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

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Saturday, February 28th, 2015

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Bunker, B.D., Nellimoottil, T.T., Boileau, R.M., Classen, A.K. and Bilder, D. (2015). The transcriptional response to tumorigenic polarity loss in Drosophila. Elife [Epub ahead of print]. PubMed ID: 25719210
Summary:
Loss of polarity correlates with progression of epithelial cancers, but how plasma membrane misorganization drives oncogenic transcriptional events remains unclear. The polarity regulators of the Drosophila Scribble (Scrib) module are potent tumor suppressors and provide a model for mechanistic investigation. RNA profiling of Scrib mutant tumors revealed multiple signatures of neoplasia, including altered metabolism and dedifferentiation. Prominent among these was upregulation of cytokine-like Unpaired (Upd) ligands, which drive tumor overgrowth. This study identified a polarity-responsive enhancer in upd3, which was activated in a coincident manner by both JNK-dependent Fos and aPKC-mediated Yki transcription. This enhancer, and Scrib mutant overgrowth in general, were also sensitive to activity of the Polycomb Group (PcG), suggesting that PcG attenuation upon polarity loss potentiated select targets for activation by JNK and Yki. These results link epithelial organization to signaling and epigenetic regulators that control tissue repair programs, and provide insight into why epithelial polarity is tumor-suppressive.

Dahlberg, O., Shilkova, O., Tang, M., Holmqvist, P. H. and Mannervik, M. (2015) P-TEFb, the super elongation complex and mediator regulate a subset of non-paused genes during early Drosophila embryo development. PLoS Genet 11: e1004971. PubMed ID: 25679530
Summary:
Positive Transcription Elongation Factor b (P-TEFb) is a kinase consisting of Cdk9 and Cyclin T that releases RNA Polymerase II (Pol II) into active elongation. It can assemble into a larger Super Elongation Complex (SEC) consisting of additional elongation factors. This study used a miRNA-based approach to knock down the maternal contribution of P-TEFb and SEC components in early Drosophila embryos. P-TEFb or SEC depletion results in loss of cells from the embryo posterior and in cellularization defects. Interestingly, the expression of many patterning genes containing promoter-proximal paused Pol II is relatively normal in P-TEFb embryos. Instead, P-TEFb and SEC are required for expression of some non-paused, rapidly transcribed genes in pre-cellular embryos, including the cellularization gene Serendipity-alpha. It was also demonstrated that another P-TEFb regulated gene, terminus, has an essential function in embryo development. Similar morphological and gene expression phenotypes were observed upon knock down of Mediator subunits (see Med19), providing in vivo evidence that P-TEFb, the SEC and Mediator collaborate in transcription control. Surprisingly, P-TEFb depletion does not affect the ratio of Pol II at the promoter versus the 3' end, despite affecting global Pol II Ser2 phosphorylation levels. Instead, Pol II occupancy is reduced at P-TEFb down-regulated genes. It is concluded that a subset of non-paused, pre-cellular genes are among the most susceptible to reduced P-TEFb, SEC and Mediator levels in Drosophila embryos.

Foos, N., Maurel-Zaffran, C., Mate, M. J., Vincentelli, R., Hainaut, M., Berenger, H., Pradel, J., Saurin, A. J., Ortiz-Lombardia, M. and Graba, Y. (2015) A flexible extension of the Drosophila Ultrabithorax homeodomain defines a novel Hox/PBC interaction mode. Structure 23: 270-279. PubMed ID: 25651060
Summary:
The patterning function of Hox proteins relies on assembling protein complexes with PBC proteins (the homeodomain proteins encoded by the Drosophila extradenticle (exd) and vertebrate pbx genes), which often involves a protein motif found in most Hox proteins, the so-called Hexapeptide (HX). Hox/PBC complexes likely gained functional diversity by acquiring additional modes of interaction. This study structurally characterized the first HX alternative interaction mode of the Hox protein Ultrabithorax based on the paralogue-specific UbdA motif and further functionally validates structure-based predictions. The UbdA motif folds as a flexible extension of the homeodomain recognition helix and defines Hox/PBC contacts that occur, compared with those mediated by the HX motif, on the opposing side of the DNA double helix. This provides a new molecular facet to Hox/PBC complex assembly and suggests possible mechanisms for the diversification of Hox protein function.

Chen, J., Nolte, V. and Schlötterer, C. (2015). Temperature stress mediates decanalization and dominance of gene expression in Drosophila melanogaster. PLoS Genet 11: e1004883. PubMed ID: 25719753
Summary:
The regulatory architecture of gene expression remains an area of active research. This report studied how the interplay of genetic and environmental variation affects gene expression by exposing Drosophila melanogaster strains to four different developmental temperatures. At 18°C they observed almost complete canalization with only very few allelic effects on gene expression. In contrast, at the two temperature extremes, 13 °C and 29°C a large number of allelic differences in gene expression were detected due to both cis- and trans-regulatory effects. Allelic differences in gene expression were mainly dominant, but for up to 62% of the genes the dominance swapped between 13 and 29°C. These results are consistent with stabilizing selection causing buffering of allelic expression variation in non-stressful environments. The study proposes that decanalization of gene expression in stressful environments is not only central to adaptation, but may also contribute to genetic disorders in human populations.

Friday, February 27th

Fletcher, G.C., Elbediwy, A., Khanal, I., Ribeiro, P.S., Tapon, N. and Thompson, B.J. (2015). The Spectrin cytoskeleton regulates the Hippo signalling pathway. EMBO J [Epub ahead of print]. PubMed ID: 25712476
Summary:
The Spectrin cytoskeleton is known to be polarised in epithelial cells, yet its role remains poorly understood. This study shows that the Spectrin cytoskeleton controls Hippo signalling. In the developing Drosophila wing and eye, loss of apical Spectrins (alpha/beta-heavy dimers) produced tissue overgrowth and mis-regulation of Hippo target genes, similar to loss of Crumbs (Crb) or the FERM-domain protein Expanded (Ex). Apical beta-heavy Spectrin bound to Ex and co-localised with it at the apical membrane to antagonise Yki activity. Interestingly, in both the ovarian follicular epithelium and intestinal epithelium of Drosophila, apical Spectrins and Crb were dispensable for repression of Yki, while basolateral Spectrins (alpha/beta dimers) were essential. Finally, the Spectrin cytoskeleton was required to regulate the localisation of the Hippo pathway effector YAP in response to cell density human epithelial cells. These findings identify both apical and basolateral Spectrins as regulators of Hippo signalling and suggest Spectrins as potential mechanosensors

Lu, W., Lakonishok, M. and Gelfand, V. I. (2015) Kinesin-1-powered microtubule sliding initiates axonal regeneration in Drosophila cultured neurons. Mol Biol Cell [Epub ahead of print]. PubMed ID: 25657321
Summary:
Understanding the mechanism underlying axon regeneration is of great practical importance to develop therapeutic treatment for traumatic brain and spinal cord injuries. Dramatic cytoskeleton reorganization occurs at the injury site, and microtubules have been implicated in the regeneration process. Previous studies have demonstrated that microtubule sliding by conventional kinesin (Kinesin-1) is required for initiation of neurite outgrowth in Drosophila embryonic neurons, and that sliding is developmentally down-regulated when neurite outgrowth is completed. This study reports that mechanical axotomy of Drosophila neurons in culture triggers axonal regeneration and regrowth. Regenerating neurons contain actively sliding microtubules; this sliding, like sliding during initial neurite outgrowth, is driven by Kinesin-1 and is required for axonal regeneration. The injury induces a fast spike of calcium, and depolymerization of microtubules near the injury site, and subsequent formation of local new microtubule arrays with mixed polarity. These events are required for reactivation of microtubule sliding at the initial stages of regeneration. Furthermore, c-Jun N-terminal kinase (JNK) pathway promotes regeneration by enhancing microtubule sliding in injured mature neurons.

Brigaud, I., Duteyrat, J.L., Chlasta, J., Le Bail, S., Couderc, J.L. and Grammont, M. (2015). Transforming Growth Factor β/activin signalling induces epithelial cell flattening during Drosophila oogenesis. Biol Open [Epub ahead of print]. PubMed ID: 25681395
Summary:
Although the regulation of epithelial morphogenesis is essential for the formation of tissues and organs in multicellular organisms, little is known about how signalling pathways control cell shape changes in space and time. In the Drosophila ovarian epithelium, the transition from a cuboidal to a squamous shape is accompanied by a wave of cell flattening and by the ordered remodelling of E-cadherin-based adherens junctions. This study shows that activation of the TGFβ pathway is crucial to determine the timing, the degree and the dynamic of cell flattening. Within these cells, TGFβ signalling controlled cell-autonomously the formation of Actin filament and the localisation of activated Myosin II, indicating that internal forces were generated and used to remodel AJ and to promote cytoskeleton rearrangement. TGFβ signalling controlled Notch activity and that its functions were partly executed through Notch. Thus, the cells that underwent the cuboidal-to-squamous transition produced active cell-shaping mechanisms, rather than passively flattening in response to a global force generated by the growth of the underlying cells. Thus, this work on TGFβ signalling provides new insights into the mechanisms through which signal transduction cascades orchestrate cell shape changes to generate proper organ structure.

Okumura, M., Sakuma, C., Miura, M. and Chihara, T. (2015) Linking cell surface receptors to microtubules: Tubulin Folding Cofactor D mediates Dscam functions during neuronal morphogenesis. J Neurosci 35: 1979-1990. PubMed ID: 25653356
Summary:
Formation of functional neural networks requires the coordination of cell surface receptors and downstream signaling cascades, which eventually leads to dynamic remodeling of the cytoskeleton. Although a number of guidance receptors affecting actin cytoskeleton remodeling have been identified, it is relatively unknown how microtubule dynamics are regulated by guidance receptors. This study used Drosophila olfactory projection neurons to study the molecular mechanisms of neuronal morphogenesis. Dendrites of each projection neuron target a single glomerulus of approximately 50 glomeruli in the antennal lobe, and the axons show stereotypical pattern of terminal arborization. In the course of genetic analysis of the dachsous mutant allele (dsUAO71), this study identified a mutation in the tubulin folding cofactor D gene (TBCD) as a background mutation. TBCD is one of five tubulin-folding cofactors required for the formation of alpha- and beta-tubulin heterodimers. Single-cell clones of projection neurons homozygous for the TBCD mutation displayed disruption of microtubules, resulting in ectopic arborization of dendrites, and axon degeneration. Interestingly, overexpression of TBCD also resulted in microtubule disruption and ectopic dendrite arborization, suggesting that an optimum level of TBCD is crucial for in vivo neuronal morphogenesis. It was further found that TBCD physically interacts with the intracellular domain of Down syndrome cell adhesion molecule (Dscam), which is important for neural development and has been implicated in Down syndrome. Genetic analyses revealed that TBCD cooperates with Dscam in vivo. This study may offer new insights into the molecular mechanism underlying the altered neural networks in cognitive disabilities of Down syndrome.

Thursday, February 26th

Ríos-Barrera, L.D., Gutiérrez-Pérez, I., Domínguez, M. and Riesgo-Escovar, J.R. (2015). acal is a long non-coding RNA in JNK signaling in epithelial shape changes during Drosophila dorsal closure. PLoS Genet 11: e1004927. PubMed ID: 25710168
Summary:
Dorsal closure is an epithelial remodeling process taking place during Drosophila embryogenesis. JNK signaling coordinates dorsal closure. This study identifies and characterizes acal as a novel negative dorsal closure regulator. acal represented a new level of JNK regulation. The acal locus coded for a conserved, long, non-coding, nuclear RNA. Long non-coding RNAs are an abundant and diverse class of gene regulators. Mutations in acal were lethal. acal mRNA expression was dynamic and was processed into a collection of 50 to 120 bp fragments. acal was downstream of raw, a pioneer protein, helping explain part of raw functions, and interacted genetically with Polycomb. acal functioned in trans regulating mRNA expression of two genes involved in JNK signaling and dorsal closure: Connector of kinase to AP1 (Cka) and anterior open (aop). Cka is a conserved scaffold protein that brings together JNK and Jun, and Aop is a transcription factor. Misregulation of Cka and aop could account for dorsal closure phenotypes in mutants.

Angrisani, A., Tafer, H., Stadler, P. F. and Furia, M. (2015) Developmentally regulated expression and expression strategies of Drosophila snoRNAs. Insect Biochem Mol Biol [Epub ahead of print]. PubMed ID: 25641266
Summary:
Small nucleolar RNAs constitute a significant portion of the eukaryotic small ncRNA transcriptome and guide site-specific methylation or pseudouridylation of target RNAs. In addition, they can play diverse regulatory roles on gene expression, acting as precursors of smaller fragments able to modulate alternative splicing or operate as microRNAs. Defining their expression strategies and the full repertory of their biological functions is a critical, but still ongoing, process in most organisms. Considering that Drosophila melanogaster is one of the most advantageous model organism for genetic, functional and developmental studies, this study analyzed the whole genomic organization of its annotated snoRNAs - whose vast majority is known to be embedded in an intronic context - and showed by GO term enrichment analysis that protein-coding genes involved in cell division and cytoskeleton organization are those mostly preferred as hosts. This finding was unexpected, and delineates an unpredicted link between snoRNA host genes and cell proliferation that might be of general relevance. Quantitative RT-PCR was used to define the expression of a representative subset of annotated specimens throughout the life cycle, providing a first overview on developmental profiling of the fly snoRNA transcriptome. Most of the tested specimens, rather than acting as housekeeping genes with uniform expression, exhibit dynamic developmental expression patterns; moreover, intronic snoRNAs harboured by the same host gene often exhibit distinct temporal profiles, indicating that they can be expressed uncoordinatedly. In addition to provide an updated outline of the fly snoRNA transcriptome, these data highlight that expression of these versatile ncRNAs can be finely regulated.

Miles, W. O., Korenjak, M., Griffiths, L. M., Dyer, M. A., Provero, P. and Dyson, N. J. (2014) Post-transcriptional gene expression control by NANOS is up-regulated and functionally important in pRb-deficient cells. EMBO J 33: 2201-2215. PubMed ID: 25100735
Summary:
Inactivation of the retinoblastoma tumor suppressor (pRb) is a common oncogenic event that alters the expression of genes important for cell cycle progression, senescence, and apoptosis. However, in many contexts, the properties of pRb-deficient cells are similar to wild-type cells suggesting there may be processes that counterbalance the transcriptional changes associated with pRb inactivation. Therefore, this study sought sets of evolutionary conserved, functionally related genes that are direct targets of pRb/E2F proteins. Expression of Nanos, a key facilitator of the Pumilio (Pum) post-transcriptional repressor complex, was shown to be directly repressed by pRb/E2F in flies and humans. In both species, Nanos expression increases following inactivation of pRb/RBF1 and becomes important for tissue homeostasis. By analyzing datasets from normal retinal tissue and pRb-null retinoblastomas, this study found a strong enrichment for putative Pum substrates among genes de-regulated in tumors. These include pro-apoptotic genes that are transcriptionally down-regulated upon pRb loss, and two such candidates, MAP2K3 and MAP3K1, were characterized as direct Pum substrates. The data suggest that Nanos increases in importance in pRb-deficient cells and helps to maintain homeostasis by repressing the translation of transcripts containing PUM Regulatory Elements (PRE).

Lindehell, H., Kim, M. and Larsson, J. (2015) Proximity ligation assays of protein and RNA interactions in the male-specific lethal complex on Drosophila melanogaster polytene chromosomes. Chromosoma [Epub ahead of print]. PubMed ID: 25694028
Summary:
In Drosophila, the male-specific lethal (MSL) complex specifically targets the male X chromosome and participates in a twofold increase in expression output leading to functional dosage compensation. The complex includes five proteins and two non-coding RNAs (ncRNAs). A number of additional associated factors have also been identified. However, the components' roles and interactions have not been fully elucidated. The in situ proximity ligation assay (PLA) provides a sensitive means to determine whether proteins and other factors have bound to chromosomes in close proximity to each other, and thus may interact. Thus, MSL complex components were modified, tested, and the assay was applied to probe interactions on polytene chromosomes. In situ PLA can detect and map both protein-protein and protein-ncRNA interactions on polytene chromosomes at high resolution. It was further shown that all five protein components of the MSL complex are in close proximity to each other, and the ncRNAs roX1 and roX2 bind the complex in close proximity to MLE. The results also indicate that JIL1, a histone H3 Ser10 kinase enriched on the male X chromosome, interacts with MSL1 and MSL2, but not MSL3 of the MSL complex. In addition, proposed interactions of the MSL complex with both CLAMP and TopoII were corroborated.

Wednesday, February 25th

Ball, R.W., Peled, E., Guerrero, G. and Isacoff, E.Y. (2015). BMP signaling and microtubule organization regulate synaptic strength. Neuroscience [Epub ahead of print]. PubMed ID: 25681521
Summary:
The strength of synaptic transmission between a neuron and multiple postsynaptic partners can vary considerably. This report has studied synaptic heterogeneity using the glutamatergic Drosophila neuromuscular junction (NMJ), which contains multiple synaptic connections of varying strength between a motor axon and muscle fiber. In larval NMJs, there was a gradient of synaptic transmission from weak proximal to strong distal boutons. The study imaged synaptic transmission with the postsynaptically targeted fluorescent calcium sensor SynapCam, to investigate the molecular pathways that determine synaptic strength and set up this gradient. Mutations in the Bone Morphogenetic Protein (BMP) signaling pathway disrupted production of strong distal boutons. Strong connections contained unbundled microtubules in the boutons, suggesting a role for microtubule organization in transmission strength. The spastin mutation, which disorganizes microtubules, disrupted the transmission gradient, supporting this interpretation. The study proposes that the BMP pathway, shown previously to function in the homeostatic regulation of synaptic growth, also boosts synaptic transmission in a spatially selective manner that depends on the microtubule system.

Verma, P., Augustine, G. J., Ammar, M. R., Tashiro, A. and Cohen, S. M. (2015) A neuroprotective role for microRNA miR-1000 mediated by limiting glutamate excitotoxicity. Nat Neurosci [Epub ahead of print]. PubMed ID: 25643297
Summary:
Evidence has begun to emerge for microRNAs as regulators of synaptic signaling, specifically acting to control postsynaptic responsiveness during synaptic transmission. This report provides evidence that Drosophila melanogaster miR-1000 acts presynaptically to regulate glutamate release at the synapse by controlling expression of the vesicular glutamate transporter (VGlut). Genetic deletion of miR-1000 led to elevated apoptosis in the brain as a result of glutamatergic excitotoxicity. The seed-similar miR-137 regulates VGluT2 expression in mouse neurons. These conserved miRNAs share a neuroprotective function in the brains of flies and mice. Drosophila miR-1000 showed activity-dependent expression, which might serve as a mechanism to allow neuronal activity to fine-tune the strength of excitatory synaptic transmission.

Kohn, E., Katz, B., Yasin, B., Peters, M., Rhodes, E., Zaguri, R., Weiss, S. and Minke, B. (2015) Functional cooperation between the IP3 receptor and Phospholipase C secures the high Sensitivity to light of Drosophila photoreceptors in vivo. J Neurosci 35: 2530-2546. PubMed ID: 25673847
Summary:
Drosophila phototransduction is a model system for the ubiquitous phosphoinositide signaling. In complete darkness, spontaneous unitary current events (dark bumps) are produced by spontaneous single Gqα activation, while single-photon responses (quantum bumps) arise from synchronous activation of several Gqα molecules. Recent studies have shown that most of the spontaneous single Gqα activations do not produce dark bumps, because of a critical phospholipase Cβ (PLCβ) activity level required for bump generation. Surpassing the threshold of channel activation depends on both PLCβ activity and cellular [Ca(2+)], which participates in light excitation via a still unclear mechanism. This study shows that in IP3 receptor (IP3R)-deficient photoreceptors, both light-activated Ca(2+) release from internal stores and light sensitivity were strongly attenuated. This was further verified by Ca(2+) store depletion, linking Ca(2+) release to light excitation. In IP3R-deficient photoreceptors, dark bumps were virtually absent and the quantum-bump rate was reduced, indicating that Ca(2+) release from internal stores is necessary to reach the critical level of PLCβ catalytic activity and the cellular [Ca(2+)] required for excitation. Combination of IP3R knockdown with reduced PLCbeta catalytic activity resulted in highly suppressed light responses that were partially rescued by cellular Ca(2+) elevation, showing a functional cooperation between IP3R and PLCβ via released Ca(2+). These findings suggest that in contrast to the current dogma that Ca(2+) release via IP3R does not participate in light excitation, this study shows that released Ca(2+) plays a critical role in light excitation. The positive feedback between PLCβ and IP3R found here may represent a common feature of the inositol-lipid signaling.

Alvarez-Fernandez, C., Tamirisa, S., Prada, F., Chernomoretz, A., Podhajcer, O., Blanco, E. and Martin-Blanco, E. (2015) Identification and functional analysis of healing regulators in Drosophila. PLoS Genet 11: e1004965. PubMed ID: 25647511
Summary:
Wound healing is an essential homeostatic mechanism that maintains the epithelial barrier integrity after tissue damage. Although the overall steps in wound healing are known, many of the underlying molecular mechanisms remain unclear. Genetically amenable systems, such as wound healing in Drosophila imaginal discs, do not model all aspects of the repair process. However, they do allow the less understood aspects of the healing response to be explored, e.g., which signal(s) are responsible for initiating tissue remodeling? How is sealing of the epithelia achieved? Or, what inhibitory cues cancel the healing machinery upon completion? Answering these and other questions first requires the identification and functional analysis of wound specific genes. A variety of different microarray analyses of murine and humans have identified characteristic profiles of gene expression at the wound site, however, very few functional studies in healing regulation have been carried out. This study developed an experimentally controlled method that is healing-permissive and that allows live imaging and biochemical analysis of cultured imaginal discs. Comparative genome-wide profiling was performed between Drosophila imaginal cells actively involved in healing versus their non-engaged siblings. Sets of potential wound-specific genes were subsequently identified. Importantly, besides identifying and categorizing new genes, this study functionally tested many of their gene products by genetic interference and overexpression in healing assays. This non-saturated analysis defines a relevant set of genes whose changes in expression level are functionally significant for proper tissue repair. Amongst these the TCP1 chaperonin complex was identified as a key regulator of the actin cytoskeleton essential for the wound healing response. There is promise that these newly identified wound-healing genes will guide future work in the more complex mammalian wound healing response.

Tuesday, February 24th

Kale, A., Li, W., Lee, C.H. and Baker, N.E. (2015). Apoptotic mechanisms during competition of ribosomal protein mutant cells: roles of the initiator caspases Dronc and Dream/Strica. Cell Death Differ [Epub ahead of print]. PubMed ID: 25613379
Summary:
Heterozygosity for mutations in ribosomal protein genes frequently leads to a dominant phenotype of retarded growth and small adult bristles in Drosophila (the Minute phenotype). Cells with Minute genotypes are subject to cell competition, characterized by their selective apoptosis and removal in mosaic tissues that contain wild-type cells. Competitive apoptosis was found to depend on the pro-apoptotic reaper, grim and head involution defective genes but was independent of p53. Rp/+ cells were protected by anti-apoptotic baculovirus p35 expression but lacked the usual hallmarks of 'undead' cells. They lacked Dronc activity, and neither expression of dominant-negative Dronc nor dronc knockdown by dsRNA prevented competitive apoptosis, which also continued in dronc null mutant cells or in the absence of the initiator caspases dredd and dream/strica. Only simultaneous knockdown of dronc and dream/strica by dsRNA was sufficient to protect Rp/+ cells from competition. By contrast, Rp/Rp cells were also protected by baculovirus p35, but Rp/Rp death was dronc-dependent, and undead Rp/Rp cells exhibited typical dronc-dependent expression of Wingless. Independence of p53 and unusual dependence on Dream/Strica distinguish competitive cell death from noncompetitive apoptosis of Rp/Rp cells and from many other examples of cell death.

Pang, Y., Bai, X. C., Yan, C., Hao, Q., Chen, Z., Wang, J. W., Scheres, S. H. and Shi, Y. (2015) Structure of the apoptosome: mechanistic insights into activation of an initiator caspase from Drosophila. Genes Dev 29: 277-287. PubMed ID: 25644603
Summary:
Apoptosis is executed by a cascade of caspase activation. The autocatalytic activation of an initiator caspase, exemplified by caspase-9 in mammals or its ortholog,Dronc, in fruit flies, is facilitated by a multimeric adaptor complex known as the apoptosome. The underlying mechanism by which caspase-9 or Dronc is activated by the apoptosome remains unknown. This study reports the electron cryomicroscopic (cryo-EM) structure of the intact apoptosome from Drosophila melanogaster at 4.0 Å resolution. Analysis of the Drosophila apoptosome, which comprises 16 molecules of the Dark protein (Apaf-1 ortholog), reveals molecular determinants that support the assembly of the 2.5-MDa complex. In the absence of dATP or ATP, Dronc zymogen potently induces formation of the Dark apoptosome, within which Dronc is efficiently activated. At 4.1 Å resolution, the cryo-EM structure of the Dark apoptosome bound to the caspase recruitment domain (CARD) of Dronc (Dronc-CARD) reveals two stacked rings of Dronc-CARD that are sandwiched between two octameric rings of the Dark protein. The specific interactions between Dronc-CARD and both the CARD and the WD40 repeats of a nearby Dark protomer are indispensable for Dronc activation. These findings reveal important mechanistic insights into the activation of initiator caspase by the apoptosome.

Jean, S., Cox, S., Nassari, S. and Kiger, A. A. (2015) Starvation-induced MTMR13 and RAB21 activity regulates VAMP8 to promote autophagosome-lysosome fusion. EMBO Rep [Epub ahead of print]. PubMed ID: 25648148
Summary:
Autophagy, the process for recycling cytoplasm in the lysosome, depends on membrane trafficking. Drosophila Sbf as a Rab21 guanine nucleotide exchange factor (GEF) that acts with Rab21 in endosomal trafficking. This study shows that Sbf/MTMR13 and Rab21 have conserved functions required for starvation-induced autophagy. Depletion of Sbf/MTMR13 or Rab21 blocks endolysosomal trafficking of VAMP8, a SNARE required for autophagosome-lysosome fusion. This study shows that starvation induces Sbf/MTMR13 GEF and RAB21 activity, as well as their induced binding to VAMP8 (or closest Drosophila homolog, Vamp7). MTMR13 is required for RAB21 activation, VAMP8 interaction and VAMP8 endolysosomal trafficking, defining a novel GEF-Rab-effector pathway. These results identify starvation-responsive endosomal regulators and trafficking that tunes membrane demands with changing autophagy status.

Weiss, S. and Minke, B. (2015). A new genetic model for calcium induced autophagy and ER-stress in Drosophila photoreceptor cells. Channels (Austin) 9: 14-20. PubMed ID: 25664921
Summary:
Cytoplasmic Ca(2+) overload is known to trigger autophagy and ER-stress. Furthermore, ER-stress and autophagy are commonly associated with degenerative pathologies, but their role in disease progression is still a matter of debate, in part, owing to limitations of existing animal model systems. The Drosophila eye is a widely used model system for studying neurodegenerative pathologies. Recently, the Drosophila protein, Calphotin, has been identified as a cytosolic immobile Ca(2+) buffer, which participates in Ca(2+) homeostasis in Drosophila photoreceptor cells. Exposure of calphotin hypomorph flies to continuous illumination, which induces Ca(2+) influx into photoreceptor cells, resulted in severe Ca(2+)-dependent degeneration. This study shows that this degeneration is autophagy and ER-stress related. These studies thus provide a new model in which genetic manipulations trigger changes in cellular Ca(2+) distribution. This model constitutes a framework for further investigations into the link between cytosolic Ca(2+), ER-stress and autophagy in human disorders and diseases.

Monday, February 23rd

Oliva, C., Molina-Fernandez, C., Maureira, M., Candia, N., Lopez, E., Hassan, B., Aerts, S., Canovas, J., Olguin, P. and Sierralta, J. (2015) Hindsight regulates photoreceptor axon targeting through transcriptional control of jitterbug/Filamin and multiple genes involved in axon guidance in Drosophila. Dev Neurobiol [Epub ahead of print]. PubMed ID: 25652545
Summary
During axon targeting, a stereotyped pattern of connectivity is achieved by the integration of intrinsic genetic programs and the response to extrinsic long and short-range directional cues. How this coordination occurs is the subject of intense study. Transcription factors play a central role due to their ability to regulate the expression of multiple genes required to sense and respond to these cues during development. This study shows that the transcription factor Hnt regulates layer-specific photoreceptor axon targeting in Drosophila through transcriptional control of jbug/Filamin and multiple genes involved in axon guidance and cytoskeleton organization. Using a microarray analysis, 235 genes were identified whose expression levels were changed by Hnt overexpression in the eye primordia. Nine candidate genes involved in cytoskeleton regulation and axon guidance were analyzed, six of which displayed significantly altered gene expression levels in hnt mutant retinas. Functional analysis confirmed the role of otk/PTK7 in photoreceptor axon targeting and uncovered Tiggrin, an integrin ligand, and Jbug/Filamin, a conserved actin- binding protein, as new factors that participate of photoreceptor axon targeting. Moreover, in silico and molecular evidence is provided that supports jbug/Filamin as a direct transcriptional target of Hnt and that Hht acts partially through Jbug/Filamin in vivo to regulate axon guidance. This work broadens the understanding of how Hnt regulates the coordinated expression of a group of genes to achieve the correct connectivity pattern in the Drosophila visual system.

Huang, Y., Ng, F. S. and Jackson, F. R. (2015)e Comparison of larval and adult Drosophila astrocytes reveals stage-specific gene expression profiles. G3 (Bethesda) [Epub ahead of print]. PubMed ID: 25653313
Summary:
The analysis of adult astrocyte glial cells has revealed a remarkable heterogeneity with regard to morphology, molecular signature and physiology. A key question in glial biology is how such heterogeneity arises during brain development. One approach to this question is to identify genes with differential astrocyte expression during development; certain genes expressed later in neural development may contribute to astrocyte differentiation. This study has utilized the Drosophila model and Translating Ribosome Affinity Purification (TRAP)-RNA-seq methods to derive the genome-wide expression profile of Drosophila larval astrocyte-like cells (hereafter referred to as astrocytes) for the first time. These studies identified hundreds of larval astrocyte-enriched genes that encode proteins important for metabolism, energy production, and protein synthesis, consistent with the known role of astrocytes in the metabolic support of neurons. Comparison of the larval profile with that observed for adults has identified genes with astrocyte-enriched expression specific to adulthood. These include genes important for metabolism and energy production, translation, chromatin modification, protein glycosylation, neuropeptide signaling, immune responses, vesicle-mediated trafficking or secretion, and the regulation of behavior. Among these functional classes, the expression of genes important for chromatin modification and vesicle-mediated trafficking or secretion is overrepresented in adult astrocytes based on Gene Ontology analysis. Certain genes with selective adult enrichment may mediate functions specific to this stage or be important for the differentiation or maintenance of adult astrocytes, the latter perhaps contributing to population heterogeneity.

Jang, A. R., Moravcevic, K., Saez, L., Young, M. W. and Sehgal, A. (2015) Drosophila TIM binds Importin alpha1, and acts as an adapter to transport PER to the nucleus. PLoS Genet 11: e1004974. PubMed ID: 25674790
Summary:
Regulated nuclear entry of clock proteins is a conserved feature of eukaryotic circadian clocks and serves to separate the phase of mRNA activation from mRNA repression in the molecular feedback loop. In Drosophila, nuclear entry of the clock proteins, Period (Per) and Timeless (Tim), is tightly controlled, and impairments of this process produce profound behavioral phenotypes. This study reports that nuclear entry of PER-TIM in clock cells, and consequently behavioral rhythms, require a specific member of a classic nuclear import pathway, Importin α1 (IMPα1). In addition to IMPα1, rhythmic behavior and nuclear expression of PER-TIM require a specific nuclear pore protein, Nup153, and Ran-GTPase. IMPα1 can also drive rapid and efficient nuclear expression of Tim and Per in cultured cells, although the effect on Per is mediated by Tim. Mapping of interaction domains between IMPα1 and TIM/PER suggests that Tim is the primary cargo for the importin machinery. This is supported by attenuated interaction of IMPalpha1 with Tim carrying a mutation previously shown to prevent nuclear entry of Tim and Per. Tim is detected at the nuclear envelope, and computational modeling suggests that it contains HEAT-ARM repeats typically found in karyopherins, consistent with its role as a co-transporter for Per. These findings suggest that although Per is the major timekeeper of the clock, Tim is the primary target of nuclear import mechanisms. Thus, the circadian clock uses specific components of the importin pathway with a novel twist in that Tim serves a karyopherin-like role for PER.

Linford, N. J., Ro, J., Chung, B. Y. and Pletcher, S. D. (2015) Gustatory and metabolic perception of nutrient stress in Drosophila. Proc Natl Acad Sci U S A. PubMed ID: 25675472
Summary:
Sleep loss is an adaptive response to nutrient deprivation that alters behavior to maximize the chances of feeding before imminent death. Organisms must maintain systems for detecting the quality of the food source to resume healthy levels of sleep when the stress is alleviated. This study determined that gustatory perception of sweetness is both necessary and sufficient to suppress starvation-induced sleep loss when animals encounter nutrient-poor food sources. It was further found that blocking specific dopaminergic neurons phenocopies the absence of gustatory stimulation, suggesting a specific role for these neurons in transducing taste information to sleep centers in the brain. Finally, it was showm that gustatory perception is required for survival, specifically in a low nutrient environment. Overall, these results demonstrate an important role for gustatory perception when environmental food availability approaches zero and illustrate the interplay between sensory and metabolic perception of nutrient availability in regulating behavioral state.

Sunday, February 22nd

Fogle, K. J., Baik, L. S., Houl, J. H., Tran, T. T., Roberts, L., Dahm, N. A., Cao, Y., Zhou, M. and Holmes, T. C. (2015) CRYPTOCHROME-mediated phototransduction by modulation of the potassium ion channel β-subunit redox sensor. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 25646452
Summary:
Blue light activation of the photoreceptor Cryptochrome (Cry) evokes rapid depolarization and increased action potential firing in a subset of circadian and arousal neurons in Drosophila melanogaster. This study shows that acute arousal behavioral responses to blue light significantly differ in mutants lacking Cry, as well as mutants with disrupted opsin-based phototransduction. Light-activated Cry couples to membrane depolarization via a well conserved redox sensor of the voltage-gated potassium (K+) channel β-subunit (Kvβ) Hyperkinetic (Hk). The neuronal light response is almost completely absent in hk-/- mutants, but is functionally rescued by genetically targeted neuronal expression of WT Hk, but not by Hk point mutations that disable Hk redox sensor function. Multiple K+ channel α-subunits that coassemble with Hk, including Shaker, Ether-a-go-go, and Ether-a-go-go-related gene, are ion conducting channels for Cry/Hk-coupled light response. Light activation of Cry is transduced to membrane depolarization, increased firing rate, and acute behavioral responses by the Kvβ subunit redox sensor.

Faville, R., Kottler, B., Goodhill, G. J., Shaw, P. J. and van Swinderen, B. (2015) How deeply does your mutant sleep? Probing arousal to better understand sleep defects in Drosophila. Sci Rep 5: 8454. PubMed ID: 25677943
Summary:
The fruitfly, Drosophila melanogaster, has become a critical model system for investigating sleep functions. Most studies use duration of inactivity to measure sleep. However, a defining criterion for sleep is decreased behavioral responsiveness to stimuli. This paper introduces the Drosophila ARousal Tracking system (DART), an integrated platform for efficiently tracking and probing arousal levels in animals. This video-based platform delivers positional and locomotion data, behavioral responsiveness to stimuli, sleep intensity measures, and homeostatic regulation effects - all in one combined system. Insight into dynamically changing arousal thresholds is shown to be crucial for any sleep study in flies. First it was found that arousal probing uncovers different sleep intensity profiles among related genetic background strains previously assumed to have equivalent sleep patterns. Then it is shown how sleep duration and sleep intensity can be uncoupled, with distinct manipulations of dopamine function producing opposite effects on sleep duration but similar sleep intensity defects. The study concludes by providing a multi-dimensional assessment of combined arousal and locomotion metrics in the mutant and background strains. This approach opens the door for deeper insights into mechanisms of sleep regulation and provides a new method for investigating the role of different genetic manipulations in controlling sleep and arousal.

Nepoux, V., Babin, A., Haag, C., Kawecki, T.J. and Le Rouzic, A. (2015). Quantitative genetics of learning ability and resistance to stress in Drosophila melanogaster. Ecol Evol 5: 543-556. PubMed ID: 25691979
Summary:
Even though laboratory evolution experiments have demonstrated genetic variation for learning ability, little is known about the underlying genetic architecture and genetic relationships with other ecologically relevant traits. With a full diallel cross among twelve inbred lines of Drosophila melanogaster originating from a natural population, this study investigated the genetic architecture of olfactory learning ability and compared it to that for another behavioral trait (unconditional preference for odors), as well as three traits quantifying the ability to deal with environmental challenges: egg-to-adult survival and developmental rate on a low-quality food, and resistance to a bacterial pathogen. Substantial additive genetic variation was detected for each trait, highlighting their potential to evolve. Genetic effects contributed more than nongenetic parental effects to variation in traits measured at the adult stage: learning, odorant perception, and resistance to infection. In contrast, the two traits quantifying larval tolerance to low-quality food were more strongly affected by parental effects. The study found no evidence for genetic correlations between traits, suggesting that these traits could evolve at least to some degree independently of one another. Finally, inbreeding adversely affected all traits.

Gaertner, B. E., Ruedi, E. A., McCoy, L. J., Moore, J. M., Wolfner, M. F. and Mackay, T. F. (2015) Heritable variation in courtship patterns in Drosophila melanogaster. G3 (Bethesda) [Epub ahead of print]. PubMed ID: 25650358
Summary:
Little is known about the genetic basis of naturally occurring variation for sexually-selected behavioral traits. Drosophila melanogaster, with its rich repertoire of courtship behavior and genomic and genetic resources, is an excellent model organism for addressing this question. This study assayed a genetically diverse panel of lines with full genome sequences, the Drosophila Genetic Reference Panel, to assess the heritability of variation in courtship behavior and mating progression. These data were subsequently used to quantify natural variation in transition probabilities between courtship behaviors. Heritable variation was found, along the expected trajectory for courtship behaviors, including the tendency to initiate courtship and rate of progression through courtship, suggesting a genetic basis to male modulation of courtship behavior based on feedback from unrelated, outbred and genetically identical females. The genetic basis of variation was assessed of the transition with the highest heritability - from copulation to no engagement with the female - and variants were identified in Serrate and Furin 1 as well as many other polymorphisms on the chromosome 3R associated with this transition.These findings suggest that courtship is a highly dynamic behavior with both social and genetic inputs, and that males may play an important role in courtship initiation and duration.

Saturday, February 21st

Shklover, J., Mishnaevski, K., Levy-Adam, F. and Kurant, E. (2015). JNK pathway activation is able to synchronize neuronal death and glial phagocytosis in Drosophila. Cell Death Dis 6: e1649. PubMed ID: 25695602
Summary:
Glial phagocytosis of superfluous neurons and damaged or aberrant neuronal material is crucial for normal development and maintenance of the CNS. However, the molecular mechanisms underlying the relationship between neuronal death and glial phagocytosis are poorly understood. This study describes a novel mechanism that is able to synchronize neuronal cell death and glial phagocytosis of dying neurons in the Drosophila embryonic CNS. This mechanism involved c-Jun N-terminal kinase (JNK) signaling, which was required for developmental apoptosis of specific neurons during embryogenesis. The dJNK pathway gain-of-function in neurons led to dJNK signaling in glia, which resulted in upregulation of glial phagocytosis. Importantly, this promotion of phagocytosis was not mediated by upregulation of the glial phagocytic receptors SIMU (Nimrod C4) and Draper, but by increasing glial capacity to degrade apoptotic particles inside phagosomes. The proposed mechanism may be important for removal of damaged neurons in the developing and mature CNS.

Organisti, C., Hein, I., Grunwald Kadow, I. C. and Suzuki, T. (2014) Flamingo, a seven-pass transmembrane cadherin, cooperates with Netrin/Frazzled in Drosophila midline guidance. Genes Cells. PubMed ID: 25440577
Summary:
During central nervous system development, several guidance cues and receptors, as well as cell adhesion molecules, are required for guiding axons across the midline and along the anterior-posterior axis. In Drosophila, commissural axons sense the midline attractants Netrin A and B (Net) through Frazzled (Fra) receptors. Despite their importance, lack of Net or Fra affects only some commissures, suggesting that additional molecules can fulfill this function. Recently, planar cell polarity (PCP) proteins have been implicated in midline axon guidance in both vertebrate and invertebrate systems. This study reports that the atypical cadherin and PCP molecule Flamingo/Starry night (Fmi/Stan) acts jointly with Net/Fra signaling during midline development. Additional removal of fmi strongly increases the guidance defects in Net/fra mutants. Rescue and domain deletion experiments suggest that Fmi signaling facilitates commissural pathfinding potentially by mediating axonal fasciculation in a partly homophilic manner. Altogether, these results indicate that contact-mediated cell adhesion via Fmi acts in addition to the Net/Fra guidance system during axon pathfinding across the midline, underlining the importance of PCP molecules during vertebrates and invertebrates midline development.

Troost, T., Schneider, M. and Klein, T. (2015) A re-examination of the selection of the sensory organ precursor of the bristle sensilla of Drosophila melanogaster. PLoS Genet 11: e1004911. PubMed ID: 25569355
Summary:
The bristle sensillum of the imago of Drosophila is made of four cells that arise from a sensory organ precursor cell (SOP). This SOP is selected within proneural clusters (PNC) through a mechanism that involves Notch signalling. PNCs are defined through the expression domains of the proneural genes, whose activities enables cells to become SOPs. They encode tissue specific bHLH proteins that form functional heterodimers with the bHLH protein Daughterless (Da). In the prevailing lateral inhibition model for SOP selection, a transcriptional feedback loop that involves the Notch pathway amplifies small differences of proneural activity between cells of the PNC. As a result only one or two cells accumulate sufficient proneural activity to adopt the SOP fate. Most of the experiments that sustained the prevailing lateral inhibition model were performed a decade ago. This study re-examined the selection process using recently available reagents. The data suggest a different picture of SOP selection. They indicate that a band-like region of proneural activity exists. In this proneural band the activity of the Notch pathway is required in combination with Emc to define the PNCs. A sub-group in the PNCs was found from which a pre-selected SOP arises. The data indicate that most imaginal disc cells are able to adopt a proneural state from which they can progress to become SOPs. They further show that bristle formation can occur in the absence of the proneural genes if the function of emc is abolished. These results suggest that the tissue specific proneural proteins of Drosophila have a similar function as in the vertebrates, which is to determine the time of emergence and position of the SOP and to stabilise the proneural state.

Mattar, P., Ericson, J., Blackshaw, S. and Cayouette, M. (2015) A conserved regulatory logic controls temporal identity in mouse neural progenitors. Neuron 85: 497-504. PubMed ID: 25654255
Summary:
Neural progenitors alter their output over time to generate different types of neurons and glia in specific chronological sequences, but this process remains poorly understood in vertebrates. This study shows that Casz1, the vertebrate ortholog of the Drosophila temporal identity factor castor, controls the production of mid-/late-born neurons in the murine retina. Casz1 is expressed from mid/late stages in retinal progenitor cells (RPCs), and conditional deletion of Casz1 increases production of early-born retinal neurons at the expense of later-born fates, whereas precocious misexpression of Casz1 has the opposite effect. In both cases, cell proliferation is unaffected, indicating that Casz1 does not control the timing of cell birth but instead biases RPC output directly. Just as Drosophila castor lies downstream of the early temporal identity factor hunchback, this study found that the hunchback ortholog Ikzf1 (Ikaros) represses Casz1. These results uncover a conserved strategy regulating temporal identity transitions from flies to mammals.

Friday, February 20th

Randall, A.S., Liu, C.H., Chu, B., Zhang, Q., Dongre, S.A., Juusola, M., Franze, K., Wakelam, M.J. and Hardie, R.C. (2015). Speed and sensitivity of phototransduction in Drosophila depend on degree of saturation of membrane phospholipids. J Neurosci 35: 2731-2746. PubMed ID: 25673862
Summary:
Drosophila phototransduction is mediated via a G-protein-coupled PLC cascade. Recent evidence, including the demonstration that light evokes rapid contractions of the photoreceptors, suggested that the light-sensitive channels (TRP and TRPL) may be mechanically gated, together with protons released by PLC-mediated PIP2 hydrolysis. If mechanical gating is involved this study predicted that the response to light should be influenced by altering the physical properties of the membrane. To achieve this, the study used diet to manipulate the degree of saturation of membrane phospholipids. In flies reared on a yeast diet, lacking polyunsaturated fatty acids (PUFAs), mass spectrometry showed that the proportion of polyunsaturated phospholipids was sevenfold reduced (from 38 to ~5%) but rescued by adding a single species of PUFA (linolenic or linoleic acid) to the diet. Photoreceptors from yeast-reared flies showed a 2- to 3-fold increase in latency and time to peak of the light response, without affecting quantum bump waveform. In the absence of Ca(2+) influx or in trp mutants expressing only TRPL channels, sensitivity to light was reduced up to ∼10-fold by the yeast diet, and essentially abolished in hypomorphic G-protein mutants (Gαq). PLC activity appeared little affected by the yeast diet; however, light-induced contractions measured by atomic force microscopy or the activation of ectopic mechanosensitive gramicidin channels were also slowed ∼2-fold. The results are consistent with mechanosensitive gating and provide a striking example of how dietary fatty acids can profoundly influence sensory performance in a classical G-protein-coupled signaling cascade.

Yu, L., Daniels, J. P., Wu, H. and Wolf, M. J. (2015). Cardiac hypertrophy induced by active Raf depends on Yorkie-mediated transcription. Sci Signal 8: ra13. PubMed ID: 25650441
Summary:
Organ hypertrophy can result from enlargement of individual cells or from cell proliferation or both. Activating mutations in the serine-threonine kinase Raf cause cardiac hypertrophy and contribute to Noonan syndrome in humans. Cardiac-specific expression of activated Raf also causes hypertrophy in Drosophila melanogaster. Yorkie (Yki), a transcriptional coactivator in the Hippo pathway that regulates organ size, is required for Raf-induced cardiac hypertrophy in flies. Although aberrant activation of Yki orthologs stimulates cardiac hyperplasia in mice, cardiac-specific expression of an activated mutant form of Yki in fruit flies caused cardiac hypertrophy without hyperplasia. Knockdown of Yki caused cardiac dilation without loss of cardiomyocytes and prevented Raf-induced cardiac hypertrophy. In flies, Yki-induced cardiac hypertrophy required the TEA domain-containing transcription factor Scalloped, and, in mammalian cells, expression of mouse RafL613V, an activated form of Raf with a Noonan syndrome mutation, increased Yki-induced Scalloped activity. Furthermore, overexpression of Tgi (a Tondu domain-containing Scalloped-binding corepressor) in the fly heart abrogated Yki- or Raf-induced cardiac hypertrophy. Thus, crosstalk between Raf and Yki occurs in the heart and can influence Raf-mediated cardiac hypertrophy.
Bae, S.J., Kim, M., Kim, S.H., Kwon, Y.E., Lee, J.H., Kim, J., Chung, C.H., Lee, W.J. and Seol, J.H. (2015). NEDD4 controls intestinal stem cell homeostasis by regulating the Hippo signalling pathway. Nat Commun 6: 6314. PubMed ID: 25692647
Summary:
The Hippo pathway plays crucial roles in regulating organ size and stem cell homeostasis. Although the signalling cascade of the core Hippo kinases is relatively well understood, little is known about the mechanisms that modulate the activity of the Hippo pathway. This study reports the identification of human NEDD4 (see Drosophila Nedd4), a HECT-type E3 ubiquitin ligase, as a regulatory component of the Hippo pathway. NEDD4 ubiquitylated and destabilized WW45 (see Drosophila Salvador) and LATS kinase (see Drosophila Warts, both of which are required for active Hippo signalling. Interestingly, MST1 protected WW45, but not LATS2, against NEDD4. The study also provided evidence indicating that NEDD4 inactivation at high cell density was a prerequisite for the elevated Hippo activity linked to contact inhibition. Moreover, NEDD4 promoted intestinal stem cell renewal in Drosophila by suppressing Hippo signalling. Collectively, the study presents a regulatory mechanism by which NEDD4 controls the Hippo pathway leading to coordinated cell proliferation and apoptosis.
Zhang, F., Qi, Y., Zhou, K., Zhang, G., Linask, K. and Xu, H. (2015). The cAMP phosphodiesterase Prune localizes to the mitochondrial matrix and promotes mtDNA replication by stabilizing TFAM. EMBO Rep. [Epub ahead of print]. PubMed ID: 25648146
Summary:
Compartmentalized cAMP signaling regulates mitochondrial dynamics, morphology, and oxidative phosphorylation. However, regulators of the mitochondrial cAMP pathway, and its broad impact on organelle function, remain to be explored. This study reports that Drosophila Prune is a cyclic nucleotide phosphodiesterase that localizes to the mitochondrial matrix. Knocking down prune in cultured cells reduces mitochondrial transcription factor A (TFAM) and mitochondrial DNA (mtDNA) levels. The data suggest that Prune stabilizes TFAM and promotes mtDNA replication through downregulation of mitochondrial cAMP signaling. In addition, this work demonstrates the prevalence of mitochondrial cAMP signaling in metazoa and its new role in mitochondrial biogenesis.

Thursday, February 19th

Arya, G.H., Magwire, M.M., Huang, W., Serrano-Negron, Y.L., Mackay, T.F. and Anholt, R.R. (2015). The genetic basis for variation in olfactory behavior in Drosophila melanogaster. Chem Senses [Epub ahead of print]. PubMed ID: 25687947
Summary:
The genetic underpinnings that contribute to variation in olfactory perception are not fully understood. To explore the genetic basis of variation in olfactory perception, this study measured behavioral responses to 14 chemically diverse naturally occurring odorants in 260400 flies from 186 lines of the Drosophila melanogaster Genetic Reference Panel, a population of inbred wild-derived lines with sequenced genomes. They observed variation in olfactory behavior for all odorants. Low to moderate broad-sense heritabilities and the large number of tests for genotype-olfactory phenotype association performed precluded any individual variant from reaching formal significance. However, the top variants (nominal P < 5×10-5) were highly enriched for genes involved in nervous system development and function, as expected for a behavioral trait. Further, pathway enrichment analyses showed that genes tagged by the top variants included components of networks centered on cyclic guanosine monophosphate and inositol triphosphate signaling, growth factor signaling, Rho signaling, axon guidance, and regulation of neural connectivity. Functional validation with RNAi and mutations showed that 15 out of 17 genes tested indeed affected olfactory behavior. These results show that in addition to chemoreceptors, variation in olfactory perception depends on polymorphisms that can result in subtle variations in synaptic connectivity within the nervous system.

Venu, I., Durisko, Z., Xu, J. and Dukas, R. (2014)S. Social attraction mediated by fruit flies' microbiome.J Exp Biol 217: 1346-1352. PubMed ID: 24744425
Summary:
Larval and adult fruit flies are attracted to volatiles emanating from food substrates that have been occupied by larvae. Tests were performed to see whether such volatiles are emitted by the larval gut bacteria by conducting tests under bacteria-free (axenic) conditions. Attraction was also tested to two bacteria species, Lactobacillus brevis, which was cultured from larvae in the lab, and L. plantarum, a common constituent of fruit flies' microbiome in other laboratory populations and in wild fruit flies. Neither larvae nor adults showed attraction to axenic food that had been occupied by axenic larvae, but both showed the previously reported attraction to standard food that had been occupied by larvae with an intact microbiome. Larvae also showed significant attraction to volatiles from axenic food and larvae to which only either L. brevis or L. plantarum, and volatiles from L. brevis reared on its optimal growth medium were added. Controlled learning experiments indicated that larvae experienced with both standard and axenic used food do not perceive either as superior, while focal larvae experienced with simulated used food, which contains burrows, perceive it as superior to unused food. Thse results suggest that flies rely on microbiome-derived volatiles for long-distance attraction to suitable food patches. Under natural settings, fruits often contain harmful fungi and bacteria, and both L. brevis and L. plantarum produce compounds that suppress the growth of some antagonistic fungi and bacteria. The larval microbiome volatiles may therefore lead prospective fruit flies towards substrates with a hospitable microbial environment.

Wasserman, S. M., Aptekar, J. W., Lu, P., Nguyen, J., Wang, A. L., Keles, M. F., Grygoruk, A., Krantz, D. E., Larsen, C. and Frye, M. A. (2015). Olfactory neuromodulation of motion vision circuitry in Drosophila. Curr Biol [Epub ahead of print]. PubMed ID: 25619767
Summary:
It is well established that perception is largely multisensory; often served by modalities such as touch, vision, and hearing that detect stimuli emanating from a common point in space; and processed by brain tissue maps that are spatially aligned. However, the neural interactions among modalities that share no spatial stimulus domain yet are essential for robust perception within noisy environments remain uncharacterized. Drosophila melanogaster makes its living navigating food odor plumes. Odor acts to increase the strength of gaze-stabilizing optomotor reflexes to keep the animal aligned within an invisible plume, facilitating odor localization in free flight. This study investigated the cellular mechanism for cross-modal behavioral interactions. A wide-field motion-selective interneuron of the lobula plate was tested that shares anatomical and physiological similarities with the "Hx" neuron identified in larger flies. Drosophila Hx exhibits cross-modal enhancement of visual responses by paired odor, and presynaptic inputs to the lobula plate are required for behavioral odor tracking but are not themselves the target of odor modulation, nor is the neighboring wide-field "HSE" neuron. Octopaminergic neurons mediating increased visual responses upon flight initiation also show odor-evoked calcium modulations and form connections with Hx dendrites. Finally, restoring synaptic vesicle trafficking within the octopaminergic neurons of animals carrying a null mutation for all aminergic signaling is sufficient to restore odor-tracking behavior. These results are the first to demonstrate cellular mechanisms underlying visual-olfactory integration required for odor localization in fruit flies, which may be representative of adaptive multisensory interactions across taxa.

Muijres, F. T., Elzinga, M. J., Iwasaki, N. A. and Dickinson, M. H. (2015). . Body saccades of Drosophila consist of stereotyped banked turns. J Exp Biol [Epub ahead of print]. PubMed ID: 25657212
Summary:
The flight pattern of many fly species consists of straight flight segments interspersed with rapid turns called body saccades, a strategy that is thought to minimize motion blur. This study analyzed the body saccades of fruit flies (Drosophila hydei), using high-speed 3D videography to track body and wing kinematics and a dynamically-scaled robot to study the production of aerodynamic forces and moments. Although the size, degree and speed of the saccades vary, the dynamics of the maneuver are remarkably stereotypic. In executing a body saccade, flies perform a quick roll and counter-roll, combined with a slower unidirectional rotation around their yaw axis. Flies regulate the size of the turn by adjusting the magnitude of torque that they produce about these control axes, while maintaining the orientation of the rotational axes in the body frame constant. In this way, body saccades are different from escape responses in the same species, in which the roll and pitch component of banking is varied to adjust turn angle. This analysis of the wing kinematics and aerodynamics showed that flies control aerodynamic torques during the saccade primarily by adjusting the timing and amount of span-wise wing rotation.

Wednesday, February 18th

Marin-Vicente, C., Domingo-Prim, J., Eberle, A.B. and Visa, N. (2015). RRP6/EXOSC10 is required for the repair of DNA double-strand breaks by homologous recombination. J Cell Sci [Epub ahead of print]. PubMed ID: 25632158
Summary:
The exosome acts on different RNA substrates and plays important roles in RNA metabolism. The fact that short non-coding RNAs are involved in the DNA damage response led this study to investigate whether the exosome factor RRP6 of Drosophila melanogaster and its human ortholog EXOSC10 play a role in DNA repair. The study shows that RRP6 and EXOSC10 are recruited to DNA double-strand breaks (DSBs) in S2 cells and HeLa cells, respectively. Depletion of RRP6/EXOSC10 did not interfere with the phosphorylation of the histone variant H2Av/H2AX, but impaired the recruitment of the homologous recombination factor RAD51 to the damaged sites, without affecting RAD51 levels. The recruitment of RAD51 to DSBs in S2 cells was also inhibited by overexpression of RRP6-Y361A-V5, a catalytically inactive RRP6 mutant. Furthermore, cells depleted of RRP6 or EXOSC10 were more sensitive to radiation, which was consistent with RRP6/EXOSC10 playing a role in DNA repair. RRP6/EXOSC10 could be co-immunoprecipitated with RAD51, which linked RRP6/EXOSC10 to the homologous recombination pathway. Altogether, these results suggest that the ribonucleolytic activity of RRP6/EXOSC10 is required for the recruitment of RAD51 to DSBs.

Lee, M., Choi, Y., Kim, K., Jin, H., Lim, J., Nguyen, T. A., Yang, J., Jeong, M., Giraldez, A. J., Yang, H., Patel, D. J. and Kim, V. N. (2014). Adenylation of maternally inherited microRNAs by Wispy. Mol Cell 56: 696-707. PubMed ID: 25454948
Summary:
Early development depends heavily on accurate control of maternally inherited mRNAs, and yet it remains unknown how maternal microRNAs are regulated during maternal-to-zygotic transition (MZT). This study found that maternal microRNAs are highly adenylated at their 3' ends in mature oocytes and early embryos. Maternal microRNA adenylation is widely conserved in fly, sea urchin, and mouse. This study identified Wispy, a noncanonical poly(A) polymerase, as the enzyme responsible for microRNA adenylation in flies. Knockout of wispy abrogates adenylation and results in microRNA accumulation in eggs, whereas overexpression of Wispy increases adenylation and reduces microRNA levels in S2 cells. Wispy interacts with Ago1 through protein-protein interaction, which may allow the effective and selective adenylation of microRNAs. Thus, adenylation may contribute to the clearance of maternally deposited microRNAs during MZT. This work provides mechanistic insights into the regulation of maternal microRNAs and illustrates the importance of RNA tailing in development.

Rieder, L. E., Savva, Y. A., Reyna, M. A., Chang, Y. J., Dorsky, J. S., Rezaei, A. and Reenan, R. A. (2015). Dynamic response of RNA editing to temperature in Drosophila. BMC Biol 13: 1. PubMed ID: 25555396
Summary:
Adenosine-to-inosine RNA editing is a highly conserved process that post-transcriptionally modifies mRNA, generating proteomic diversity, particularly within the nervous system of metazoans. Transcripts encoding proteins involved in neurotransmission predominate as targets of such modifications. Previous reports suggest that RNA editing is responsive to environmental inputs in the form of temperature alterations. However, the molecular determinants underlying temperature-dependent RNA editing responses are not well understood. Using the poikilotherm Drosophila, this study shows that acute temperature alterations within a normal physiological range result in substantial changes in RNA editing levels. Examination of particular sites reveals diversity in the patterns with which editing responds to temperature, and these patterns are conserved across five species of Drosophilidae representing over 10 million years of divergence. In addition, it was shown that expression of the editing enzyme, ADAR, is dramatically decreased at elevated temperatures, partially, but not fully, explaining some target responses to temperature. Interestingly, this reduction in editing enzyme levels at elevated temperature is only partially reversed by a return to lower temperatures. Lastly, it was showm that engineered structural variants of the most temperature-sensitive editing site, in a sodium channel transcript, perturb thermal responsiveness in RNA editing profile for a particular RNA structure. These results suggest that the RNA editing process responds to temperature alterations via two distinct molecular mechanisms: through intrinsic thermosensitivity of the RNA structures that direct editing, and due to temperature sensitive expression or stability of the RNA editing enzyme. Environmental cues, in this case temperature, rapidly reprogram the Drosophila transcriptome through RNA editing, presumably resulting in altered proteomic ratios of edited and unedited proteins.

Kern, A. D., Barbash, D. A., Mell, J. C., Hupalo, D. and Jensen, A. (2015). Highly constrained intergenic Drosophila ultraconserved elements are candidate ncRNAs. Genome Biol Evol [Epub ahead of print]. PubMed ID: 25618141
Summary:
Eukaryotes contain short (~80-200 bp) regions that have few or no substitutions among species that represent hundreds of millions of years of evolutionary divergence. These ultraconserved elements (UCEs) are candidates for containing essential functions, but their biological roles remain largely unknown. This study reports the discovery and characterization of UCEs from 12 sequenced Drosophila species. 98 elements were identified >/= 80 bp long, with very high conservation across the Drosophila phylogeny. Population genetic analyses reveal that these UCEs are not present in mutational cold spots. Instead it is inferred that they experience a level of selective constraint almost 10-fold higher compared to missense mutations in protein-coding sequences, which is substantially higher than that observed previously for human UCEs. About one-half of these Drosophila UCEs overlap the transcribed portion of genes, with many of those that are within coding sequences likely to correspond to sites of ADAR-dependent RNA editing. For the remaining UCEs that are in non-genic regions, it was found that many are potentially capable of forming RNA secondary structures. Among 10 chosen for further analysis it was discovered that the majority are transcribed in multiple tissues of Drosophila melanogaster. It is concluded that Drosophila species are rich with UCEs and that many of them may correspond to novel non-coding RNAs.

Tuesday, February 17th

Crocker, J., Abe, N., Rinaldi, L., McGregor, A. P., Frankel, N., Wang, S., Alsawadi, A., Valenti, P., Plaza, S., Payre, F., Mann, R. S. and Stern, D. L. (2015). Low affinity binding site clusters confer hox specificity and regulatory robustness. Cell 160: 191-203. PubMed ID: 25557079
Summary:
In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox, because different Hox proteins bind with high affinity in vitro to similar DNA sequences.This study demonstrates that the Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) binds specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture-clusters of low affinity binding sites-is maintained and required for enhancer function. Natural selection therefore works at the level of the enhancer, requiring a particular density of low affinity Ubx sites to confer both specific and robust expression.

Lee, J.E., Oney, M., Frizzell, K., Phadnis, N. and Hollien, J. (2015). Drosophila melanogaster Activating Transcription Factor 4 regulates glycolysis during endoplasmic reticulum stress. G3 (Bethesda) [Epub ahead of print]. PubMed ID: 25681259
Summary:
Endoplasmic reticulum (ER) stress results from an imbalance between the load of proteins entering the secretory pathway and the ability of the ER to fold and process them. The response to ER stress is mediated by a collection of signaling pathways termed the unfolded protein response (UPR), which plays important roles in development and disease. This study shows that in Drosophila melanogaster S2 cells, ER stress induces a coordinated change in the expression of genes involved in carbon metabolism. Genes encoding enzymes that carry out glycolysis were up-regulated, whereas genes encoding proteins in the TCA cycle and respiratory chain complexes were down-regulated. The UPR transcription factor Atf4 was necessary for the up-regulation of glycolytic enzymes and Lactate dehydrogenase (Ldh). Furthermore, Atf4 binding motifs in promoters for these genes could partially account for their regulation during ER stress. Finally, flies up-regulated Ldh and produced more lactate when subjected to ER stress. Together these results suggest that Atf4 mediates a shift from a metabolism based on oxidative phosphorylation to one more heavily reliant on glycolysis, reminiscent of aerobic glycolysis or the Warburg effect observed in cancer and other proliferative cells.
Busser, B. W., Haimovich, J., Huang, D., Ovcharenko, I. and Michelson, A. M. (2015). Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila. Nucleic Acids Res [Epub ahead of print]. PubMed ID: 25609699
Summary:
This study used discriminative training methods to uncover the chromatin, transcription factor (TF) binding and sequence features of enhancers underlying gene expression in individual cardiac cells. Machine learning with TF motifs and ChIP data for a core set of cardiogenic TFs and histone modifications were used to classify Drosophila cell-type-specific cardiac enhancer activity. The classifier models can be used to predict cardiac cell subtype cis-regulatory activities. Associating the predicted enhancers with an expression atlas of cardiac genes further uncovered clusters of genes with transcription and function limited to individual cardiac cell subtypes. Further, the cell-specific enhancer models revealed chromatin, TF binding and sequence features that distinguish enhancer activities in distinct subsets of heart cells. Collectively, these results show that computational modeling combined with empirical testing provides a powerful platform to uncover the enhancers, TF motifs and gene expression profiles which characterize individual cardiac cell fates.

Hadzic, T., Park, D., Abruzzi, K. C., Yang, L., Trigg, J. S., Rohs, R., Rosbash, M. and Taghert, P. H. (2015). Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED. Nucleic Acids Res [Epub ahead of print]. PubMed ID: 25634895
Summary:
Neuroendocrine (NE) cells use large dense core vesicles (LDCVs) to traffic, process, store and secrete neuropeptide hormones through the regulated secretory pathway. The Dimmed (Dimm) basic helix-loop-helix transcription factor of Drosophila controls the level of regulated secretory activity in NE cells. To pursue its mechanisms, two independent genome-wide analyses of DIMM's activities were performed: (1) in vivo chromatin immunoprecipitation (ChIP) to define genomic sites of Dimm occupancy and (2) deep sequencing of purified Dimm neurons to characterize their transcriptional profile. By this combined approach, Dimm was shown to binds to conserved E-boxes in enhancers of 212 genes whose expression is enriched in Dimm-expressing NE cells. Dimm binds preferentially to certain E-boxes within first introns of specific gene isoforms. Statistical machine learning revealed that flanking regions of putative Dimm binding sites contribute to its DNA binding specificity. Dimm's transcriptional repertoire features at least 20 large dense core vesicle (LDCV_ constituents. In addition, Dimm notably targets the pro-secretory transcription factor, creb-A, but significantly, Dimm does not target any neuropeptide genes. Dimm therefore prescribes the scale of secretory activity in NE neurons, by a systematic control of both proximal and distal points in the regulated secretory pathway.

Monday, February 16th

König, A. and Shcherbata, H.R. (2015). Soma influences GSC progeny differentiation via the cell adhesion-mediated steroid-let-7-Wingless signaling cascade that regulates chromatin dynamics. Biol Open [Epub ahead of print]. PubMed ID: 25661868
Summary:
It is known that signaling from the germline stem cell niche is required to maintain germline stem cell identity in Drosophila. However, it is not clear whether the germline stem-cell daughters differentiate by default (because they are physically distant from the niche) or whether additional signaling is necessary to initiate the differentiation program. Previously, these authors showed that ecdysteroid signaling cell non-autonomously regulates early germline differentiation via its soma-specific co-activator and co-repressor, Taiman and Abrupt. This study demonstrates that this regulation is modulated by the miRNA let-7, which acts in a positive feedback loop to confer ecdysone signaling robustness via targeting its repressor, the transcription factor Abrupt. This feedback loop adjusted ecdysteroid signaling in response to some stressful alterations in the external and internal conditions, which included temperature stress and aging, but not nutritional deprivation. Upon let-7 deficit, escort cells failed to properly differentiate: their shape, division, and cell adhesive characteristics were perturbed. These cells had confused cellular identity and formed columnar-like rather than squamous epithelium and failed to send protrusions in between differentiating germline cysts, affecting soma-germline communication. Particularly, levels of the homophilic cell adhesion protein Cadherin, which recruits Wg signaling transducer &beta;-catenin, were increased in mutant escort cells and, correspondingly, in the adjacent germline cells. Readjustment of heterotypic (soma-germline) cell adhesion modulated Wg signaling intensity in the germline, which in turn regulated histone modifications that promoted expression of the genes necessary to trigger early germline differentiation. Thus, these data first show the intrinsic role for Wg signaling in the germline and support a model where the soma influences the tempo of germline differentiation in response to external conditions.

Escobar, D.J., Desai, R., Ishiyama, N., Folmsbee, S.S., Novak, M.N., Flozak, A.S., Daugherty, R.L., Mo, R., Nanavati, D., Sarpal, R., Leckband, D., Ikura, M., Tepass, U., and Gottardi, C.J. (2015). α-catenin phosphorylation promotes intercellular adhesion through a dual-kinase mechanism. J Cell Sci [Epub ahead of print]. PubMed ID: 25653389
Summary:
The cadherin-catenin adhesion complex is a key contributor to epithelial tissue stability and dynamic cell movements during development and tissue renewal. How this complex is regulated to accomplish these functions is not fully understood. This study identified several phosphorylation sites in mammalian αE-catenin and Drosophila α-Catenin within a flexible linker located between the middle (M)-region and the carboxyl-terminal actin-binding domain. This phospho-linker (P-linker) was the main phosphorylated region of α-catenin in cells and was sequentially modified at Casein Kinase 2 and 1 consensus sites. In Drosophila, the P-linker was required for normal α-catenin function during development and collective cell migration, although no obvious defects were found in cadherin-catenin complex assembly or adherens junction formation. In mammalian cells, non-phosphorylatable forms of α-catenin showed defects in intercellular adhesion using a mechanical dispersion assay. Epithelial sheets expressing phospho-mimic forms of α-catenin showed faster and more coordinated migrations after scratch wounding. These findings suggest that phosphorylation and dephosphorylation of the α-catenin P-linker are required for normal cadherin-catenin complex function in Drosophila and mammalian cells.

Arya, R., Sarkissian, T., Tan, Y. and White, K. (2015). Neural stem cell progeny regulate stem cell death in a Notch and Hox dependent manner. Cell Death Differ [Epub ahead of print]. PubMed ID: 25633198
Summary:
Cell death is a prevalent, well-controlled and fundamental aspect of development, particularly in the nervous system. In Drosophila, specific neural stem cells are eliminated by apoptosis during embryogenesis. In the absence of apoptosis, these stem cells continue to divide, resulting in a dramatically hyperplastic central nervous system and adult lethality. Although core cell death pathways have been well described, the spatial, temporal and cell identity cues that activate the cell death machinery in specific cells are largely unknown. This study identified a cis-regulatory region that controls the transcription of the cell death activators reaper, grim and sickle exclusively in neural stem cells. Using a reporter generated from this regulatory region, this study found that Notch activity is required for neural stem cell death. Notch regulates the expression of the AbdominalA homeobox protein, which provides important spatial cues for death. Importantly, this study shows that pro-apoptotic Notch signaling is activated by the Delta ligand expressed on the neighboring progeny of the stem cell. Thus a previously undescribed role for progeny has been identified in regulating the proper developmental death of their parental stem cells.

Birdsey, G. M., Shah, A. V., Dufton, N., Reynolds, L. E., Osuna Almagro, L., Yang, Y., Aspalter, I. M., Khan, S. T., Mason, J. C., Dejana, E., Gottgens, B., Hodivala-Dilke, K., Gerhardt, H., Adams, R. H. and Randi, A. M. (2015). The Endothelial Transcription factor ERG promotes vascular stability and growth through Wnt/β-Catenin signaling. Dev Cell 32: 82-96. PubMed ID: 25584796
Summary:
Blood vessel stability is essential for embryonic development; in the adult, many diseases are associated with loss of vascular integrity. The ETS transcription factor ERG (see Drosophila Pointed) drives expression of VE-cadherin (see Drosophila Shotgun) and controls junctional integrity. Constitutive endothelial deletion of ERG (ErgcEC-KO) in mice causes embryonic lethality with vascular defects. Inducible endothelial deletion of ERG (ErgiEC-KO) results in defective physiological and pathological angiogenesis in the postnatal retina and tumors, with decreased vascular stability. ERG controls the Wnt/beta-catenin pathway by promoting β-catenin stability, through signals mediated by VE-cadherin and the Wnt receptor Frizzled-4. Wnt signaling is decreased in ERG-deficient endothelial cells; activation of Wnt signaling with lithium chloride, which stabilizes beta-catenin levels, corrects vascular defects in ErgcEC-KO embryos. Finally, overexpression of ERG in vivo reduces permeability and increases stability of VEGF-induced blood vessels. These data demonstrate that ERG is an essential regulator of angiogenesis and vascular stability through Wnt signaling.

Sunday, February 15th

Lenz, O., Xiong, J., Nelson, M.D., Raizen, D.M. and Williams, J.A. (2015). FMRFamide signaling promotes stress-induced sleep in Drosophila. Brain Behav Immun [Epub ahead of print]. PubMed ID: 25668617
Summary:
Enhanced sleep in response to cellular stress is a conserved adaptive behavior across multiple species, but the mechanism of this process is poorly understood. Drosophila melanogaster increases sleep following exposure to septic or aseptic injury, and Caenorhabditis elegans displays sleep-like quiescence following exposure to high temperatures that stress cells. This study shows that, similar to C. elegans, Drosophila responds to heat stress with an increase in sleep. In contrast to Drosophila infection-induced sleep, heat-induced sleep was not sensitive to the time-of-day of the heat pulse. Moreover, the sleep response to heat stress did not require Relish, the NFκB transcription factor that is necessary for infection-induced sleep, indicating that sleep was induced by multiple mechanisms from different stress modalities. The study identified a sleep-regulating role for a signaling pathway involving FMRFamide neuropeptides and their receptor FR. Animals mutant for either FMRFamide or for the FMRFamide receptor (FR) had a reduced recovery sleep in response to heat stress. FR mutants, in addition, showed reduced sleep responses following infection with Serratia marcescens, and succumbed to infection at a faster rate than wild-type controls. Together, these findings support the hypothesis that FMRFamide and its receptor promote an adaptive increase in sleep following stress. Because an FMRFamide-like neuropeptide plays a similar role in C. elegans, the study proposes that FRMFamide neuropeptide signaling is an ancient regulator of recovery sleep which occurs in response to cellular stress.

Rezaei, A., Krishna, M.S. and Santhosh, H.T. (2015). Male age affects female mate preference, quantity of accessory gland proteins, and sperm traits and female fitness in D. melanogaster. Zoolog Sci 32: 16-24. PubMed ID: 25660692
Summary:
For species in which mating is resource-independent and offspring do not receive parental care, theoretical models of age-based female mate preference predict that females should prefer to mate with older males as they have demonstrated ability to survive. Thus, females should obtain a fitness benefit from mating with older males. However, male aging is often associated with reductions in quantity of sperm. The adaptive significance of age-based mate choice is therefore unclear. Various hypotheses have made conflicting predictions concerning this issue, because published studies have not investigated the effect of age on accessory gland proteins and sperm traits. D. melanogaster exhibits resource-independent mating, and offspring do not receive parental care, making this an appropriate model for studying age-based mate choice. In the present study, it was found that D. melanogaster females of all ages preferred to mate with the younger of two competing males. Young males performed significantly greater courtship attempts and females showed least rejection for the same than middle-aged and old males. Young males had small accessory glands that contained very few main cells that were larger than average. Nevertheless, compared with middle-aged or old males, the young males transferred greater quantities of accessory gland proteins and sperm to mated females. As a result, females that mated with young male produced more eggs and progeny than those that mated with older males. Furthermore, mating with young male reduced female's lifespan. These studies indicate that quantity of accessory gland proteins and sperm traits decrease with male age and females obtain direct fitness benefit from mating with preferred young males.

Yang, C. H., He, R. and Stern, U. (2015). Behavioral and circuit basis of sucrose rejection by Drosophila females in a simple decision-making task. J Neurosci 35: 1396-1410. PubMed ID: 25632118
Summary:
Drosophila melanogaster egg-laying site selection offers a genetic model to study a simple form of value-based decision. Drosophila females consistently reject a sucrose-containing substrate and choose a plain (sucrose-free) substrate for egg laying in a sucrose versus plain decision assay. However, either substrate is accepted when it is the sole option. This study describes the neural mechanism that underlies females' sucrose rejection in the sucrose versus plain assay. First, it was demonstrated that females explored the sucrose substrate frequently before most egg-laying events, suggesting that they actively suppress laying eggs on the sucrose substrate as opposed to avoiding visits to it. Second, it was shown that activating a specific subset of dopamine (DA) neurons triggered a preference for laying eggs on the sucrose substrate over the plain one, suggesting that activating these DA neurons can increase the value of the sucrose substrate for egg laying. Third, it was demonstrated that neither ablating nor inhibiting the mushroom body (MB), a known Drosophila learning and decision center, affected females' egg-laying preferences in the sucrose versus plain assay, suggesting that MB does not mediate this specific decision-making task. It is proposed that the value of a sucrose substrate- as an egg-laying option-can be adjusted by the activities of a specific DA circuit. Once the sucrose substrate is determined to be the lesser valued option, females execute their decision to reject this inferior substrate not by stopping their visits to it, but by actively suppressing their egg-laying motor program during their visits.

Schleyer, M., Miura, D., Tanimura, T. and Gerber, B. (2015). Learning the specific quality of taste reinforcement in larval Drosophila. Elife 4 [Epub ahead of print]. PubMed ID: 25622533
Summary:
The only property of reinforcement insects are commonly thought to learn about is its value. This study shows that larval Drosophila not only remember the value of reinforcement (How much?), but also its quality (What?). This is demonstrated both within the appetitive domain by using sugar vs amino acid as different reward qualities, and within the aversive domain by using bitter vs high-concentration salt as different qualities of punishment. From the available literature, such nuanced memories for the quality of reinforcement are unexpected and pose a challenge to present models of how insect memory is organized. Given that animals as simple as larval Drosophila, endowed with but 10,000 neurons, operate with both reinforcement value and quality, it is suggested that both are fundamental aspects of mnemonic processing-in any brain.

Saturday, February 14th


Schaub, C., März, J., Reim, I. and Frasch, M. (2015). Org-1-dependent lineage reprogramming generates the ventral longitudinal musculature of the Drosophila heart. Curr Biol [Epub ahead of print]. PubMed ID: 25660543
Summary:
Only few examples of transdifferentiation, which denotes the conversion of one differentiated cell type to another, are known to occur during normal development, and more often, it is associated with regeneration processes. With respect to muscles, dedifferentiation/redifferentiation processes have been documented during post-traumatic muscle regeneration in blastema of newts as well as during myocardial regeneration. As shown in this study, the ventral longitudinal muscles of the adult Drosophila heart arise from specific larval alary muscles in a process that represents the first known example of syncytial muscle transdifferentiation via dedifferentiation into mononucleate myoblasts during normal development. This unique process was dependent on the reinitiation of a transcriptional program previously employed for embryonic alary muscle development, in which the factors Org-1 (Drosophila Tbx1) and Tailup (Drosophila Islet1) are key components. During metamorphosis, the action of these factors combined with cell-autonomous inputs from the ecdysone steroid and the Hox gene Ultrabithorax, which provide temporal and spatial specificity to the transdifferentiation events. Following muscle dedifferentiation, inductive cues, particularly from the remodeling heart tube, were required for the redifferentiation of myoblasts into ventral longitudinal muscles. These results provide new insights into mechanisms of lineage commitment and cell-fate plasticity during development.

Jang, A.R., Moravcevic, K., Saez, L., Young, M.W. and Sehgal A. (2015). Drosophila TIM binds Importin α1, and acts as an adapter to transport PER to the nucleus. PLoS Genet 11: e1004974. PubMed ID: 25674790
Summary:
Regulated nuclear entry of clock proteins is a conserved feature of eukaryotic circadian clocks and serves to separate the phase of mRNA activation from mRNA repression in the molecular feedback loop. In Drosophila, nuclear entry of the clock proteins, Period (Per) and Timeless (Tim), is tightly controlled, and impairments of this process produce profound behavioral phenotypes. This study reports that nuclear entry of Per-Tim in clock cells, and consequently behavioral rhythms, require a specific member of a classic nuclear import pathway, Importin α1 (IMPα1). In addition to IMPα1, rhythmic behavior and nuclear expression of Per-Tim required a specific nuclear pore protein, Nup153, and Ran-GTPase. IMPα1 could also drive rapid and efficient nuclear expression of Tim and Per in cultured cells, although the effect on PER was mediated by TIM. Mapping of interaction domains between IMPα1 and Tim/Per suggested that Tim was the primary cargo for the importin machinery. This was supported by attenuated interaction of IMPα1 with Tim carrying a mutation previously shown to prevent nuclear entry of Tim and Per. Tim was detected at the nuclear envelope, and computational modeling suggested that it contains HEAT-ARM repeats typically found in karyopherins, consistent with its role as a co-transporter for Per. These findings suggested that although Per was the major timekeeper of the clock, Tim was the primary target of nuclear import mechanisms. Thus, the circadian clock uses specific components of the importin pathway with a novel twist in that Tim serves a karyopherin-like role for Per.

Kain, P. and Dahanukar, A. (2015). Secondary taste neurons that convey sweet taste and starvation in the Drosophila brain. Neuron [Epub ahead of print]. PubMed ID: 25661186
Summary:
The gustatory system provides vital sensory information to determine feeding and appetitive learning behaviors. Very little is known, however, about higher-order gustatory circuits in the highly tractable model for neurobiology, Drosophila melanogaster. This study reports second-order sweet gustatory projection neurons (sGPNs) in the Drosophila brain using a powerful behavioral screen. Silencing neuronal activity reduced appetitive behaviors, whereas inducible activation resulted in food acceptance via proboscis extensions. sGPNs showed functional connectivity with Gr5a+ sweet taste neurons and were activated upon sucrose application to the labellum. By tracing sGPN axons, the study identified the antennal mechanosensory and motor center (AMMC) as an immediate higher-order processing center for sweet taste. Interestingly, starvation increased sucrose sensitivity of the sGPNs in the AMMC, suggesting that hunger modulated the responsiveness of the secondary sweet taste relay. Together, these results provide a foundation for studying gustatory processing and its modulation by the internal nutrient state.

Hong, E. J. and Wilson, R. I. (2015). Simultaneous encoding of odors by channels with diverse sensitivity to inhibition. Neuron 85: 573-589. PubMed ID: 25619655
Summary:
Odorant receptors in the periphery map precisely onto olfactory glomeruli ("coding channels") in the brain. However, the odor tuning of a glomerulus is not strongly correlated with its spatial position. This raises the question of whether lateral inhibition between glomeruli is specific or nonspecific. This study shows that, in the Drosophila brain, focal activation of even a single glomerulus recruits GABAergic interneurons in all glomeruli. Moreover, the relative level of interneuron activity in different glomeruli is largely odor invariant. Although interneurons are recruited nonspecifically, glomeruli differ dramatically in their sensitivity to interneuron activity, and this is explained by their varying sensitivity to GABA. Interestingly, a stimulus is typically encoded in parallel by channels having high and low sensitivity to inhibition. Because lateral inhibition confers both costs and benefits, the brain might rely preferentially on "high" and "low" channels in different behavioral contexts.

Friday, February 13th

Rikhy, R., Mavrakis, M. and Lippincott-Schwartz, J. (2015). Dynamin regulates metaphase furrow formation and plasma membrane compartmentalization in the syncytial Drosophila embryo. Biol Open [Epub ahead of print]: PubMed ID: 25661871
Summary:
The successive nuclear division cycles in the syncytial Drosophila embryo are accompanied by ingression and regression of plasma membrane furrows, which surround individual nuclei at the embryo periphery, playing a central role in embryo compartmentalization prior to cellularization. This study demonstrates that cell cycle changes in dynamin localization and activity at the plasma membrane (PM) regulate metaphase furrow formation and PM organization in the syncytial embryo. Dynamin was localized on short PM furrows during interphase, mediating endocytosis of PM components. Dynamin redistributed off ingressed PM furrows in metaphase, correlating with stabilized PM components and the associated actin regulatory machinery on long furrows. Acute inhibition of dynamin in the temperature sensitive shibire mutant embryo resulted in morphogenetic consequences in the syncytial division cycle. These included inhibition of metaphase furrow ingression, randomization of proteins normally polarized to intercap PM and disruption of the diffusion barrier separating PM domains above nuclei. Based on these findings, the study proposes that cell cycle changes in dynamin orchestrate recruitment of actin regulatory machinery for PM furrow dynamics during the early mitotic cycles in the Drosophila embryo.

Winstanley, J., Sawala, A., Baldock, C. and Ashe, H.L. (2015). Synthetic enzyme-substrate tethering obviates the Tolloid-ECM interaction during Drosophila BMP gradient formation. Elife 4. PubMed ID: 25642644
Summary:
Members of the Tolloid family of metalloproteinases liberate BMPs from inhibitory complexes to regulate BMP gradient formation during embryonic dorsal-ventral axis patterning. This study determines mechanistically how Tolloid activity is regulated by its non-catalytic CUB domains in the Drosophila embryo. Tolloid, via its N-terminal CUB domains, interacted with Collagen IV, which enhanced Tolloid activity towards its substrate Sog, and facilitated Tsg-dependent stimulation of cleavage. In contrast, the two most C-terminal Tld CUB domains mediated Sog interaction to facilitate its processing as, based on structural data, Tolloid curvature positions bound Sog in proximity to the protease domain. Having ascribed functions to the Tolloid non-catalytic domains, the study recapitulated embryonic BMP gradient formation in their absence, by artificially tethering the Tld protease domain to Sog. The study highlights how the bipartite function of Tolloid CUB domains, in substrate and ECM interactions, fine-tune protease activity to a particular developmental context.

Staller, M. V., Fowlkes, C. C., Bragdon, M. D., Wunderlich, Z., Estrada, J. and DePace, A. H. (2015). A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate. Development 142: 587-596. PubMed ID: 25605785
Summary:
In developing embryos, gene regulatory networks drive cells towards discrete terminal fates, a process called canalization. This paper reports a study of the behavior of the anterior-posterior segmentation network in Drosophila melanogaster embryos by depleting a key maternal input, bicoid (bcd), and measuring gene expression patterns of the network at cellular resolution. This method results in a gene expression atlas containing the levels of mRNA or protein expression of 13 core patterning genes over six time points for every cell of the blastoderm embryo. This is the first cellular resolution dataset of a genetically perturbed Drosophila embryo that captures all cells in 3D. The technical developments are described that are required to build this atlas along with how the method can be employed and extended by others. This novel dataset was analyzed to characterize the degree and timing of cell fate canalization in the segmentation network. In two layers of this gene regulatory network, following depletion of bcd, individual cells rapidly canalize towards normal cell fates. This result supports the hypothesis that the segmentation network directly canalizes cell fate, rather than an alternative hypothesis whereby cells are initially mis-specified and later eliminated by apoptosis. The gene expression atlas provides a high resolution picture of a classic perturbation and will enable further computational modeling of canalization and gene regulation in this transcriptional network.

Drake, M., Furuta, T., Suen, K. M., Gonzalez, G., Liu, B., Kalia, A., Ladbury, J. E., Fire, A. Z., Skeath, J. B. and Arur, S. (2014). A requirement for ERK-dependent Dicer phosphorylation in coordinating oocyte-to-embryo transition in C. elegans. Dev Cell 31: 614-628. PubMed ID: 25490268
Summary:
Signaling pathways and small RNAs direct diverse cellular events, but few examples are known of defined signaling pathways directly regulating small RNA biogenesis. This study shows that ERK (see Drosophila Rolled) phosphorylates Dicer on two conserved residues in its RNase IIIb and double-stranded RNA (dsRNA)-binding domains and that phosphorylation of these residues is necessary and sufficient to trigger Dicer's nuclear translocation in worms, mice, and human cells. Phosphorylation of Dicer on either site inhibits Dicer function in the female germline and dampens small RNA repertoire. These data demonstrate that ERK phosphorylates and inhibits Dicer during meiosis I for oogenesis to proceed normally in Caenorhabditis elegans and that this inhibition is released before fertilization for embryogenesis to proceed normally. The conserved Dicer residues, their phosphorylation by ERK, and the consequences of the resulting modifications implicate an ERK-Dicer nexus as a fundamental component of the oocyte-to-embryo transition and an underlying mechanism coupling extracellular cues to small RNA production.

Thursday, February 12th

Bhandari, P., Song, M. and Dorn, G. W., (2014). Dissociation of mitochondrial from sarcoplasmic reticular stress in Drosophila cardiomyopathy induced by molecularly distinct mitochondrial fusion defects. J Mol Cell Cardiol 80C: 71-80. PubMed ID: 25555803
Summary: Mitochondrial dynamism (fusion and fission) is responsible for remodeling interconnected mitochondrial networks in some cell types. Adult cardiac myocytes lack mitochondrial networks, and their mitochondria are inherently "fragmented". Mitochondrial fusion/fission is so infrequent in cardiomyocytes as to not be observable under normal conditions, suggesting that mitochondrial dynamism may be dispensable in this cell type. However, cardiomyocyte-specific genetic suppression of mitochondrial fusion factors Optic atrophy 1 (Opa1) and mitofusin/MARF evokes cardiomyopathy in Drosophila hearts. It was posited that fusion-mediated remodeling of mitochondria may be critical for cardiac homeostasis, although never directly observed. Alternately, inner membrane Opa1 and outer membrane mitofusin/MARF might have other as-yet poorly described roles that affect mitochondrial and cardiac function. This study compared heart tube function in three models of mitochondrial fragmentation in Drosophila cardiomyocytes: Drp1 expression, Opa1 RNAi, and mitofusin MARF RNAi. Mitochondrial fragmentation evoked by enhanced Drp1-mediated fission did not adversely impact heart tube function. In contrast, RNAi-mediated suppression of either Opa1 or mitofusin/MARF induced cardiac dysfunction associated with mitochondrial depolarization and ROS production. Inhibiting ROS by overexpressing Superoxide dismutase (SOD) or suppressing ROMO1 prevented mitochondrial and heart tube dysfunction provoked by Opa1 RNAi, but not by mitofusin/MARF RNAi. In contrast, enhancing the ability of endoplasmic/sarcoplasmic reticulum to handle stress by expressing Xbp1 rescued the cardiomyopathy of mitofusin/MARF insufficiency without improving that caused by Opa1 deficiency. It is concluded that decreased mitochondrial size is not inherently detrimental to cardiomyocytes. Rather, preservation of mitochondrial function by Opa1 located on the inner mitochondrial membrane, and prevention of ER stress by mitofusin/MARF located on the outer mitochondrial membrane, are central functions of these "mitochondrial fusion proteins".

Khalil, B., El Fissi, N., Aouane, A., Cabirol-Pol, M. J., Rival, T. and Lievens, J. C. (2015). PINK1-induced mitophagy promotes neuroprotection in Huntington's disease. Cell Death Dis 6: e1617. PubMed ID: 25611391
Summary: Huntington's disease (HD) is a fatal neurodegenerative disorder caused by aberrant expansion of CAG repeat in the huntingtin gene. Mutant Huntingtin (mHtt) alters multiple cellular processes, leading to neuronal dysfunction and death. Among those alterations, impaired mitochondrial metabolism seems to have a major role in HD pathogenesis. In this study, the Drosophila model system was used to further investigate the role of mitochondrial damages in HD. The impact of mHtt on mitochondrial morphology was examined, and surprisingly, the formation of abnormal ring-shaped mitochondria was observed in photoreceptor neurons. Because such mitochondrial spheroids were previously detected in cells where mitophagy is blocked, the effect of PTEN-induced putative kinase 1 (PINK1), which controls Parkin-mediated mitophagy, was examined. Consistently, PINK1 overexpression was found to alleviate mitochondrial spheroid formation in HD flies. More importantly, PINK1 ameliorated ATP levels, neuronal integrity and adult fly survival, demonstrating that PINK1 counteracts the neurotoxicity of mHtt. This neuroprotection was Parkin-dependent and required mitochondrial outer membrane proteins, mitofusin/ and the voltage-dependent anion channel. Consistent with these observations in flies, it was demonstrated that the removal of defective mitochondria was impaired in HD striatal cells derived from HdhQ111 knock-in mice, and that overexpressing PINK1 in these cells partially restored mitophagy. The presence of mHtt did not affect Parkin-mediated mitochondrial ubiquitination but decreased the targeting of mitochondria to autophagosomes. Altogether, these findings suggest that mitophagy is altered in the presence of mHtt and that increasing PINK1/Parkin mitochondrial quality control pathway may improve mitochondrial integrity and neuroprotection in HD.

Omata, Y., Lim, Y. M., Akao, Y. and Tsuda, L. (2014). Age-induced reduction of autophagy-related gene expression is associated with onset of Alzheimer's disease. Am J Neurodegener Dis 3: 134-142. PubMed ID: 25628964
Summary: Aging is a major risk factor for Alzheimer's disease (AD). Aggregation of amyloid β (Aβ) in cerebral cortex and hippocampus is a hallmark of AD. Many factors have been identified as causative elements for onset and progression of AD; for instance, tau seems to mediate the neuronal toxicity of Aβ, and downregulation of macroautophagy (autophagy) is thought to be a causative element of AD pathology. Expression of autophagy-related genes is reduced with age, which leads to increases in oxidative stress and aberrant protein accumulation. This study found that expression of the autophagy-related genes atg1, atg8a, and atg18 in Drosophila melanogaster was regulated with aging as well as their own activities. In addition, the level of atg18 was maintained by dfoxo (foxo) and dsir2 (sir2) activities in concert with aging. These results indicate that some autophagy-related gene expression is regulated by foxo/sir2-mediated aging processes. It was further found that reduced autophagy activity correlated with late-onset neuronal dysfunction caused by neuronal induction of Aβ. These data support the idea that age-related dysfunction of autophagy is a causative element in onset and progression of AD.

Leshchiner, E. S., Parkhitko, A., Bird, G. H., Luccarelli, J., Bellairs, J. A., Escudero, S., Opoku-Nsiah, K., Godes, M., Perrimon, N. and Walensky, L. D. (2015). Direct inhibition of oncogenic KRAS by hydrocarbon-stapled SOS1 helices. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 25624485
Summary: Activating mutations in the Kirsten rat sarcoma viral oncogene homolog (KRAS) underlie the pathogenesis and chemoresistance of approximately 30% of all human tumors, yet the development of high-affinity inhibitors that target the broad range of KRAS mutants remains a formidable challenge. This study reports the development and validation of stabilized alpha helices of son of sevenless 1 (SAH-SOS1; see Drosophila Son of sevenless) as prototype therapeutics that directly inhibit wild-type and mutant forms of KRAS. SAH-SOS1 peptides bound in a sequence-specific manner to KRAS and its mutants, and dose-responsively blocked nucleotide association. Importantly, this functional binding activity correlated with SAH-SOS1 cytotoxicity in cancer cells expressing wild-type or mutant forms of KRAS. The mechanism of action of SAH-SOS1 peptides was demonstrated by sequence-specific down-regulation of the ERK-MAP kinase phosphosignaling cascade in KRAS-driven cancer cells and in a Drosophila melanogaster model of Ras85DV12 activation. These studies provide evidence for the potential utility of SAH-SOS1 peptides in neutralizing oncogenic KRAS in human cancer.

Wednesday, February 11th

Lipinszki, Z., Lefevre, S., Savoian, M. S., Singleton, M. R., Glover, D. M. and Przewloka, M. R. (2015). Centromeric binding and activity of Protein Phosphatase 4. Nat Commun 6: 5894. PubMed ID: 25562660
Summary: The cell division cycle requires tight coupling between protein phosphorylation and dephosphorylation. However, understanding the cell cycle roles of multimeric protein phosphatases has been limited by the lack of knowledge of how their diverse regulatory subunits target highly conserved catalytic subunits to their sites of action. Phosphoprotein phosphatase 4 (PP4) has been recently shown to participate in the regulation of cell cycle progression. This study finds that the EVH1 domain of the regulatory subunit 3 of Drosophila PP4, Falafel (Flfl), directly interacts with the centromeric protein C (CENP-C). Unlike other EVH1 domains that interact with proline-rich ligands, the crystal structure of the Flfl amino-terminal EVH1 domain bound to a CENP-C peptide reveals a new target-recognition mode for the phosphatase subunit. This study also shows that binding of Flfl to CENP-C is required to bring PP4 activity to centromeres to maintain CENP-C and attached core kinetochore proteins at chromosomes during mitosis.

Yu, Z., et al. (2015). Dynamic phosphorylation of CENP-A at ser68 orchestrates its cell-cycle-dependent deposition at centromeres. Dev Cell 32: 68-81. PubMed ID: 25556658
Summary: The H3 histone variant CENP-A (see Drosophila Centromere identifier) is an epigenetic marker critical for the centromere identity and function. However, the precise regulation of the spatiotemporal deposition and propagation of CENP-A at centromeres during the cell cycle is still poorly understood. This study shows that CENP-A is phosphorylated at Ser68 during early mitosis by Cdk1. These results demonstrate that phosphorylation of Ser68 eliminates the binding of CENP-A to the assembly factor HJURP, thus preventing the premature loading of CENP-A to the centromere prior to mitotic exit. Because Cdk1 activity is at its minimum at the mitotic exit, the ratio of Cdk1/PP1alpha activity changes in favor of Ser68 dephosphorylation, thus making CENP-A available for centromeric deposition by HJURP. Thus, this study reveals that dynamic phosphorylation of CENP-A Ser68 orchestrates the spatiotemporal assembly of newly synthesized CENP-A at active centromeres during the cell cycle.

Sabherwal, N., Thuret, R., Lea, R., Stanley, P. and Papalopulu, N. (2014). aPKC phosphorylates p27Xic1, providing a mechanistic link between apicobasal polarity and cell-cycle control. Dev Cell 31: 559-571. PubMed ID: 25490266
Summary: During the development of the nervous system, apicobasally polarized stem cells are characterized by a shorter cell cycle than nonpolar progenitors, leading to a lower differentiation potential of these cells. However, how polarization might be directly linked to the kinetics of the cell cycle is not understood. This study reports that apicobasally polarized neuroepithelial cells in Xenopus laevis have a shorter cell cycle than nonpolar progenitors, consistent with mammalian systems. The apically localized serine/threonine kinase aPKC (see Drosophila aPKC) directly phosphorylates an N-terminal site of the cell-cycle inhibitor p27Xic1 (see Drosophila Dacapo) and reduces its ability to inhibit the cyclin-dependent kinase 2 (Cdk2; see Drosophila Cdc2), leading to shortening of G1 and S phases. Overexpression of activated aPKC blocks the neuronal differentiation-promoting activity of p27Xic1. These findings provide a direct mechanistic link between apicobasal polarity and the cell cycle, which may explain how proliferation is favored over differentiation in polarized neural stem cells.

Powell, S. K., MacAlpine, H. K., Prinz, J. A., Li, Y., Belsky, J. A. and MacAlpine, D. M. (2015). Dynamic loading and redistribution of the Mcm2-7 helicase complex through the cell cycle. EMBO J [Epub ahead of print]. PubMed ID: 25555795
Summary: Eukaryotic replication origins are defined by the ORC-dependent loading of the Mcm2-7 helicase complex onto chromatin in G1. Paradoxically, there is a vast excess of Mcm2-7 relative to ORC assembled onto chromatin in G1. These excess Mcm2-7 complexes exhibit little co-localization with ORC or replication foci and can function as dormant origins. This study dissected the mechanisms regulating the assembly and distribution of the Mcm2-7 complex in the Drosophila genome. In the absence of cyclin E/Cdk2 activity, there was a 10-fold decrease in chromatin-associated Mcm2-7 relative to the levels found at the G1/S transition. The minimal amounts of Mcm2-7 loaded in the absence of cyclin E/Cdk2 activity were strictly localized to ORC binding sites. In contrast, cyclin E/Cdk2 activity was required for maximal loading of Mcm2-7 and a dramatic genome-wide reorganization of the distribution of Mcm2-7 that is shaped by active transcription. Thus, increasing cyclin E/Cdk2 activity over the course of G1 is not only critical for Mcm2-7 loading, but also for the distribution of the Mcm2-7 helicase prior to S-phase entry.

Tuesday, February 10th

Lu, W., Lakonishok, M. and Gelfand, V.I. (2015). Kinesin-1-powered microtubule sliding initiates axonal regeneration in Drosophila cultured neurons. Mol Biol Cell [Epub ahead of print]. PubMed ID: 25657321
Summary: Understanding the mechanism underlying axon regeneration is of great practical importance to develop therapeutic treatment for traumatic brain and spinal cord injuries. Dramatic cytoskeleton reorganization occurs at the injury site, and microtubules have been implicated in the regeneration process. Previously, these authors demonstrated that microtubule sliding by conventional kinesin (Kinesin-1) is required for initiation of neurite outgrowth in Drosophila embryonic neurons, and that sliding is developmentally down-regulated when neurite outgrowth is completed. This study reports that mechanical axotomy of Drosophila neurons in culture triggers axonal regeneration and regrowth. Regenerating neurons contained actively sliding microtubules; this sliding, like sliding during initial neurite outgrowth, was driven by Kinesin-1 and was required for axonal regeneration. The injury induced a fast spike of calcium, and depolymerization of microtubules near the injury site, and subsequent formation of local new microtubule arrays with mixed polarity. These events were required for reactivation of microtubule sliding at the initial stages of regeneration. Furthermore, c-Jun N-terminal kinase (JNK) pathway promoted regeneration by enhancing microtubule sliding in injured mature neurons.

Eom, T. Y., Stanco, A., Guo, J., Wilkins, G., Deslauriers, D., Yan, J., Monckton, C., Blair, J., Oon, E., Perez, A., Salas, E., Oh, A., Ghukasyan, V., Snider, W. D., Rubenstein, J. L. and Anton, E. S. (2014). Differential regulation of microtubule severing by APC underlies distinct patterns of projection neuron and interneuron migration. Dev Cell 31: 677-689. PubMed ID: 25535916
Summary: Coordinated migration of distinct classes of neurons to appropriate positions leads to the formation of functional neuronal circuitry in the cerebral cortex. The two major classes of cortical neurons, interneurons and projection neurons, utilize distinctly different modes (radial versus tangential) and routes of migration to arrive at their final positions in the cerebral cortex. this study shows that adenomatous polyposis coli (APC; see Drosophila APC) modulates microtubule (MT) severing in interneurons to facilitate tangential mode of interneuron migration, but not the glial-guided, radial migration of projection neurons. APC regulates the stability and activity of the MT-severing protein p60-katanin (see Drosophila Katanin-60) in interneurons to promote the rapid remodeling of neuronal processes necessary for interneuron migration. These findings reveal how severing and restructuring of MTs facilitate distinct modes of neuronal migration necessary for laminar organization of neurons in the developing cerebral cortex.

Rotty, J. D., Wu, C., Haynes, E. M., Suarez, C., Winkelman, J. D., Johnson, H. E., Haugh, J. M., Kovar, D. R. and Bear, J. E. (2015). Profilin-1 serves as a gatekeeper for actin assembly by arp2/3-dependent and -independent pathways. Dev Cell 32: 54-67. PubMed ID: 25543281
Summary: Cells contain multiple F-actin assembly pathways, including the Arp2/3 complex, formins, and Ena/VASP (see Drosophila Arpc1, Diaphanous and Enabled respectively), which have largely been analyzed separately. They collectively generate the bulk of F-actin from a common pool of G-actin; however, the interplay and/or competition between these pathways remains poorly understood. Using fibroblast lines derived from an Arpc2 conditional knockout mouse, matched-pair cells were established with and without the Arp2/3 complex. Arpc2-/- cells lack lamellipodia and migrate more slowly than WT cells but have F-actin levels indistinguishable from controls. Actin assembly in Arpc2-/- cells was resistant to cytochalasin-D and was highly dependent on profilin-1 (see Drosophila Chickadee) and Ena/VASP but not formins. Profilin-1 depletion in WT cells increased F-actin and Arp2/3 complex in lamellipodia. Conversely, addition of exogenous profilin-1 inhibited Arp2/3 complex actin nucleation in vitro and in vivo. Antagonism of the Arp2/3 complex by profilin-1 in cells appears to maintain actin homeostasis by balancing Arp2/3 complex-dependent and -independent actin assembly pathways.

Wakayama, Y., Fukuhara, S., Ando, K., Matsuda, M. and Mochizuki, N. (2015). Cdc42 mediates Bmp-induced sprouting angiogenesis through Fmnl3-driven assembly of endothelial filopodia in Zebrafish. Dev Cell 32: 109-122. PubMed ID: 25584797
Summary: During angiogenesis in vivo, endothelial cells (ECs) at the tips of vascular sprouts actively extend filopodia that are filled with bundles of linear actin filaments. To date, signaling pathways involved in the formation of endothelial filopodia have been studied using in-vitro-cultured ECs that behave differently from those in vivo. This study delineated a signaling pathway that governs the assembly of endothelial filopodia during angiogenic sprouting of the caudal vein plexus (CVP) in zebrafish. During CVP formation, bone morphogenetic protein induces the extension of endothelial filopodia and their migration via Arhgef9b-mediated activation of Cdc42 (see Drosophila Cdc2). Active Cdc42 binds to and stimulates Formin-like 3 (see Drosophila Diaphanous), an actin-regulatory protein of the formin family, which, in turn, promotes the extension of endothelial filopodia to facilitate angiogenic sprouting of the CVP. Thus, this study has elucidated molecular mechanisms underlying the formation of endothelial filopodia and their role in angiogenesis in vivo.

Monday, February 9th

Kumar, A., Gupta, T., Berzsenyi, S. and Giangrande, A. (2015). N-cadherin negatively regulates collective Drosophila glial migration via actin cytoskeleton remodeling. J Cell Sci. PubMed ID: 25593128
Summary: Cell migration is an essential and highly regulated process. During development, glia and neurons migrate over long distances, in most cases collectively, to reach their final destination and build the sophisticated architecture of the nervous system, the most complex tissue of the body. Collective migration is highly stereotyped and efficient, defects in the process leading to severe human diseases that include mental retardation. This dynamic process entails extensive cell communication and coordination, hence the real challenge is to analyze it in the whole organism and at cellular resolution. This study investigate the impact of the N-cadherin adhesion molecule on collective glial migration using the Drosophila developing wing and cell-type specific manipulation of gene expression. N-cadherin timely accumulates in glial cells and that its levels affect migration efficiency. N-cadherin works as a molecular brake in a dosage dependent manner by negatively controlling actin nucleation and cytoskeleton remodeling through α/β catenins. This is the first in vivo evidence for N-cadherin negatively and cell autonomously controlling collective migration.

Pflanz, R., Voigt, A., Yakulov, T. and Jackle, H. (2015). Drosophila gene tao-1 encodes proteins with and without a Ste20 kinase domain that affect cytoskeletal architecture and cell migration differently. Open Biol 5. PubMed ID: 25589578
Summary: Tao-1, the single representative of the Sterile 20 kinase subfamily in Drosophila, is best known for destabilizing microtubules at the actin-rich cortex, regulating the cytoskeletal architecture of cells. More recently, Tao-1 was shown to act in the Salvador-Warts-Hippo pathway by phosphorylating Hippo, regulating cell growth as well as cell polarity. This study shows that tao-1 encodes two proteins, one with the Sterile 20 kinase domain (Tao-L) and one without it (Tao-S), and that they act in an antagonistic manner. Tao-L expression causes lamellipodia-like cell protrusions, whereas Tao-S expression results in filopodia-like structures that make cells stick to the surface they attach to. Ectopic Tao-1 expression in the anterior region of Drosophila embryos results in pole cell formation as normally observed at the posterior end. Tao-S expression causes primordial germ cells (PGCs) to adhere to the inner wall of the gut primordia and prevents proper transepithelial migration to the gonads. Conversely, RNAi knockdowns of Tao-1 cause disordered migration of PGCs out of the gut epithelium, their dispersal within the embryo and cell death. The results reveal a novel function of Tao-1 in cell migration, which is based on antagonistic activities of two proteins encoded by a single gene.

Suarez, C., Carroll, R. T., Burke, T. A., Christensen, J. R., Bestul, A. J., Sees, J. A., James, M. L., Sirotkin, V. and Kovar, D. R. (2015). Profilin regulates F-Actin network homeostasis by favoring formin over Arp2/3 complex. Dev Cell 32: 43-53. PubMed ID: 25543282
Summary: Fission yeast cells use Arp2/3 (see Drosophila Arpc1) complex and formin (see Drosophila Diaphanous) to assemble diverse filamentous actin (F-actin) networks within a common cytoplasm for endocytosis, division, and polarization. Although these homeostatic F-actin networks are usually investigated separately, competition for a limited pool of actin monomers (G-actin) helps to regulate their size and density. However, the mechanism by which G-actin is correctly distributed between rival F-actin networks is not clear. Using a combination of cell biological approaches and in vitro reconstitution of competition between actin assembly factors, this study found that the small G-actin binding protein profilin (see Drosophila Profilin) directly inhibits Arp2/3 complex-mediated actin assembly. Profilin is therefore required for formin to compete effectively with excess Arp2/3 complex for limited G-actin and to assemble F-actin for contractile ring formation in dividing cells.

Wu, Y., Kanchanawong, P. and Zaidel-Bar, R. (2015). Actin-delimited adhesion-independent clustering of E-cadherin forms the nanoscale building blocks of adherens junctions. Dev Cell 32: 139-154. PubMed ID: 25600236
Summary: E-cadherin (see Drosophila Shotgun) is the major adhesion receptor in epithelial adherens junctions, which connect cells to form tissues and are essential for morphogenesis and homeostasis. The mechanism by which E-cadherin monomers cluster and become organized in adherens junctions remains poorly understood. Using superresolution microscopy techniques in combination with structure-informed functional mutations, this study found that loosely organized clusters of approximately five E-cadherin molecules that form independently of cis or trans interactions, and that are delimited by the cortical F-actin meshwork, are the precursors of trans-ligated adhesive clusters that make up the adherens junction. The density of E-cadherin clusters was wide ranged, and notably, densities consistent with the crystal lattice structure at the core of adhesive clusters were detected that were dependent on extracellular domain interactions. Thus, these results elucidate the nanoscale architecture of adherens junctions, as well as the molecular mechanisms driving its assembly.

Sunday, February 8th

de Madrid, B.H., Greenberg, L. and Hatini, V. (2015). RhoGAP68F controls transport of adhesion proteins in Rab4 endosomes to modulate epithelial morphogenesis of Drosophila leg discs. Dev Biol [Epub ahead of print]. PubMedID: 25617722
Summary: Elongation and invagination of epithelial tissues are fundamental developmental processes that contribute to the morphogenesis of embryonic and adult structures and are dependent on coordinated remodeling of cell-cell contacts. The morphogenesis of Drosophila leg imaginal discs depends on extensive remodeling of cell contacts and thus provides a useful system with which to investigate the underlying mechanisms. The small Rho GTPase regulator RhoGAP68F has been previously implicated in leg morphogenesis. It consists of an N-terminal Sec14 domain and a C-terminal GAP domain. This study examines the molecular function and role of RhoGAP68F in epithelial remodeling. Depletion of RhoGAP68F impaired epithelial remodeling from a pseudostratified to simple, while overexpression of RhoGAP68F caused tears of lateral cell-cell contacts and thus impaired epithelial integrity. The RhoGAP68F protein localized to Rab4 recycling endosomes and formed a complex with the Rab4 protein. The Sec14 domain was sufficient for localizing to Rab4 endosomes, while the activity of the GAP domain was dispensable. RhoGAP68F, in turn, inhibited the scission and movement of Rab4 endosomes involved in transport the adhesion proteins Fasciclin3 and E-cadherin back to cell-cell contacts. Expression of RhoGAP68F was upregulated during prepupal development suggesting that RhoGAP68F decreases the transport of key adhesion proteins to the cell surface during this developmental stage to decrease the strength of adhesive cell-cell contacts and thereby facilitate epithelial remodeling and leg morphogenesis.

Wu, J., Bakerink, K. J., Evangelista, M. E. and Thomas, G. H. (2014). Cytoplasmic capes are nuclear envelope intrusions that are enriched in endosomal proteins and depend upon betaH-spectrin and Annexin B9. PLoS One 9: e93680. PubMed ID: 24705398
Summary: It is increasingly recognized that non-erythroid spectrins have roles remote from the plasma membrane, notably in endomembrane trafficking. The large spectrin isoform, βH, partners with Annexin B9 to modulate endosomal processing of internalized proteins. This modulation is focused on the early endosome through multivesicular body steps of endocytic processing and loss of either protein appears to cause a traffic jam before removal of ubiquitin at the multivesicular body. It has been previously reported that betaH/Annexin B9 influenced EGF receptor signaling. While investigating this effect it was noticed that mSpitz, the membrane bound precursor of the secreted EGF receptor ligand sSpitz, is located in striking intrusions of the nuclear membrane. This study characterized these structures and identified them as 'cytoplasmic capes', which were previously identified in old ultrastructural studies and probably coincide with recently recognized sites of non-nuclear-pore RNA export. Thus study shows that cytoplasmic capes contain multiple endosomal markers and that their existence is dependent upon betaH and Annexin B9. Diminution of these structures does not lead to a change in mSpitz processing. These results extend the endosomal influence of betaH and its partner Annexin B9 to this unusual compartment at the nuclear envelope.

Morelli, E., Ginefra, P., Mastrodonato, V., Beznoussenko, G. V., Rusten, T. E., Bilder, D., Stenmark, H., Mironov, A. A. and Vaccari, T. (2014). Multiple functions of the SNARE protein Snap29 in autophagy, endocytic, and exocytic trafficking during epithelial formation in Drosophila. Autophagy: 0. PubMed ID: 25551675
Summary: How autophagic degradation is linked to endosomal trafficking routes is little known. This study screened a collection of uncharacterized Drosophila mutants affecting membrane transport to identify new genes that also have a role in autophagy. A loss of function mutant was isolated in Snap29 (Synaptosomal-associated protein 29 kDa), the gene encoding the Drosophila homolog of the human protein SNAP29; and its function was characterized in vivo. Snap29 contains 2 soluble NSF attachment protein receptor (SNARE) domains and a asparagine-proline-phenylalanine (NPF motif) at its N terminus and rescue experiments indicate that both SNARE domains are required for function, whereas the NPF motif is in part dispensable. Snap29 was found to interact with SNARE proteins, localizes to multiple trafficking organelles, and is required for protein trafficking and for proper Golgi apparatus morphology. Developing tissue lacking Snap29 displays distinctive epithelial architecture defects and accumulates large amounts of autophagosomes, highlighting a major role of Snap29 in autophagy and secretion. Mutants for autophagy genes do not display epithelial architecture or secretion defects, suggesting that the these alterations of the Snap29 mutant are unlikely to be caused by the impairment of autophagy. In contrast, evidence was found of elevated levels of hop-Stat92E (hopscotch-signal transducer and activator of transcription protein at 92E) ligand, receptor, and associated signaling, which might underlie the epithelial defects. In summary, these findings support a role of Snap29 at key steps of membrane trafficking, and predict that signaling defects may contribute to the pathogenesis of cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma (CEDNIK), a human congenital syndrome due to loss of Snap29

Nagaoka, T., Ohashi, R., Inutsuka, A., Sakai, S., Fujisawa, N., Yokoyama, M., Huang, Y. H., Igarashi, M. and Kishi, M. (2014). The Wnt/planar cell polarity pathway component Vangl2 induces synapse formation through direct control of N-cadherin. Cell Rep 6: 916-927. PubMed ID: 24582966
Summary: Although regulators of the Wnt/planar cell polarity (PCP) pathway are widely expressed in vertebrate nervous systems, their roles at synapses are unknown. This study shows that Vangl2 (Drosophila homolog; Van Gogh) is a postsynaptic factor crucial for synaptogenesis and that it coprecipitates with N-cadherin (see Drosophila Shotgun) and PSD-95 (see Drosophila Discs large) from synapse-rich brain extracts. Vangl2 directly binds N-cadherin and enhances its internalization in a Rab5-dependent manner. This physical and functional interaction is suppressed by β-catenin (see Drosophila Armadillo), which binds the same intracellular region of N-cadherin as Vangl2. In hippocampal neurons expressing reduced Vangl2 levels, dendritic spine formation as well as synaptic marker clustering is significantly impaired. Furthermore, Prickle2 (see Drosophila Prickle), another postsynaptic PCP component, inhibits the N-cadherin-Vangl2 interaction and is required for normal spine formation. These results demonstrate direct control of classic cadherin by PCP factors; this control may play a central role in the precise formation and maturation of cell-cell adhesions at the synapse

Saturday, January 7th

Walkinshaw, E., Gai, Y., Farkas, C., Richter, D., Nicholas, E., Keleman, K. and Davis, R.L. (2015). Identification of genes that promote or inhibit olfactory memory formation in Drosophila. Genetics [Epub ahead of print]. PubMed ID: 25644700
Summary: Genetic screens in Drosophila melanogaster and other organisms have been pursued in order to filter the genome for genetic functions important for memory formation. Such screens have employed primarily chemical or transposon-mediated mutagenesis and have identified numerous mutants including classical memory mutants, dunce and rutabaga. This study reports the results of a large screen using pan-neuronal RNAi expression to identify additional genes critical for memory formation. It identified more than 500 genes that compromised memory when inhibited (low hits), either by disrupting the development and normal function of the adult animal or by participating in the neurophysiological mechanisms underlying memory formation. It also identified more than 40 genes that enhanced memory when inhibited (high hits). The dunce gene was identified as one of the low hits and further experiments were performed to map the effects of the dunce RNAi to the α/β and γ mushroom body neurons. Additional behavioral experiments suggested that dunce knockdown in the mushroom body neurons impaired memory without significantly affecting acquisition. The study also characterized one high hit, sickie, to show that RNAi knockdown of this gene enhanced memory through effects in dopaminergic neurons without apparent effects on acquisition. These studies further understanding of two genes involved in memory formation, provide a valuable list of genes that impair memory that may be important for understanding the neurophysiology of memory or neurodevelopmental disorders and offer a new resource of memory suppressor genes that will aid in understanding restraint mechanisms employed by the brain to optimize resources.

Slater, G., Levy, P., Chan, K.L. and Larsen, C. (2015). A central neural pathway controlling odor tracking in Drosophila. J Neurosci 35: 1831-1848. PubMed ID: 25653345
Summary: Chemotaxis is important for the survival of most animals. How the brain translates sensory input into motor output beyond higher olfactory processing centers is largely unknown. This study describes a group of excitatory neurons, termed Odd neurons, which are important for Drosophila larval chemotaxis. Odd neurons received synaptic input from projection neurons in the calyx of the mushroom body and project axons to the central brain. Functional imaging showed that some of the Odd neurons responded to odor. Larvae in which Odd neurons were silenced were less efficient at odor tracking than controls and sampled the odor space more frequently. Larvae in which the excitability of Odd neurons was increased were better at odor intensity discrimination and odor tracking. Thus, the Odd neurons represent a distinct pathway that regulates the sensitivity of the olfactory system to odor concentrations, demonstrating that efficient chemotaxis depends on processing of odor strength downstream of higher olfactory centers.

Wolff, G. H. and Strausfeld, N. J. (2015). Genealogical correspondence of mushroom bodies across invertebrate phyla. Curr Biol 25: 38-44. PubMed ID: 25532890
Summary: Except in species that have undergone evolved loss, paired lobed centers referred to as "mushroom bodies" occur across invertebrate phyla. Unresolved is the question of whether these centers, which support learning and memory in insects, correspond genealogically or whether their neuronal organization suggests convergent evolution. Anatomical and immunohistological observations demonstrate that across phyla, mushroom body-like centers share a neuroanatomical ground pattern and proteins required for memory formation. Paired lobed or dome-like neuropils characterize the first brain segment (protocerebrum) of mandibulate and chelicerate arthropods and the nonganglionic brains of polychaete annelids, polyclad planarians, and nemerteans. Structural and cladistic analyses resolve an ancestral ground pattern common to all investigated taxa: chemosensory afferents supplying thousands of intrinsic neurons, the parallel processes of which establish orthogonal networks with feedback loops, modulatory inputs, and efferents. Shared ground patterns and their selective labeling with antisera against proteins required for normal mushroom body function in Drosophila are indicative of genealogical correspondence and thus an ancestral presence predating arthropod and lophotrochozoan origins. Implications of this are considered in the context of mushroom body function and early ecologies of ancestral bilaterians.

Kacsoh, B. Z., Bozler, J., Hodge, S., Ramaswami, M. and Bosco, G. (2015). Non-associative long-term memory formation in Drosophila requires mushroom body specific functions to maintain predator-induced changes in oviposition behavior. Genetics [Epub ahead of print]. PubMed ID: 25633088
Summary: Learning processes in Drosophila have been studied through the use of Pavlovian associative memory tests, and these paradigms have been extremely useful in identifying both genetic factors and neuroanatomical structures that are essential to memory formation. Whether these same genes and brain compartments also contribute to memory formed from non-associative experiences is not well understood. Exposures to environmental stressors such as predators are known to induce innate behavioral responses and can lead to new memory formation that allows a predator response to persist for days after the predator-threat has been removed. This study has utilized a unique form of non-associative behavior in Drosophila where female flies detect the presence of endoparasitoid predatory wasps and alter their oviposition behavior to lay eggs in food containing high levels of alcohol. The predator-induced change in fly oviposition preference is maintained for days after wasps are removed, and this persistence in behavior requires a minimum continuous exposure time of 14 hours. Maintenance of this behavior is dependent on multiple long-term memory genes, including orb2, dunce, rutabaga, amnesiac and Fmr1. Maintenance of the behavior also requires intact synaptic transmission of the mushroom body. Surprisingly, synaptic output from the mushroom body or the functions of any of these learning and memory genes are not required for the change in behavior when female flies are in constant contact with wasps. This suggests that perception of this predator that leads to an acute change in oviposition behavior is not dependent on the mushroom body or dependent on learning and memory gene functions. Because wasp induced oviposition behavior can last for days, its maintenance requires a functional mushroom body and the wild-type products of several known learning and memory genes, it is suggested that this constitutes a paradigm for a bona fide form of non-associative long-term memory that is not dependent on associated experiences.

Friday, February 6th

Alfa, R.W., Park, S., Skelly, K.R., Poffenberger, G., Jain, N., Gu, X., Kockel, L., Wang, J., Liu, Y., Powers, A.C. and Kim, S.K. (2015). Suppression of insulin production and secretion by a Decretin hormone. Cell Metab 21: 323-333. PubMed ID: 25651184
Summary: Decretins, hormones induced by fasting that suppress insulin production and secretion, have been postulated from classical human metabolic studies. From genetic screens, this study identified Drosophila Limostatin (Lst), a peptide hormone that suppresses insulin secretion. Lst is induced by nutrient restriction in gut-associated endocrine cells. limostatin deficiency leads to hyperinsulinemia, hypoglycemia, and excess adiposity. A conserved 15-residue polypeptide encoded by limostatin suppresses secretion by insulin-producing cells. Targeted knockdown of CG9918, a Drosophila ortholog of mammalian Neuromedin U receptors (NMURs), in insulin-producing cells phenocopied limostatin deficiency and attenuated insulin suppression by purified Lst, suggesting CG9918 encodes an Lst receptor. Human NMUR1 is expressed in islet &beta; cells, and purified NMU suppressed insulin secretion from human islets. A human mutant NMU variant that co-segregates with familial early-onset obesity and hyperinsulinemia failed to suppress insulin secretion. The study proposes Lst as an index member of an ancient hormone class called decretins, which suppress insulin output.

Merino, M. M., Rhiner, C., Lopez-Gay, J. M., Buechel, D., Hauert, B. and Moreno, E. (2015). Elimination of unfit cells maintains tissue health and prolongs lifespan. Cell [Epub ahead of print]. PubMed ID: 25601460
Summary: Viable yet damaged cells can accumulate during development and aging. Although eliminating those cells may benefit organ function, identification of this less fit cell population remains challenging. A previous study identified a molecular mechanism, based on 'fitness fingerprints' displayed on cell membranes, which allows direct fitness comparison among cells in Drosophila. This study addressed the physiological consequences of efficient cell selection for the whole organism. Fitness-based cell culling was found to be naturally used to maintain tissue health, delay aging, and extend lifespan in Drosophila. A gene, azot, was identified that ensures the elimination of less fit cells. Lack of azot increases morphological malformations and susceptibility to random mutations and accelerates tissue degeneration. On the contrary, improving the efficiency of cell selection is beneficial for tissue health and extends lifespan.

Luan, Z., Quigley, C. and Li, H. S. (2015). The putative Na(+)/Cl(-)-dependent neurotransmitter/osmolyte transporter Inebriated in the Drosophila hindgut is essential for the maintenance of systemic water homeostasis. Sci Rep 5: 7993. PubMed ID: 25613130
Summary: Most organisms are able to maintain systemic water homeostasis over a wide range of external or dietary osmolarities. The excretory system, composed of the kidneys in mammals and the Malpighian tubules and hindgut in insects, can increase water conservation and absorption to maintain systemic water homeostasis, which enables organisms to tolerate external hypertonicity or desiccation. However, the mechanisms underlying the maintenance of systemic water homeostasis by the excretory system have not been fully characterized. The present study found that the putative Na(+)/Cl(-)-dependent neurotransmitter/osmolyte transporter inebriated (ine) is expressed in the basolateral membrane of anterior hindgut epithelial cells. This was confirmed by comparison with a known basolateral localized protein, the alpha subunit of Na(+)-K(+) ATPase (ATPalpha). Under external hypertonicity, loss of ine in the hindgut epithelium results in severe dehydration without damage to the hindgut epithelial cells, implicating a physiological failure of water conservation/absorption. It was also found that hindgut expression of ine is required for water conservation under desiccating conditions. Importantly, specific expression of ine in the hindgut epithelium can completely restore disrupted systemic water homeostasis in ine mutants under both conditions. Therefore, ine in the Drosophila hindgut is essential for the maintenance of systemic water homeostasis.

von Stockum, S., Giorgio, V., Trevisan, E., Lippe, G., Glick, G. D., Forte, M. A., Da-Re, C., Checchetto, V., Mazzotta, G., Costa, R., Szabo, I. and Bernardi, P. (2014). F-ATPase of D. melanogaster forms 53 pS channels responsible for mitochondrial Ca2+-induced Ca2+ release. J Biol Chem [Epub ahead of print]. PubMed ID: 25550160
Summary: Mitochondria of Drosophila undergo Ca2+-induced Ca2+ release through a putative channel (mCrC) that has several regulatory features of the permeability transition pore (PTP). The PTP is an inner membrane channel that forms from F-ATPase, possessing a conductance of 500 pS in mammals and of 300 pS in yeast. In contrast to the PTP, the mCrC of Drosophila is not permeable to sucrose and appears to be selective for Ca2+ and H+. This study shows (1) that like the PTP, the mCrC is affected by the sense of rotation of F-ATPase, by Bz-423 and Mg2+/ADP; (2) that expression of human cyclophilin D in mitochondria of Drosophila S2R+ cells sensitizes the mCrC to Ca2+ but does not increase its apparent size; and (3) that purified dimers of Drosophila F-ATPase reconstituted into lipid bilayers form 53 pS channels activated by Ca2+ and thiol oxidants, and inhibited by Mg2+/gamma-imino ATP. These findings indicate that the mCrC is the 'PTP' of Drosophila, and that the signature conductance of F-ATPase channels depends on unique structural features that may underscore specific roles in different species.

Thursday, February 5th

Yang, C.C., Graves, H.K., Moya, I.M., Tao, C., Hamaratoglu, F., Gladden, A.B. and Halder, G. (2015). Differential regulation of the Hippo pathway by adherens junctions and apical-basal cell polarity modules. Proc Natl Acad Sci USA [Epub ahead of print]. PubMed ID: 25624491
Summary: Adherens junctions (AJs) and cell polarity complexes are key players in the establishment and maintenance of apical-basal cell polarity. Loss of AJs or basolateral polarity components promotes tumor formation and metastasis. Recent studies in vertebrate models show that loss of AJs or loss of the basolateral component Scribble (Scrib) cause deregulation of the Hippo tumor suppressor pathway and hyperactivation of its downstream effectors Yes-associated protein (YAP; see Drosophila Yorkie) and Transcriptional coactivator with PDZ-binding motif (TAZ). However, whether AJs and Scrib act through the same or independent mechanisms to regulate Hippo pathway activity is not known. This study dissects how disruption of AJs or loss of basolateral components affect the activity of the Drosophila YAP homolog Yorkie (Yki) during imaginal disc development. Surprisingly, disruption of AJs and loss of basolateral proteins produced very different effects on Yki activity. Yki activity was cell-autonomously decreased but non-cell-autonomously elevated in tissues where the AJ components E-cadherin (E-cad) or α catenin (α-cat) were knocked down. In contrast, scrib knockdown caused a predominantly cell-autonomous activation of Yki. Moreover, disruption of AJs or basolateral proteins had different effects on cell polarity and tissue size. Simultaneous knockdown of &alpha;-cat and scrib induced both cell-autonomous and non-cell-autonomous Yki activity. In mammalian cells, knockdown of E-cad or α-cat caused nuclear accumulation and activation of YAP without overt effects on Scrib localization and vice versa. Therefore, these results indicate the existence of multiple, genetically separable inputs from AJs and cell polarity complexes into Yki/YAP regulation.

Zadorozny, E. V., Little, J. C. and Kalderon, D. (2015). Contributions of Costal 2-Fused interactions to Hedgehog signaling in Drosophila. Development [Epub ahead of print]. PubMed ID: 25633354
Summary: The Drosophila kinesin-family protein Costal 2 (Cos2) and its mammalian ortholog Kif7 play dual roles in Hedgehog (Hh) signaling. In the absence of Hh, Cos2 and Kif7 contribute to proteolytic processing and silencing of the Hh-regulated transcription factors, Drosophila Cubitus interruptus (Ci) and mammalian Gli proteins. Cos2 and Kif7 are also necessary for full activation of full-length Ci-155 and Gli transcription factors in response to Hh proteins. This study used classical fused alleles and transgenic Cos2 products deficient for Fused (Fu) association to show that Cos2 must bind to Fu to support efficient Ci-155 processing. Residual Ci-155 processing in the absence of Cos2-Fu interaction did not require Suppressor of Fused, which has been implicated in processing mammalian Gli proteins. Evidence is provided that Cos2 binding to the CORD domain of Ci-155 contributes to both Ci-155 processing and Ci-155 silencing in the absence of Hh. In the presence of Hh, Ci-155 processing is blocked and Cos2 now promotes activation of Ci-155, which requires Fu kinase activity. Normal Ci-155 activation by Hh was shown to require Cos2 binding to Fu, supporting the hypothesis that Cos2 mediates the apposition of Fu molecules suitable for cross-phosphorylation and consequent full activation of Fu kinase. Phosphorylation of Cos2 by Fu at two previously mapped sites, S572 and S931, which is thought to mediate Ci-155 activation, is not required for normal activation of Ci-155 by Hh or by activated Fu.

Chakrabarti, P., Kolay, S., Yadav, S., Kumari, K., Nair, A., Trivedi, D. and Raghu, P. (2015). A dPIP5K dependent pool of Phosphatidylinositol 4,5 Bisphosphate (PIP2) is required for G-Protein coupled signal transduction in Drosophila photoreceptors. PLoS Genet 11: e1004948. PubMed ID: 25633995
Summary: Multiple PIP2 dependent molecular processes including receptor activated phospholipase C activity occur at the neuronal plasma membranes, yet levels of this lipid at the plasma membrane are remarkably stable. Although the existence of unique pools of PIP2 supporting these events has been proposed, the mechanism by which they are generated is unclear. In Drosophila photoreceptors, the hydrolysis of PIP2 by G-protein coupled phospholipase C activity is essential for sensory transduction of photons. This study identified dPIP5K as an enzyme essential for PIP2 re-synthesis in photoreceptors. Loss of dPIP5K causes profound defects in the electrical response to light and light-induced PIP2 dynamics at the photoreceptor membrane. Overexpression of dPIP5K was able to accelerate the rate of PIP2 synthesis following light induced PIP2 depletion. Other PIP2 dependent processes such as endocytosis and cytoskeletal function were unaffected in photoreceptors lacking dPIP5K function. These results provide evidence for the existence of a unique dPIP5K dependent pool of PIP2 required for normal Drosophila phototransduction. These results define the existence of multiple pools of PIP2 in photoreceptors generated by distinct lipid kinases and supporting specific molecular processes at neuronal membranes.

Cook, M., Bolkan, B. J. and Kretzschmar, D. (2014). Increased actin polymerization and stabilization interferes with neuronal function and survival in the AMPKgamma mutant Loechrig. PLoS One 9: e89847. PubMed ID: 24587072
Summary: loechrig (loe) mutant flies are characterized by progressive neuronal degeneration, behavioral deficits, and early death. The mutation is due to a P-element insertion in the gene for the γ-subunit of the trimeric AMP-activated protein kinase (AMPK) complex, whereby the insertion affects only one of several alternative transcripts encoding a unique neuronal isoform. AMPK is a cellular energy sensor that regulates a plethora of signaling pathways, including cholesterol and isoprenoid synthesis via its downstream target hydroxy-methylglutaryl (HMG)-CoA reductase. Recent studies have shown that loe interferes with isoprenoid synthesis and increases the prenylation and thereby activation of RhoA. During development, RhoA plays an important role in neuronal outgrowth by activating a signaling cascade that regulates actin dynamics. This study shows that the effect of loe/AMPKγ on RhoA prenylation leads to a hyperactivation of this signaling pathway, causing increased phosphorylation of the actin depolymerizating factor cofilin and accumulation of filamentous actin. Furthermore, the results show that the resulting cytoskeletal changes in loe interfere with neuronal growth and disrupt axonal integrity. Surprisingly, these phenotypes were enhanced by expressing the Slingshot (SSH) phosphatase, which during development promotes actin depolymerization by dephosphorylating cofilin. However, these studies suggest that in the adult SSH promotes actin polymerization, supporting in vitro studies using human SSH1 that suggested that SSH can also stabilize and bundle filamentous actin. Together with the observed increase in SSH levels in the loe mutant, these experiments suggest that in mature neurons SSH may function as a stabilization factor for filamentous actin instead of promoting actin depolymerization.

Wednesday, February 4th

Bonfini, A., Wilkin, M.B. and Baron, M. (2015). Reversible regulation of stem cell niche size associated with dietary control of Notch signalling. BMC Dev Biol [Epub ahead of print]. PubMed ID: 25637382
Summary: Stem cells can respond to environmental and physiological inputs to adaptively remodel tissues. Little is known about whether stem cell niches are similarly responsive. The Drosophila ovary germline stem cell (GSC) niche is a well-studied model, which is comprised of cap cells that provide anchorage and maintenance signals for GSCs to maintain oogenesis. Previous studies have shown a strong link between diet and the regulation of oogenesis, making this a useful model system in which to investigate dietary regulation of the niche and its associated stem cells. This study shows that the Drosophila ovary GSC cap cell niche is a dynamic structure, which can contract and expand in fluctuating dietary conditions. Cap cells were lost when adult flies were shifted to nutrient poor diet and were restored after returning flies to nutrient-rich medium. Notch signalling in cap and escort cells was similarly reduced and restored by dietary shifts to nutrient poor and rich media. In old flies decreased Notch signalling was associated with decreased robustness of the niche to dietary changes. The study demonstrated using a Notch temperature sensitive allele that removal and restoration of Notch signalling also led to a reduction and re-expansion of the niche. Changes in niche size were not associated with apoptosis or cell division. Two distinct roles for Notch were identified in the adult germarium. Notch could act in cap cells to prevent their loss while activation of Notch in the flanking escort cells resulted in expansion of the niche. This study provided evidence that dietary changes alone were sufficient to alter Notch signalling and reversibly change niche size in the adult in wild type flies. It showed that Notch acted in different cells to maintain and re-expand the niche and proposed a model in which cell fate transitions between cap cells and flanking somatic cells accounted for niche dynamics. These findings reveal an unexpected reversible plasticity of the GSC niche whose responses provide an integrated read out of the physiological status of the fly that is modulated by diet and age.

Lengil, T., Gancz, D. and Gilboa, L. (2015). Activin signaling balances proliferation and differentiation of ovarian niche precursors and enables adjustment of niche numbers. Development [Epub ahead of print]. PubMed ID: 25633355
Summary: How the numbers of niches and resident stem cells within a particular organ are determined during development and how they may be modulated or corrected is a question with significant medical implications. In the larval ovary of Drosophila melanogaster, somatic precursors for niches, and germ cells that will become germline stem cells, co-develop. Somatic precursors proliferate during the first 3 days of larval development. By mid-third instar, adult terminal filament (TF) (part of the germline stem cell niche) cells first appear, and differentiation terminates 24 h later when 16-20 TFs fully form. The developmental sequence responsible for TF cell determination and final TF numbers is only partially understood. This study shows that TF formation proceeds through several, hitherto uncharacterized stages, which include an early exit from the cell cycle to form TF precursors and two steps of cell shape change to form the mature TF cells. The Activin receptor Baboon (Babo) is required for somatic precursor cell proliferation and therefore determines the pool of TF precursors available for TF differentiation. During the final differentiation stage, Babo facilitates TF and germ cell differentiation, and promotes the accumulation of Broad-Z1, which is also a target of the steroid hormone ecdysone. Epistasis analysis shows that Activin controls cell proliferation in an ecdysone-independent manner and TF differentiation by affecting ecdysone targets. It is further proposed that this mode of function allows Activin to balance proliferation and differentiation, and to equilibrate niche numbers. These results suggest a novel model for how niche numbers are corrected during development.

Sarikaya, D.P. and Extavour, C.G. (2015). The Hippo pathway regulates homeostatic growth of stem cell niche precursors in the Drosophila ovary. PLoS Genet 11: e1004962. PubMed ID: 25643260
Summary: The Hippo pathway regulates organ size, stem cell proliferation and tumorigenesis in adult organs. Whether the Hippo pathway influences establishment of stem cell niche size to accommodate changes in organ size, however, has received little attention. This study asks whether Hippo signaling influences the number of stem cell niches that are established during development of the Drosophila larval ovary, and whether it interacts with the same or different effector signaling pathways in different cell types. Canonical Hippo signaling regulated autonomous proliferation of the soma, while a novel hippo-independent activity of Yorkie regulated autonomous proliferation of the germ line. Hippo signaling mediates non-autonomous proliferation signals between germ cells and somatic cells, and contributes to maintaining the correct proportion of these niche precursors. Finally, the Hippo pathway interacts with different growth pathways in distinct somatic cell types, and interacted with EGFR and JAK/STAT pathways to regulate non-autonomous proliferation of germ cells. The study provides evidence for novel roles of the Hippo pathway in establishing the precise balance of soma and germ line, the appropriate number of stem cell niches, and ultimately regulating adult female reproductive capacity.

Eikenes, A. H., Malerod, L., Christensen, A. L., Steen, C. B., Mathieu, J., Nezis, I. P., Liestol, K., Huynh, J. R., Stenmark, H. and Haglund, K. (2015). ALIX and ESCRT-III coordinately control cytokinetic abscission during germline stem cell division in vivo. PLoS Genet 11: e1004904. PubMed ID: 25635693
Summary: Abscission is the final step of cytokinesis that involves the cleavage of the intercellular bridge connecting the two daughter cells. Recent studies have given novel insight into the spatiotemporal regulation and molecular mechanisms controlling abscission in cultured yeast and human cells. The mechanisms of abscission in living metazoan tissues are however not well understood. This study shows that ALIX and the ESCRT-III component Shrub are required for completion of abscission during Drosophila female germline stem cell (fGSC) division. Loss of ALIX or Shrub function in fGSCs leads to delayed abscission and the consequent formation of stem cysts in which chains of daughter cells remain interconnected to the fGSC via midbody rings and fusome. ALIX and Shrub interact and that they co-localize at midbody rings and midbodies during cytokinetic abscission in fGSCs. Mechanistically, this study shows that the direct interaction between ALIX and Shrub is required to ensure cytokinesis completion with normal kinetics in fGSCs. It is concluded that ALIX and ESCRT-III coordinately control abscission in Drosophila fGSCs and that their complex formation is required for accurate abscission timing in GSCs in vivo.

Tuesday, February 3rd

Li, Z., Liu, S. and Cai, Y. (2015). EGFR/MAPK signaling regulates the proliferation of Drosophila renal and nephric stem cells. J Genet Genomics 42: 9-20. PubMed ID: 25619598
Summary: Tissue homeostasis, accomplished through the self-renewal and differentiation of resident stem cells, is critical for the maintenance of adult tissues throughout an animal's lifetime. Adult Drosophila Malpighian tubules (MTs or fly kidney) are maintained by renal and nephric stem cells (RNSCs) via self-renewing divisions, however, it is unclear how RNSC proliferation and differentiation are regulated. This study shows that EGFR/MAPK signaling is dispensable for RNSC maintenance, but required for RNSC proliferation in vivo. Inactivation of the EGFR/MAPK pathway blocked or greatly retarded RNSC cell cycle progression; conversely, over-activation of EGFR/MAPK signaling resulted in RNSC over-proliferation and disrupted the normal differentiation of renablasts (RBs), the immediate daughters of RNSC divisions. The data further suggest that EGFR/MAPK signaling functioned independently of JAK/STAT signaling and that dMyc and CycE partially mediated EGFR/MAPK signaling in MTs. Together, the data suggests a principal role of EGFR/MAPK signaling in regulating RNSC proliferation, which may provide important clues for understanding mammalian kidney repair and regeneration following injury.

Laws, K. M., Sampson, L. L. and Drummond-Barbosa, D. (2015). Insulin-independent role of adiponectin receptor signaling in Drosophila germline stem cell maintenance. Dev Biol [Epub ahead of print]. PubMed ID: 25576925
Summary: Adipocytes have a key endocrine role, mediated in large part by secreted protein hormones termed adipokines. The adipokine adiponectin is well known for its role in sensitizing peripheral tissues to insulin, and several lines of evidence suggest that adiponectin might also modulate stem cells/precursors. It remains unclear, however, how adiponectin signaling controls stem cells and whether this role is secondary to its insulin-sensitizing effects or distinct. Drosophila adipocytes also function as an endocrine organ and, although no obvious adiponectin homolog has been identified, Drosophila AdipoR encodes a well-conserved homolog of mammalian adiponectin receptors. This study generated a null AdipoR allele and used clonal analysis to demonstrate an intrinsic requirement for AdipoR in germline stem cell (GSC) maintenance in the Drosophila ovary. AdipoR null GSCs are not fully responsive to bone morphogenetic protein ligands from the niche and have a slight reduction of E-cadherin at the GSC-niche junction. Conversely, germline-specific overexpression of AdipoR inhibits natural GSC loss, suggesting that reduction in adiponectin signaling might contribute to the normal decline in GSC numbers observed over time in wild-type females. Surprisingly, AdipoR is not required for insulin sensitization of the germline, leading to a speculation that insulin sensitization is a more recently acquired function than stem cell regulation in the evolutionary history of adiponectin signaling. These findings establish Drosophila female GSCs as a new system for future studies addressing the molecular mechanisms whereby adiponectin receptor signaling modulates stem cell fate.

Loza-Coll, M. A., Southall, T. D., Sandall, S. L., Brand, A. H. and Jones, D. L. (2014). Regulation of Drosophila intestinal stem cell maintenance and differentiation by the transcription factor Escargot. EMBO J [Epub ahead of print]. PubMed ID: 25433031
Summary: Tissue stem cells divide to self-renew and generate differentiated cells to maintain homeostasis. Although influenced by both intrinsic and extrinsic factors, the genetic mechanisms coordinating the decision between self-renewal and initiation of differentiation remain poorly understood. The escargot (esg) gene encodes a transcription factor that is expressed in stem cells in multiple tissues in Drosophila melanogaster, including intestinal stem cells (ISCs). This study demonstrates that Esg plays a pivotal role in intestinal homeostasis, maintaining the stem cell pool while influencing fate decisions through modulation of Notch activity. Loss of esg induced ISC differentiation, a decline in Notch activity in daughter enteroblasts (EB), and an increase in differentiated enteroendocrine (EE) cells. Amun, an inhibitor of Notch in other systems, was identified as a target of Esg in the intestine. Decreased expression of esg resulted in upregulation of Amun, while downregulation of Amun rescued the ectopic EE cell phenotype resulting from loss of esg. Thus, these findings provide a framework for further comparative studies addressing the conserved roles of Snail factors in coordinating self-renewal and differentiation of stem cells across tissues and species.

Lu, Y. and Li, Z. (2015). Notch signaling downstream target E(spl)mβ is dispensable for adult midgut homeostasis in Drosophila. Gene [Epub ahead of print]. PubMed ID: 25637572
Summary: Adult tissue homeostasis is maintained by residential stem cells through the proper balance of stem cell self-renewal and differentiation. The adult midgut of Drosophila contains multipotent intestinal stem cells (ISCs), and Notch signaling plays critical roles in the proliferation and differentiation of these ISCs. However, how Notch signaling downstream targets regulate ISC proliferation and differentiation still remains unclear. This study finds that Notch signaling downstream targets E(spl)mβ and E(spl)mα are differentially expressed in ISCs and their progeny. Interestingly, midgut homeostasis was not affected in E(spl)mβ null mutant. No obvious defects were observed in the intestines ectopically expressing E(spl)mβ or E(spl)mα. Importantly, the defects in ISC proliferation and differentiation observed in Notch mutant could not be rescued by ectopic expression of E(spl)mβ or E(spl)mα. Together, these data indicate that the proliferation and differentiation of ISCs are not regulated by individual Notch downstream targets, but by different downstream targets collectively.

Monday, February 2nd

Kavi, H., Lu, X., Xu, N., Bartholdy, B.A., Vershilova, E., Skoultchi, A.I. and Fyodorov, D.V. (2015). A genetic screen and transcript profiling reveal a shared regulatory program for Drosophila linker Histone H1 and chromatin remodeler CHD1. G3 (Bethesda) [Epub ahead of print]. PubMed ID: 25628309
Summary: Chromatin structure and activity can be modified through ATP-dependent repositioning of nucleosomes and post-translational modifications of core histone tails within nucleosome core particles and by deposition of linker histones into the oligonucleosome fiber. The linker histone H1 is essential in metazoans. It has a profound effect on organization of chromatin into higher-order structures and on recruitment of histone-modifying enzymes to chromatin. This study describes a genetic screen for modifiers of the lethal phenotype caused by depletion of H1 in Drosophila melanogaster. It identified 41 mis-expression alleles that enhanced and 20 that suppressed the effect of His1 depletion in vivo. Most of them were important for chromosome organization, transcriptional regulation and cell signaling. Specifically, the reduced viability of H1-depleted animals was strongly suppressed by ubiquitous mis-expression of the ATP-dependent chromatin remodeling enzyme CHD1. Comparison of transcript profiles in H1-depleted and Chd1 null mutant larvae revealed that H1 and CHD1 had common transcriptional regulatory programs in vivo. H1 and CHD1 share roles in repression of numerous developmentally regulated and extracellular stimulus-responsive transcripts, including immunity- and stress response-related genes. Thus, linker histone H1 participates in various regulatory programs in chromatin to alter gene expression.

Gambetta, M. C. and Muller, J. (2014). O-GlcNAcylation prevents aggregation of the Polycomb group repressor polyhomeotic. Dev Cell 31: 629-639. PubMed ID: 25468754
Summary: The glycosyltransferase Ogt adds O-linked N-Acetylglucosamine (O-GlcNAc) moieties to nuclear and cytosolic proteins. Drosophila embryos lacking Ogt protein arrest development with a remarkably specific Polycomb phenotype, arising from the failure to repress Polycomb target genes. The Polycomb protein Polyhomeotic (Ph), an Ogt substrate, forms large aggregates in the absence of O-GlcNAcylation both in vivo and in vitro. O-GlcNAcylation of a serine/threonine (S/T) stretch in Ph is critical to prevent nonproductive aggregation of both Drosophila and human Ph via their C-terminal sterile alpha motif (SAM) domains in vitro. Full Ph repressor activity in vivo requires both the SAM domain and O-GlcNAcylation of the S/T stretch. Ph mutants lacking the S/T stretch reproduce the phenotype of ogt mutants, suggesting that the S/T stretch in Ph is the key Ogt substrate in Drosophila. It is proposed that O-GlcNAcylation is needed for Ph to form functional, ordered assemblies via its SAM domain.

Stern, S., Snir, O., Mizrachi, E., Galili, M., Zaltsman, I. and Soen, Y. (2014). Reduction in maternal Polycomb levels contributes to transgenerational inheritance of a response to toxic stress in flies. J Physiol 592: 2343-2355. PubMed ID: 24535443
Summary: Transgenerational persistence of parental responses to environmental stimuli has been reported in various organisms, but the underlying mechanisms remain underexplored. In one of these reported examples, it was shown that exposure of fly larvae to G418 antibiotic leads to non-Mendelian inheritance of ectopic induction of certain developmental genes. This study investigated if this inheritance involves changes in mRNA composition within the early, maternal-stage offspring embryos of exposed flies. Exposure to G418 in F1 modified the maternal RNA levels of many genes in their early (F2) embryos. This includes reduction of maternal Polycomb group genes which persisted in the following generation of embryos (F3). To investigate the functional meaning of this reduction, genetically normal embryos of Polycomb mutant females were compared to normal embryos of normal females. Analysis with two different alleles of Polycomb, Pc1 and Pc3, revealed that maternal reduction in Polycomb gene dosage has a positive influence on the inheritance of induced expression. Together, this shows that exposure to G418 stress reduces the maternal levels of Polycomb in the offspring embryos and this reduction contributes to the inheritance of induced expression.

Feller, C., Forne, I., Imhof, A. and Becker, P. B. (2015). Global and specific responses of the histone acetylome to systematic perturbation. Mol Cell [Epub ahead of print]. PubMed ID: 25578876
Summary: Regulation of histone acetylation is fundamental to the utilization of eukaryotic genomes in chromatin. Aberrant acetylation contributes to disease and can be clinically combated by inhibiting the responsible enzymes. Knowledge of the histone acetylation system is patchy because the methodology to describe acetylation patterns and their genesis by integrated enzyme activities has been lacking. This study devised a generally applicable, mass spectrometry-based strategy to precisely and accurately quantify combinatorial modification motifs. This was applied to generate a comprehensive inventory of acetylation motifs on histones H3 and H4 in Drosophila cells. Systematic depletion of known or suspected acetyltransferases and deacetylases revealed specific alterations of histone acetylation signatures, established enzyme-substrate relationships, and unveiled an extensive crosstalk between neighboring modifications. Unexpectedly, overall histone acetylation levels remained remarkably constant upon depletion of individual acetyltransferases. Conceivably, the acetylation level is adjusted to maintain the global charge neutralization of chromatin and the stability of nuclei.

Sunday, February 1st

Eirin-Lopez, J. M. and Sanchez, L. (2015). The comparative study of five sex-determining proteins across insects unveils high rates of evolution at basal components of the sex determination cascade. Dev Genes Evol [Epub ahead of print]. PubMed ID: 25613749
Summary: In insects, the sex determination cascade is composed of genes that interact with each other in a strict hierarchical manner, constituting a coadapted gene complex built in reverse order from bottom to top. Accordingly, ancient elements at the bottom are expected to remain conserved ensuring the correct functionality of the cascade. The present work studied the levels of variation displayed by five key components of the sex determination cascade across 59 insect species, including Sex-lethal, transformer, transformer-2, fruitless, doublesex, and sister-of-Sex-lethal (a paralog of Sxl encompassing sex-independent functions). Surprisingly, the results reveal that basal components of the cascade (doublesex, fruitless) seem to evolve more rapidly than previously suspected. Indeed, in the case of Drosophila, these proteins evolve more rapidly than the master regulator Sex-lethal. These results agree with the notion suggesting that genes involved in early aspects of development will be more constrained due to the large deleterious pleiotropic effects of mutations, resulting in increased levels of purifying selection at top positions of the cascade. The analyses of the selective episodes involved in the recruitment of Sxl into sex-determining functions further support this idea, suggesting the presence of bursts of adaptive selection in the common ancestor of drosophilids, followed by the onset of purifying selection preserving the master regulatory role of this protein on top of the Drosophila sex determination cascade. Altogether, these results underscore the importance of the position of sex determining genes in the cascade, constituting a major constraint shaping the molecular evolution of the insect sex determination pathway.

Guillen, Y., et al. (2014). Genomics of ecological adaptation in cactophilic Drosophila. Genome Biol Evol. PubMed ID: 25552534
Summary: Cactophilic Drosophila species provide a valuable model to study gene-environment interactions and ecological adaptation. D. buzzatii and D. mojavensis are two cactophilic species that belong to the repleta group, but have very different geographical distributions and primary host plants. To investigate the genomic basis of ecological adaptation, the genome and developmental transcriptome of D. buzzatii was sequence and its gene content was compared to that of D. mojavensis and two other non-cactophilic Drosophila species in the same subgenus. The newly sequenced D. buzzatii genome (161.5 Mb) comprises 826 scaffolds (> 3 kb) and contains 13,657 annotated protein-coding genes. Using RNA-Seq data of five life-stages, expression was found of 15,026 genes, 80% protein-coding genes and 20% ncRNA genes. In total, 1,294 genes were found putatively under positive selection. Interestingly, among genes under positive selection in the D. mojavensis lineage, there is an excess of genes involved in metabolism of heterocyclic compounds that are abundant in Stenocereus cacti and toxic to nonresident Drosophila species. 117 orphan genes were found in the shared D. buzzatii-D. mojavensis lineage. In addition, gene duplication analysis identified lineage-specific expanded families with functional annotations associated with proteolysis, zinc ion binding, chitin binding, sensory perception, ethanol tolerance, immunity, physiology and reproduction. In summary this study identified genetic signatures of adaptation in the shared D. buzzatii-D. mojavensis lineage, and in the two separate D. buzzatii and D. mojavensis lineages. Many of the novel lineage-specific genomic features are promising candidates for explaining the adaptation of these species to their distinct ecological niches.

Chakraborty, M. and Fry, J. D. (2015). Parallel functional changes in independent testis-specific duplicates of Aldehyde dehydrogenase in Drosophila. Mol Biol Evol [Epub ahead of print]. PubMed ID: 25564519
Summary: A large proportion of duplicates, originating from ubiquitously expressed genes, acquire testis-biased expression. Identifying the underlying cause of this observation requires determining whether the duplicates have altered functions relative to the parental genes. Typically, statistical methods are used to test for positive selection, signature of which in protein sequence of duplicates implies functional divergence. When assumptions are violated, however, such tests can lead to false inference of positive selection. More convincing evidence for naturally selected functional changes would be the occurrence of structural changes with similar functional consequences in independent duplicates of the same gene. Two testis-specific duplicates were tested of the broadly expressed enzyme gene Aldehyde dehydrogenase (Aldh) that arose in different Drosophila lineages. The duplicates show a typical pattern of accelerated amino-acid substitutions relative to their broadly expressed paralogs, with statistical evidence for positive selection in both cases. Importantly, in both duplicates, width of the entrance to the substrate binding site, known a priori to influence substrate specificity, and otherwise conserved throughout the genus Drosophila, has been reduced, resulting in narrowing of the entrance. Protein structure modeling suggests that the reduction of the size of the enzyme's substrate entry channel, which is likely to shift substrate specificity toward smaller aldehydes, is accounted for by the positively selected parallel substitutions in one duplicate but not the other. Evolution of the testis-specific duplicates was accompanied by reduction in expression of the ancestral Aldh in males, supporting the hypothesis that the duplicates may have helped resolve intralocus sexual conflict over Aldh function.

Charlesworth, B. (2015). Causes of natural variation in fitness: Evidence from studies of Drosophila populations. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 25572964
Summary: DNA sequencing has revealed high levels of variability within most species. Statistical methods based on population genetics theory have been applied to the resulting data and suggest that most mutations affecting functionally important sequences are deleterious but subject to very weak selection. Quantitative genetic studies have provided information on the extent of genetic variation within populations in traits related to fitness and the rate at which variability in these traits arises by mutation. This paper attempts to combine the available information from applications of the two approaches to populations of the fruitfly Drosophila in order to estimate some important parameters of genetic variation, using a simple population genetics model of mutational effects on fitness components. Analyses based on this model suggest the existence of a class of mutations with much larger fitness effects than those inferred from sequence variability and that contribute most of the standing variation in fitness within a population caused by the input of mildly deleterious mutations. However, deleterious mutations explain only part of this standing variation, and other processes such as balancing selection appear to make a large contribution to genetic variation in fitness components in Drosophila.

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