learning but also provides general insights into how a sparse sensory code is read out (Hige, 2015).

Li, Q. and Gong, Z. (2015). Cold-sensing regulates Drosophila growth through insulin-producing cells. Nat Commun 6: 10083. PubMed ID: 26648410
Summary:
Across phyla, body size is linked to climate. For example, rearing fruit flies at lower temperatures results in bigger body sizes than those observed at higher temperatures. The underlying molecular basis of this effect is poorly understood. This study provides evidence that the temperature-dependent regulation of Drosophila body size depends on a group of cold-sensing neurons and insulin-producing cells (IPCs). Electrically silencing IPCs completely abolishes the body size increase induced by cold temperature. IPCs are directly innervated by cold-sensing neurons. Stimulation of these cold-sensing neurons activates IPCs, promotes synthesis and secretion of Drosophila insulin-like peptides and induces a larger body size, mimicking the effects of rearing the flies in cold temperature. Taken together, these findings reveal a neuronal circuit that mediates the effects of low temperature on fly growth.

Thursday, January 7th

Karak, S., Jacobs, J. S., Kittelmann, M., Spalthoff, C., Katana, R., Sivan-Loukianova, E., Schon, M. A., Kernan, M. J., Eberl, D. F. and Gopfert, M. C. (2015). Diverse roles of axonemal dyneins in Drosophila auditory neuron function and mechanical amplification in hearing. Sci Rep 5: 17085. PubMed ID: 26608786
Summary:
Much like vertebrate hair cells, the chordotonal sensory neurons that mediate hearing in Drosophila are motile and amplify the mechanical input of the ear. Because the neurons bear mechanosensory primary cilia whose microtubule axonemes display dynein arms, it was hypothesized that their motility is powered by dyneins. This study describes two axonemal dynein proteins that are required for Drosophila auditory neuron function, localize to their primary cilia, and differently contribute to mechanical amplification in hearing. Promoter fusions revealed that the two axonemal dynein genes Dmdnah3 (=CG17150) and Dmdnai2 (=CG6053) are expressed in chordotonal neurons, including the auditory ones in the fly's ear. Null alleles of both dyneins equally abolished electrical auditory neuron responses, yet whereas mutations in Dmdnah3 facilitated mechanical amplification, amplification was abolished by mutations in Dmdnai2. Epistasis analysis revealed that Dmdnah3 acts downstream of Nan-Iav channels in controlling the amplificatory gain. Dmdnai2, in addition to being required for amplification, is essential for outer dynein arms in auditory neuron cilia. Mutant defects in sperm competition suggest that both dyneins also function in sperm motility.

Sakuma, C., Okumura, M., Umehara, T., Miura, M. and Chihara, T. (2015). A STRIPAK component Strip regulates neuronal morphogenesis by affecting microtubule stability. Sci Rep 5: 17769. PubMed ID: 26644129
Summary:
During neural development, regulation of microtubule stability is essential for proper morphogenesis of neurons. Recently, the striatin-interacting phosphatase and kinase (STRIPAK) complex was revealed to be involved in diverse cellular processes. However, there is little evidence that STRIPAK components regulate microtubule dynamics, especially in vivo. This study shows that one of the core STRIPAK components, Strip, is required for microtubule organization during neuronal morphogenesis. Knockdown of Strip causes a decrease in the level of acetylated alpha-tubulin in Drosophila S2 cells, suggesting that Strip influences the stability of microtubules. Strip physically and genetically interacts with tubulin folding cofactor D (TBCD), an essential regulator of alpha- and beta-tubulin heterodimers. Furthermore, the genetic interaction is demonstrated between strip and Down syndrome cell adhesion molecule (Dscam), a cell surface molecule that is known to work with TBCD. Thus, it is proposed that Strip regulates neuronal morphogenesis by affecting microtubule stability.

Ito, A. and Goshima, G. (2015). Microcephaly protein Asp focuses the minus ends of spindle microtubules at the pole and within the spindle. J Cell Biol 211: 999-1009. PubMed ID: 26644514
Summary:
Depletion of Drosophila melanogaster Asp, an orthologue of microcephaly protein ASPM, causes spindle pole unfocusing during mitosis. However, it remains unclear how Asp contributes to pole focusing, a process that also requires the kinesin-14 motor Ncd. This study shows that Asp localizes to the minus ends of spindle microtubule (MT) bundles and focuses them to make the pole independent of Ncd. A critical domain in Asp was identified exhibiting MT cross-linking activity in vitro. Asp was also localized to, and focuses the minus ends of, intraspindle MTs that were nucleated in an augmin-dependent manner and translocated toward the poles by spindle MT flux. Ncd, in contrast, functions as a global spindle coalescence factor not limited to MT ends. A revised molecular model is proposed for spindle pole focusing in which Asp at the minus ends cross-links MTs at the pole and within the spindle. Additionally, this study provides new insight into the dynamics of intraspindle MTs by using Asp as a minus end marker.

Girdler, G. C., Applewhite, D. A., Perry, W. M., Rogers, S. L. and Roper, K. (2015). The Gas2 family protein Pigs is a microtubule +TIP that affects cytoskeleton organisation. J Cell Sci [Epub ahead of print]. PubMed ID: 26585311
Summary:
Coordination between different cytoskeletal systems is crucial for many cell biological functions, including cell migration and mitosis, and also plays an important role during tissue morphogenesis. Proteins of the class of cytoskeletal crosslinkers or cytolinkers have the ability to interact with more than one cytoskeletal system at a time and are prime candidates to mediate any coordination. One such class comprises the Gas2-like proteins, combining a conserved Calponin-homology-type actin-binding domain and a Gas2 domain predicted to bind microtubules (MTs). This domain combination is also found in spectraplakins, huge cytolinkers that play important roles in many tissues in both invertebrates and vertebrates. This study dissects the ability of the single Drosophila Gas2-like protein Pigs (Pickled eggs) to interact with both actin and MT cytoskeletons, both in vitro and in vivo, and illustrate complex regulatory interactions that determine Pigs' localisation to and its effects on the cytoskeleton.

Wednesday, January 6th

Park, J., Lee, N., Kavoussi, A., Seo, J.T., Kim, C.H. and Moon, S.J. (2015). Ciliary phosphoinositide regulates ciliary protein trafficking in Drosophila. Cell Rep 13: 2808-2816. PubMed ID: 26723017
Summary:
Cilia are highly specialized antennae-like cellular organelles. Inositol polyphosphate 5-phosphatase E (INPP5E) converts PI(4,5)P2 into PI4P and is required for proper ciliary function. Although Inpp5e mutations are associated with ciliopathies in humans and mice, the precise molecular role INPP5E plays in cilia remains unclear. This study reports that Drosophila INPP5E (dINPP5E) regulates ciliary protein trafficking by controlling the phosphoinositide composition of ciliary membranes. Mutations in dInpp5e lead to hearing deficits due to the mislocalization of dTULP and mechanotransduction channels, Inactive and NOMPC, in chordotonal cilia. Both loss of dINPP5E and ectopic expression of the phosphatidylinositol-4-phosphate 5-kinase Skittles increase PI(4,5)P2 levels in the ciliary base. The fact that Skittles expression phenocopies the dInpp5e mutants confirms a central role for PI(4,5)P2 in the regulation of dTULP, Inactive, and NOMPC localization. These data suggest that the spatial localization and levels of PI(4,5)P2 in ciliary membranes are important regulators of ciliary trafficking and function. 

Khoshnood, B., Dacklin, I. and Grabbe, C. (2015). Urm1: an essential regulator of JNK signaling and oxidative stress in Drosophila melanogaster. Cell Mol Life Sci [Epub ahead of print]. PubMed ID: 26715182
Summary:
Ubiquitin-related modifier 1 (Urm1) is a ubiquitin-like molecule (UBL) with the dual capacity to act both as a sulphur carrier and posttranslational protein modifier. This study characterizes the Drosophila homologues of Urm1 (CG33276) and its E1 activating enzyme Uba4 (CG13090) and shows that they function together to induce protein urmylation in vivo. Urm1 conjugation to target proteins in general, and to the evolutionary conserved substrate Peroxiredoxin 5 (Prx5) specifically, is dependent on Uba4. A complete loss of Urm1 is lethal in flies, although a small number of adult zygotic Urm1 n123 mutant escapers can be recovered. These escapers display a decreased general fitness and shortened lifespan, but in contrast to their S. cerevisiae counterparts, they are resistant to oxidative stress. Providing a molecular explanation, this study demonstrates that cytoprotective JNK signaling is increased in Urm1 deficient animals. In agreement, molecular and genetic evidence suggest that elevated activity of the JNK downstream target genes Jafrac1 (thioredoxin peroxidase 1) and gstD1 (Glutathione S transferase D1) strongly contributes to the tolerance against oxidative stress displayed by Urm1 n123 null mutants. In conclusion, Urm1 is a UBL that is involved in the regulation of JNK signaling and the response against oxidative stress in the fruit fly.

Pares, G. and Ricardo, S. (2015). FGF control of E-cadherin targeting in the Drosophila midgut impacts on primordial germ cell motility. J Cell Sci [Epub ahead of print]. PubMed ID: 26604222
Summary:
Embryo formation requires tight regulation and coordination of adhesion in multiple cell types. By imaging, 3D reconstructions and genetic analysis during posterior midgut morphogenesis in Drosophila, a novel requirement was found for the conserved FGF signaling pathway in maintenance of epithelial cell adhesion, by modulation of zygotic E-cadherin. During Drosophila gastrulation, primordial germ cells (PGC) are transported with the posterior midgut while it undergoes dynamic cell shape changes. In Branchless and Breathless mutant embryos zygotic E-cadherin is not targeted to AJs causing midgut pocket collapse impacting on PGC movement. The ventral midline also requires FGF signaling to maintain cell-cell adhesion. FGF signaling regulates the distribution of zygotic E-cadherin during early embryonic development to maintain cell-cell adhesion in the posterior midgut and the ventral midline, a role that is likely crucial in other tissues undergoing active cell shape changes with higher adhesive needs.

Liu, Y., Singh, S. R., Zeng, X., Zhao, J. and Hou, S. X. (2015). The nuclear matrix protein Megator regulates stem cell asymmetric division through the mitotic checkpoint complex in Drosophila testes. PLoS Genet 11: e1005750. PubMed ID: 26714316
Summary:
In adult Drosophila testis, asymmetric division of germline stem cells (GSCs) is specified by an oriented spindle and cortically localized adenomatous coli tumor suppressor homolog 2 (Apc2). However, the molecular mechanism underlying these events remains unclear. This study identified Megator (Mtor), a nuclear matrix protein, which regulates GSC maintenance and asymmetric division through the spindle assembly checkpoint (SAC) complex. Loss of Mtor function results in Apc2 mis-localization, incorrect centrosome orientation, defective mitotic spindle formation, and abnormal chromosome segregation that lead to the eventual GSC loss. Expression of mitotic arrest-deficient-2 (Mad2) and monopolar spindle 1 (Mps1) of the SAC complex effectively rescues the GSC loss phenotype associated with loss of Mtor function. Collectively these results define a new role of the nuclear matrix-SAC axis in regulating stem cell maintenance and asymmetric division.

Tuesday, January 5th

Savitsky, M., Kim, M., Kravchuk, O. and Schwartz, Y.B. (2015). Distinct roles of chromatin insulator proteins in control of the Drosophila bithorax complex. Genetics [Epub ahead of print]. PubMed ID: 26715665
Summary:
Chromatin insulators are remarkable regulatory elements that can bring distant genomic sites together and block unscheduled enhancer-promoter communications. Insulators act via associated insulator proteins of two classes: sequence-specific DNA binding factors and "bridging" proteins. The latter are required to mediate interactions between distant insulator elements. Chromatin insulators are critical for correct expression of complex loci however their mode of action is poorly understood. This study uses the Drosophila bithorax complex as a model to investigate the roles of the "bridging" proteins Cp190 and Mod(mdg4). The bithorax complex consists of three evolutionary conserved homeotic genes Ubx, abd-A and Abd-B, which specify anterior-posterior identity of the last thoracic and all abdominal segments of the fly. Looking at effects of CTCF, mod(mdg4) and Cp190 mutations on expression of the bithorax complex genes, the study provides the first functional evidence that Mod(mdg4) acts in concert with the DNA binding insulator protein CTCF. It was found that Mod(mdg4) and Cp190 are not redundant and may have distinct functional properties. It was, for the first time, demonstrated that Cp190 is critical for correct regulation of the bithorax complex and that Cp190 is required at an exceptionally strong Fub insulator to partition the bithorax complex into two topological domains.

Boltengagen, M., Huang, A., Boltengagen, A., Trixl, L., Lindner, H., Kremser, L., Offterdinger, M. and Lusser, A. (2015). A novel role for the histone acetyltransferase Hat1 in the CENP-A/CID assembly pathway in Drosophila melanogaster. Nucleic Acids Res [Epub ahead of print]. PubMed ID: 26586808
Summary:
The incorporation of CENP-A (Centromere identifier) into centromeric chromatin is an essential prerequisite for kinetochore formation. Yet, the molecular mechanisms governing this process are surprisingly divergent in different organisms. While CENP-A loading mechanisms have been studied in some detail in mammals, there are still large gaps to understanding of CENP-A/Cid loading pathways in Drosophila. This study reports on the characterization and delineation of at least three different CENP-A preloading complexes in Drosophila. Two complexes contain the CENP-A chaperones CAL1, FACT (subunit Dre4) and/or Caf1/Rbap48. Notably, a novel complex was identified consisting of the histone acetyltransferase Hat1, Caf1 and CENP-A/H4. Hat1 is required for proper CENP-A loading into chromatin, since knock-down in S2 cells leads to reduced incorporation of newly synthesized CENP-A. In addition,CENP-A/Cid interacts with the HAT1 complex via an N-terminal region, which is acetylated in cytoplasmic but not in nuclear CENP-A. Since Hat1 is not responsible for acetylation of CENP-A/Cid, these results suggest a histone acetyltransferase activity-independent escort function for Hat1. Thus, these results point toward intriguing analogies between the complex processing pathways of newly synthesized CENP-A and canonical histones.

Kawaguchi, T. and Hirose, T. (2015). Chromatin remodeling complexes in the assembly of long noncoding RNA-dependent nuclear bodies. Nucleus [Epub ahead of print] PubMed ID: 26709446
Summary:
Paraspeckles are subnuclear structures that assemble on nuclear paraspeckle assembly transcript 1 (NEAT1) long noncoding (lnc)RNA. Paraspeckle formation requires appropriate NEAT1 biogenesis and subsequent assembly with multiple prion-like domain (PLD) containing RNA-binding proteins. SWI/SNF chromatin remodeling complexes (see Drosophila Brahma) were found to function as paraspeckle components that interact with paraspeckle proteins (PSPs) and NEAT1. SWI/SNF complexes play an essential role in paraspeckle formation that does not require their ATP-dependent chromatin remodeling activity. Instead, SWI/SNF complexes facilitate organization of the PSP interaction network required for intact paraspeckle assembly. SWI/SNF complexes may collectively bind multiple PSPs to recruit them onto NEAT1. SWI/SNF complexes are also required for Sat III (Satellite III) lncRNA-dependent formation of nuclear stress bodies under heat shock conditions. Organization of the lncRNA-dependent omega speckle in Drosophila also depends on the chromatin remodeling complex. These findings raise the possibility that a common mechanism controls the formation of lncRNA-dependent nuclear body architecture.

Kim, S., Bugga, L., Hong, E. S., Zabinsky, R., Edwards, R. G., Deodhar, P. A. and Armstrong, J. A. (2015). An RNAi-based candidate screen for modifiers of the CHD1 chromatin remodeler and assembly factor in Drosophila melanogaster.G3 (Bethesda) [Epub ahead of print]. PubMed ID: 26596648
Summary:
The conserved chromatin remodeling and assembly factor CHD1 (chromodomains, helicase, DNA-binding domain) is present at active genes where it participates in histone turnover and recycling during transcription. In order to gain a more complete understanding of the mechanism of action of CHD1 during development a novel genetic assay was created in Drosophila melanogaster to evaluate potential functional interactions between CHD1 and other chromatin factors. Over-expression of the CHD1 results in defects in wing development, and this fully penetrant and reliable phenotype was used to conduct a small-scale RNAi-based candidate screen to identify genes that functionally interact with Chd1 in vivo. The results indicate that CHD1 may act in opposition to other remodeling factors, including INO80, and that the recruitment of CHD1 to active genes by RTF1 is conserved in flies.

Monday, January 4th

Berndt, A. J., Tang, J. C., Ridyard, M. S., Lian, T., Keatings, K. and Allan, D. W. (2015).. Gene regulatory mechanisms underlying the spatial and temporal regulation of target-dependent gene expression in Drosophila neurons. PLoS Genet 11: e1005754. PubMed ID: 26713626
Summary:
Neuronal differentiation often requires target-derived signals from the cells they innervate. These signals typically activate neural subtype-specific genes, but the gene regulatory mechanisms remain largely unknown. Highly restricted expression of the FMRFa neuropeptide in Drosophila Tv4 neurons requires target-derived BMP signaling and a transcription factor code that includes Apterous. Using integrase transgenesis of enhancer reporters, this study functionally dissected the Tv4-enhancer of FMRFa within its native cellular context. Two essential but discrete cis-elements were identified, a BMP-response element (BMP-RE) that binds BMP-activated pMad, and a homeodomain-response element (HD-RE) that binds Apterous. These cis-elements have low activity and must be combined for Tv4-enhancer activity. Concatemers of the HD-RE and BMP-RE cis-elements were found to independently generate the same spatiotemporal expression as the Tv4-enhancer. The activation of target-dependent genes is assumed to 'wait' for target contact. This was tested directly, and it was unexpectedly found that premature BMP activity could not induce early FMRFa expression; also, that the BMP-insensitive HD-RE cis-element is activated at the time of target contact. seven up (svp) was uncovered as a repressor of FMRFa induction prior to target contact. Svp is normally downregulated immediately prior to target contact, and maintaining Svp expression prevents cis-element activation, whereas reducing svp gene dosage prematurely activates cis-element activity. It is concluded that the target-dependent FMRFa gene is repressed prior to target contact, and that target-derived BMP signaling directly activates FMRFa gene expression through an atypical gene regulatory mechanism.

Gurdziel, K., Lorberbaum, D. S., Udager, A. M., Song, J. Y., Richards, N., Parker, D. S., Johnson, L. A., Allen, B. L., Barolo, S. and Gumucio, D. L. (2015). Identification and validation of novel Hedgehog-responsive enhancers predicted by computational analysis of Ci/Gli binding site density. PLoS One 10: e0145225. PubMed ID: 26710299
Summary:
The Hedgehog (Hh) signaling pathway directs a multitude of cellular responses during embryogenesis and adult tissue homeostasis. Stimulation of the pathway results in activation of Hh target genes by the transcription factor Ci/Gli, which binds to specific motifs in genomic enhancers. In Drosophila, only a few enhancers (patched, decapentaplegic, wingless, stripe, knot, hairy, orthodenticle) have been shown by in vivo functional assays to depend on direct Ci/Gli regulation. All but one (orthodenticle) contain more than one Ci/Gli site, prompting this study to directly test whether homotypic clustering of Ci/Gli binding sites is sufficient to define a Hh-regulated enhancer. A computational algorithm was developed to identify Ci/Gli clusters that are enriched over random expectation, within a given region of the genome. Candidate genomic regions containing Ci/Gli clusters were functionally tested in chicken neural tube electroporation assays and in transgenic flies. Of the 22 Ci/Gli clusters tested, seven novel enhancers (and the previously known patched enhancer) were identified as Hh-responsive and Ci/Gli-dependent in one or both of these assays, including: Cuticular protein 100A (Cpr100A); invected (inv), which encodes an engrailed-related transcription factor expressed at the anterior/posterior wing disc boundary; roadkill (rdx), the fly homolog of vertebrate Spop; the segment polarity gene gooseberry (gsb); and two previously untested regions of the Hh receptor-encoding patched (ptc) gene. It is concluded that homotypic Ci/Gli clustering is not sufficient information to ensure Hh-responsiveness; however, it can provide a clue for enhancer recognition within putative Hedgehog target gene loci.

Chechenova, M. B., Maes, S. and Cripps, R. M. (2015). Expression of the Troponin C at 41C gene in adult Drosophila tubular muscles depends upon both positive and negative regulatory inputs.PLoS One 10: e0144615. PubMed ID: 26641463
Summary:
Most animals express multiple isoforms of structural muscle proteins to produce tissues with different physiological properties. In Drosophila, the adult muscles include tubular-type muscles and the fibrillar indirect flight muscles. This study analyzed the transcriptional regulation of TpnC41C, a Troponin C gene expressed in the tubular jump muscles, but not in the fibrillar flight muscles. A 300-bp promoter fragment of TpnC41C is sufficient for the fiber-specific reporter expression. Two sites necessary for the activation of the enhancer were identified. Mutations in each resulted in 70% reduction of enhancer activity. One was characterized as a binding site for Myocyte Enhancer Factor-2. In addition, a repressive element was identified that prevents activation of the enhancer in other muscle fiber types. Mutation of this site increased jump muscle-specific expression of the reporter, but more importantly reporter expression expanded into the indirect flight muscles. These findings demonstrate that expression of the TpnC41C gene in jump muscles requires integration of multiple positive and negative transcriptional inputs. Identification of the transcriptional regulators binding the cis-elements that were identified will reveal the regulatory pathways controlling muscle fiber differentiation.

Kamps-Hughes, N., Preston, J. L., Randel, M. A. and Johnson, E. A. (2015). Genome-wide identification of hypoxia-induced enhancer regions. PeerJ 3: e1527. PubMed ID: 26713262
Summary:
This study presents a genome-wide method for de novo identification of enhancer regions. This approach enables massively parallel empirical investigation of DNA sequences that mediate transcriptional activation and provides a platform for discovery of regulatory modules capable of driving context-specific gene expression. The method links fragmented genomic DNA to the transcription of randomer molecule identifiers and measures the functional enhancer activity of the library by massively parallel sequencing. A Drosophila melanogaster library was transfected into S2 cells in normoxia and hypoxia, and 4,599,881 genomic DNA fragments were assayed in parallel. The locations of the enhancer regions strongly correlate with genes up-regulated after hypoxia and previously described enhancers. Novel enhancer regions were identified and integrated with RNAseq data and transcription factor motifs to describe the hypoxic response on a genome-wide basis as a complex regulatory network involving multiple stress-response pathways. Of particular interest, an intronic enhancer in Sima was identified that contains both HIF-1 and NF-&kapppa;B binding sites, suggesting HIF-1 autoregulation and integration of NF-&kapppa;B signaling at a basal level in the hypoxic response. The enhancer region, while intronic to the full-length Sima transcript isoforms, is upstream of an alternative transcriptional start site that produces a transcript isoform that is up-regulated after hypoxia,

Sunday, January 3rd

Kong, Y., Wu, J., Zhang, D., Wan, C. and Yuan, L. (2015). The role of miR-124 in Drosophila Alzheimer's disease model by targeting Delta in Notch signaling pathway. Curr Mol Med 15: 980-989. PubMed ID: 26592243
Summary:
Alzheimer's disease (AD) is a neurodegenerative disorder which mainly affects elderly population. MicroRNAs (miRNA) are small RNA molecules that fine-tune gene expression at posttranscriptional level and exert important functions in AD. MicroRNA-124 (miR-124) is a kind of miRNA abundantly expressed in the central nervous system. It is highly conserved from Caenorhabditis elegans to humans. However, its function in AD is still elusive. This study found miR-124 is significantly down-regulated in AD flies. miR-124 mutant flies show impaired climbing ability and shortened lifespan. In contrast, miR-124 expression rescues locomotive defects of AD flies. Using microarray analysis to test gene expression profiles of miR-124 mutant flies, Notch signaling pathway was found to be potentially targeted by miR-124. Further experiments showed that miR-124 regulates Notch ligand Delta expression by acting on specific site of Delta 3'UTR. In addition, reduced Delta expression by RNA interference extends lifespan and ameliorates learning defects of AD Drosophila. Notch inhibitor DAPT can also alleviate AD phenotypes. In conclusion, this study indicates that miR-124 plays neuroprotective roles in AD Drosophila by targeting Delta in Notch signaling pathway, which helps further in the understanding of miRNAs in the molecular pathology of AD.

Kyotani, A., Azuma, Y., Yamamoto, I., Yoshida, H., Mizuta, I., Mizuno, T., Nakagawa, M., Tokuda, T. and Yamaguchi, M. (2015). Knockdown of the Drosophila FIG4 induces deficient locomotive behavior, shortening of motor neuron, axonal targeting aberration, reduction of life span and defects in eye development. Exp Neurol [Epub ahead of print]. PubMed ID: 26708557
Summary:
Mutations in Factor-Induced-Gene 4 (FIG4) gene have been identified in Charcot-Marie-Tooth disease type 4J (CMT4J), Yunis-Varon syndrome and epilepsy with polymicrogyria. FIG4 protein regulates a cellular abundance of phosphatidylinositol 3,5-bisphosphate (PI3,5P2), a signaling lipid on the cytosolic surface of membranes of the late endosomal compartment. PI3,5P2 is required for retrograde membrane trafficking from lysosomal and late endosomal compartments to the Golgi. However, it is still unknown how the neurodegeneration that occurs in these diseases is related to the loss of FIG4 function. Drosophila has CG17840 (dFIG4) as a human FIG4 homologue. This study specifically knocked down dFIG4 in various tissues, and investigated their phenotypes. Neuron-specific knockdown of dFIG4 results in axonal targeting aberrations of photoreceptor neurons, shortened presynaptic terminals of motor neurons in 3rd instar larvae and reduced climbing ability in adulthood and life span. Fat body-specific knockdown of dFIG4 results in enlarged lysosomes in cells that were detected by staining with LysoTracker. In addition, eye imaginal disc-specific knockdown of dFIG4 disrupts differentiation of pupal ommatidial cell types, such as cone cells and pigment cells, suggesting an additional role of dFIG4 during eye development.

Li, F. and Scott, M. J. (2015). CRISPR/Cas9-mediated mutagenesis of the white and Sex lethal loci in the invasive pest, Drosophila suzukii. Biochem Biophys Res Commun [Epub ahead of print]. PubMed ID: 26721433
Summary:
Drosophila suzukii (commonly called spotted wing Drosophila) is an invasive pest of soft-skinned fruit (e.g. blueberries, strawberries). A high quality reference genome sequence is available but functional genomic tools, such as used in Drosophila melanogaster, remain to be developed. This study used the CRISPR/Cas9 system to introduce site-specific mutations in the D. suzukii white (w) and Sex lethal (Sxl) genes. Hemizygous males with w mutations develop white eyes and the mutant genes are transmissible to the next generation. Somatic mosaic females that carry mutations in the Sxl gene develop abnormal genitalia and reproductive tissue. The D. suzukii Sxl gene could be an excellent target for a Cas9-mediated gene drive to suppress populations of this highly destructive pest.

Haddadi, M., Nongthomba, U., Jahromi, S. R. and Ramesh, S. R. (2015). Transgenic Drosophila model to study apolipoprotein E4-induced neurodegeneration. Behav Brain Res [Epub ahead of print]. PubMed ID: 26706888
Summary:
The ε4 isoform of Apolipoprotein E (ApoE4) that is involved in neuron-glial lipid metabolism has been demonstrated as the main genetic risk factor in late-onset of Alzheimer's disease. However, the mechanism underlying ApoE4-mediated neurodegeneration remains unclear. This study created a transgenic model of neurodegenerative disorder by expressing ε3 and ε4 isoforms of human ApoE in the Drosophila. The genetic models exhibited progressive neurodegeneration, shortened lifespan and memory impairment. Genetic interaction studies between amyloid precursor protein and ApoE in axon pathology of the disease revealed that over expression of hApoE in Appl-expressing neurons of Drosophila brain causes neurodegeneration. This Drosophila model may facilitate analysis of the molecular and cellular events implicated in hApoE4 neurotoxicity.

Saturday, January 2nd

Shenoi, V. N., Syed, Z. A. and Prasad, N. G. (2015). Evolution of increased adult longevity in Drosophila melanogaster populations selected for adaptation to larval crowding. J Evol Biol [Epub ahead of print]. PubMed ID: 26575793
Summary:
In holometabolous animals such as Drosophila melanogaster, larval crowding can affect a wide range of larval and adult traits. Adults emerging from high larval density cultures have smaller body size and increased mean life span compared to flies emerging from low larval density cultures. Therefore, adaptation to larval crowding could potentially affect adult longevity as a correlated response. This issue was addressed by studying a set of large, outbred populations of D. melanogaster, experimentally evolved for adaptation to larval crowding for 83 generations. Longevity of adult flies from both selected (MCUs) and control populations (MBs) was assayed after growing them at different larval densities. MCUs have evolved increased mean longevity compared to MBs at all larval densities. The interaction between selection regime and larval density was not significant, indicating that the density dependence of mean longevity had not evolved in the MCU populations. The increase in longevity in MCUs can be partially attributed to their lower rates of aging. It is also noteworthy that reaction norm of dry body weight, a trait probably under direct selection in these populations, has indeed evolved in MCU populations. This is the first report of the evolution of adult longevity as a correlated response of adaptation to larval crowding.

Yu, D., Shi, W. and Zhang, Y. E. (2015). Underrepresentation of active histone modification marks in evolutionarily young genes. Insect Sci [Epub ahead of print]. PubMed ID: 26607206
Summary:
It is known that evolutionarily new genes can rapidly evolve essential roles in fundamental biological processes. Nevertheless, the underlying molecular mechanism of how they acquire their novel transcriptional pattern is less characterized except for the role of cis-regulatory evolution. Epigenetic modification offers an alternative potential possibility. This study examined how histone modifications have changed among different gene age groups in Drosophila melanogaster by integrative analyses of an updated new gene dataset and published epigenomic data. A robust pattern was found across various datasets where both the coverage and intensity of active histone modifications, Histone 3 lysine 4 trimethylation and lysine 36 trimethylation, increased with the evolutionary age. Such a temporal correlation is negative and much weaker for the repressive histone mark, lysine 9 trimethylation, which is expected given its major association with heterochromatin. By the further comparison with neighboring old genes, the depletion of active marks of new genes could be only partially explained by the local epigenetic context. All these data are consistent with the observation that older genes bear relatively higher expression level and suggest that the evolution of histone modifications could be implicated in transcriptional evolution after gene birth.

Sved, J. A., Chen, Y., Shearman, D., Frommer, M. and Gilchrist, A. S. (2015). Extraordinary conservation of entire chromosomes in insects over long evolutionary periods. Evolution [Epub ahead of print] PubMed ID: 26639450
Summary:
Comparison of the genomes of different Drosophila species has shown that six different chromosomes, the so-called 'Muller elements', constitute the building blocks for all Drosophila species. This study confirmed previous results suggesting that this conservation of the Muller elements extends far beyond Drosophila, to at least tephritid fruit flies, thought to have diverged from drosophilids 60 -70 mYr ago. Less than ten percent of genes differ in chromosome location between the two insect groups. Within chromosomes, however, the order is highly scrambled, as expected from the comparison between Drosophila species. The data also support the notion that the sex chromosomes of tephritid flies originated from an ancestor of the dot chromosome 4 of Drosophila. Overall, therefore, no new chromosome has been created for perhaps a billion generations over the two evolutionary lines. This stability at the chromosome level, which appears to extend to all Diptera including mosquitoes, is in stark contrast to other groups such as mammals, birds, fish and plants, in which chromosome numbers and organisation vary enormously among species that have diverged over much fewer generations.

Izutsu, M., Toyoda, A., Fujiyama, A., Agata, K. and Fuse, N. (2015). Dynamics of Dark-Fly genome under environmental selections. G3 (Bethesda) [Epub ahead of print]. PubMed ID: 26637434
Summary:
Environmental adaptation is one of the most fundamental features of organisms. This study utilized "Dark-fly", a Drosophila melanogaster line maintained in a constant dark condition for more than 60 years to discover how genes contribute to adaptive traits and how traits are selected under an environment in the course of evolution. Previous analysis identified 220,000 single nucleotide polymorphisms (SNPs) in the Dark-fly genome, but did not clarify which SNPs of Dark-fly are truly adaptive for living in the dark. This study found that Dark-fly dominated over the wild-type fly in a mixed population under dark conditions, and based on this domination an experiment was designed for genome re-selection to identify adaptive genes of Dark-fly. For this experiment, large mixed populations of Dark-fly and the wild-type fly were maintained in light conditions or in dark conditions, and the frequencies of Dark-fly SNPs were compared between these populations across the whole genome. Condition-dependent selections was thereby detected towards approximately 6% of the genome. In addition, the time-course trajectory of SNP frequency was observed in the mixed populations through generations 0, 22, and 49; this revealed notable categorization of the selected SNPs into three types with different combinations of positive and negative selections. The data provided a list of about 100 strong candidate genes associated with the adaptive traits of Dark-fly.

Friday, January 1st

Rodriguez-Fernandez, I. A. and Dell'Angelica, E. C. (2015). Identification of Atg2 and ArfGAP1 as candidate genetic modifiers of the eye pigmentation phenotype of Adaptor Protein-3 (AP-3) mutants in Drosophila melanogaster. PLoS One 10: e0143026. PubMed ID: 26565960
Summary:
The Adaptor Protein (AP)-3 complex is a molecular sorting device that mediates the intracellular trafficking of proteins to lysosomes. Genetic defects in AP-3 subunits lead to impaired biogenesis of lysosome-related organelles (LROs) such as mammalian melanosomes and insect eye pigment granules. A forward screening was performed for genetic modifiers of the eye pigmentation AP-3 (carmine) gene in Drosophila. One modifier was the Atg2 gene, encoding a conserved protein involved in autophagy. Loss of one copy of Atg2 ameliorated the pigmentation defects of mutants in AP-3 subunits as well as in two other genes previously implicated in LRO biogenesis, Biogenesis of lysosome-related organelles complex 1, subunit 1 (Blos1) and lightoid (Rab32), and even increased the eye pigment content of wild-type flies. A second modifier was the ArfGAP1 gene, encoding a conserved GTPase-activating protein. Loss of a single copy of the ArfGAP1 gene ameliorated the pigmentation phenotype of AP-3 mutants. Strikingly, loss of the second copy of the gene elicited early lethality in males and abnormal eye morphology when combined with mutations in Blos1 or lightoid. These results provide evidence for functional links connecting the machinery for biogenesis of LROs with autophagy and small GTPase regulation.

Hebbar, S., Sahoo, I., Matysik, A., Argudo Garcia, I., Osborne, K. A., Papan, C., Torta, F., Narayanaswamy, P., Fun, X. H., Wenk, M. R., Shevchenko, A., Schwudke, D. and Kraut, R. (2015). Ceramides and stress signalling intersect with autophagic defects in neurodegenerative Drosophila blue cheese (bchs) mutants. Sci Rep 5: 15926. PubMed ID: 26639035
Summary:
Sphingolipid metabolites are involved in the regulation of autophagy, a degradative recycling process that is required to prevent neuronal degeneration. Drosophila blue cheese mutants neurodegenerate due to perturbations in autophagic flux, and consequent accumulation of ubiquitinated aggregates. This study demonstrates that blue cheese mutant brains exhibit an elevation in total ceramide levels; surprisingly, however, degeneration is ameliorated when the pool of available ceramides is further increased, and exacerbated when ceramide levels are decreased by altering sphingolipid catabolism or blocking de novo synthesis. Exogenous ceramide is seen to accumulate in autophagosomes, which are fewer in number and show less efficient clearance in blue cheese mutant neurons. Sphingolipid metabolism is also shifted away from salvage toward de novo pathways, while pro-growth Akt and MAP pathways are down-regulated, and ER stress is increased. All these defects are reversed under genetic rescue conditions that increase ceramide generation from salvage pathways. This constellation of effects suggests a possible mechanism whereby the observed deficit in a potentially ceramide-releasing autophagic pathway impedes survival signaling and exacerbates neuronal death.

Jacomin, A. C., Bescond, A., Soleilhac, E., Gallet, B., Schoehn, G., Fauvarque, M. O. and Taillebourg, E. (2015). The deubiquitinating enzyme UBPY is required for lysosomal biogenesis and productive autophagy in Drosophila. PLoS One 10: e0143078. PubMed ID: 26571504
Summary:
Autophagy is a catabolic process that delivers cytoplasmic components to the lysosomes. Protein modification by ubiquitination is involved in this pathway: it regulates the stability of autophagy regulators such as BECLIN-1 and it also functions as a tag targeting specific substrates to autophagosomes. In order to identify deubiquitinating enzymes (DUBs) involved in autophagy, a genetic screen was performed in the Drosophila larval fat body. This screen identified Ubiquitin carboxy-terminal hydrolase L5 ortholog (Uch-L3), Usp45, Usp12 and Ubpy (Ubiquitin specific protease 8). This paper shows that Ubpy loss of function results in the accumulation of autophagosomes due to a blockade of the autophagy flux. Furthermore, analysis by electron and confocal microscopy of Ubpy-depleted fat body cells revealed altered lysosomal morphology, indicating that Ubpy inactivation affects lysosomal maintenance and/or biogenesis. Lastly, shRNA mediated inactivation of UBPY in HeLa cells affects autophagy in a different way: in UBPY-depleted HeLa cells autophagy is deregulated.

Tracy, K., Velentzas, P. D. and Baehrecke, E. H. (2015). Ral GTPase and the exocyst regulate autophagy in a tissue-specific manner. EMBO Rep [Epub ahead of print]. PubMed ID: 26598552
Summary:
Autophagy traffics cellular components to the lysosome for degradation. Ral GTPase and the exocyst have been implicated in the regulation of stress-induced autophagy, but it is unclear whether they are global regulators of this process. This study investigated Ral function in different cellular contexts in Drosophila and found that it is required for autophagy during developmentally regulated cell death in salivary glands, but does not affect starvation-induced autophagy in the fat body. Furthermore, knockdown of exocyst subunits has a similar effect, preventing autophagy in dying cells but not in cells of starved animals. Notch activity is elevated in dying salivary glands, this change in Notch signaling is influenced by Ral, and decreased Notch function influences autophagy. These data indicate that Ral and the exocyst regulate autophagy in a context-dependent manner, and that in dying salivary glands, Ral mediates autophagy, at least in part, by regulation of Notch.

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