PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (123)
 

Clipboard (0)
None

Select a Filter Below

Journals
Year of Publication
1.  A simplified and efficient germline-specific CRISPR/Cas9 system for Drosophila genomic engineering 
Fly  2013;8(1):52-57.
The type II CRISPR/Cas9 system (clustered regularly interspaced short palindromic repeats/CRISPR-associated) has recently emerged as an efficient and simple tool for site-specific engineering of eukaryotic genomes. To improve its applications in Drosophila genome engineering, we simplified the standard two-component CRISPR/Cas9 system by generating a stable transgenic fly line expressing the Cas9 endonuclease in the germline (Vasa-Cas9 line). By injecting vectors expressing engineered target-specific guide RNAs into Vasa-Cas9 fly embryos, mutations were generated from site-specific DNA cleavages and efficiently transmitted into progenies. Because Cas9 endonuclease is the universal component of the type II CRISPR/Cas9 system, site-specific genomic engineering based on this improved platform can be achieved with lower complexity and toxicity, greater consistency, and excellent versatility.
doi:10.4161/fly.26828
PMCID: PMC3974895  PMID: 24141137
CRISPR/Cas9; genomic engineering; germline; engineered endonuclease; RNA-guided DNA cleavage
2.  Bridging the divide 
Fly  2013;8(1):13-18.
Ring canals are made from arrested cleavage furrows, and provide direct cytoplasmic connections among sibling cells. They are well documented for their participation in Drosophila oogenesis, but little is known about their role in several somatic tissues in which they are also found. Using a variety of genetic tools in live and fixed tissue, we recently demonstrated that rapid intercellular exchange occurs through somatic ring canals by diffusion, and presented evidence that ring canals permit equilibration of protein among transcriptionally mosaic cells. We also used a novel combination of markers to evaluate the extent of protein movement within and across mitotic clones in follicle cells and imaginal discs, providing evidence of robust movement of GFP between the 2 sides of mitotic clones and frequently into non-recombined cells. These data suggest that, depending on the experimental setup and proteins of interest, inter-clonal diffusion of protein may alter the interpretation of clonal data in follicle cells. Here, we discuss these results and provide additional insight into the impact of ring canals in Drosophila somatic tissues.
doi:10.4161/fly.27016
PMCID: PMC3974888  PMID: 24406334
Drosophila; egg chamber; follicle cells; intercellular bridge; ring canal; imaginal discs
3.  Diverse roles for the Drosophila fructose sensor Gr43a 
Fly  2013;8(1):19-25.
The detection of nutrients, both in food and within the body, is crucial for the regulation of feeding behavior, growth, and metabolism. While the molecular basis for sensing food chemicals by the taste system has been firmly linked to specific taste receptors, relatively little is known about the molecular nature of the sensors that monitor nutrients internally. Recent reports of taste receptors expressed in other organ systems, foremost in the gastrointestinal tract of mammals and insects, has led to the proposition that some taste receptors may also be used as sensors of internal nutrients. Indeed, we provided direct evidence that the Drosophila gustatory receptor 43a (Gr43a) plays a critical role in sensing internal fructose levels in the fly brain. In addition to the brain and the taste system, Gr43a is also expressed in neurons of the proventricular ganglion and the uterus. Here, we discuss the multiple potential roles of Gr43a in the fly. We also provide evidence that its activation in the brain is likely mediated by the neuropeptide Corazonin. Finally, we posit that Gr43a may represent only a precedent for other taste receptors that sense internal nutrients, not only in flies but, quite possibly, in other animals, including mammals.
doi:10.4161/fly.27241
PMCID: PMC3974889  PMID: 24406333
brain; corazonin; fructose; nutrient sensor; proventriculus; receptor; taste; uterus; valence
4.  Roles of Hox genes in the patterning of the central nervous system of Drosophila 
Fly  2013;8(1):26-32.
One of the key aspects of functional nervous systems is the restriction of particular neural subtypes to specific regions, which permits the establishment of differential segment-specific neuromuscular networks. Although Hox genes play a major role in shaping the anterior-posterior body axis during animal development, our understanding of how they act in individual cells to determine particular traits at precise developmental stages is rudimentary. We have used the abdominal leucokinergic neurons (ABLKs) to address this issue. These neurons are generated during both embryonic and postembryonic neurogenesis by the same progenitor neuroblast, and are designated embryonic and postembryonic ABLKs, respectively. We report that the genes of the Bithorax-Complex, Ultrabithorax (Ubx) and abdominal-A (abd-A) are redundantly required to specify the embryonic ABLKs. Moreover, the segment-specific pattern of the postembryonic ABLKs, which are restricted to the most anterior abdominal segments, is controlled by the absence of Abdominal-B (Abd-B), which we found was able to repress the expression of the neuropeptide leucokinin. We discuss this and other examples of how Hox genes generate diversity within the central nervous system of Drosophila.
doi:10.4161/fly.27424
PMCID: PMC3974890  PMID: 24406332
development; Hox genes; central nervous system; Drosophila; cell fate specification
5.  Drosophila chemotaxis 
Fly  2013;8(1):3-6.
Chemotaxis, the ability to direct movements according to chemical cues in the environment, is important for the survival of most organisms. In our original article, we combined a quantitative behavioral assay with genetic manipulations to dissect the neural substrate for chemotaxis. In this Extra View article, we offer a more chronological narration of the findings leading to our key conclusion that aversion engages specific motor-related circuits and kinematics. We speculate on the separation and crosstalk between aversion and attraction circuits in the brain and the ventral nerve cord, and the implication for valence encoding in the olfactory system.
doi:10.4161/fly.26685
PMCID: PMC3974891  PMID: 24091819
behavior; neurobiology; olfaction; neurogenetics; locomotion; ventral nerve cord; ellipsoid body; aversion; attraction; chemotaxis; octopamine
6.  Mind the gap 
Fly  2014;8(1):33-35.
Nature presents plenty of examples of cellular behavior that determines the shape of an organ during development, such as epithelial polarity and cell division orientation. Little is known, however, about how organs regenerate or how cellular behavior affects regeneration. One of the most exciting aspects of regeneration biology is understanding how proliferation and patterning are coordinated, since it means that cells not only have to proliferate but also have to do so in an ordered manner so that organs are reconstructed proportionally. Drosophila wing imaginal discs and adult wings are models used in different approaches to investigate this issue; they have recently been used to reveal that, after localized cell death, neighboring cells change their cell division orientation toward the damaged zone. During this process, cell polarity and spindle orientation operate in coordination with cell proliferation to regenerate proper organ size and shape.
doi:10.4161/fly.27690
PMCID: PMC3974892  PMID: 24406337
regeneration; cell division; wound healing; imaginal discs; cell polarity
7.  Hedgehog and extramacrochaetae in the Drosophila eye 
Fly  2014;8(1):36-42.
During the third and final larval instar stage, thousands of pluripotent cells within the Drosophila eye imaginal disc are transformed into a near perfect neurocrystalline lattice of 800 unit eyes called ommatidia. This transformation begins with the initiation of the morphogenetic furrow at the posterior margin of the eye field. The furrow, which marks the leading edge of a wave of differentiation, passes across the epithelium transforming unpatterned and undifferentiated cells into rows of periodically spaced clusters of photoreceptor neurons. As cells enter and exit the furrow they undergo dramatic alterations in cellular architecture and gene expression, many of which are required to propel the furrow forward and for proper cell fate specification. The Decapentaplegic (Dpp) and Hedgehog (Hh) signaling pathways are required for the initiation and progression of the furrow, respectively. Consistent with a role in furrow progression, the loss of Hh pathway activity results in a “furrow stop” phenotype. In contrast, reductions in levels of the helix-loop-helix transcription factor, Extramacrochaetae (Emc), lead to the polar opposite phenotype—the furrow accelerates. Recently, we demonstrated that the furrow stop and furrow acceleration phenotypes are molecularly connected. Emc appears to serve as a brake on the furrow by dampening the activity of the Hh pathway. Loss of Emc leads to an upsurge in Hh pathway activity and a faster moving furrow. The acceleration of the furrow appears to be due to an increase in levels of the full-length isoform of Cubitus Interruptus (Ci155) and Suppressor of Fused [Su(fu)]. Here we will briefly review the mechanisms by which Hh drives and Emc impedes the progression of the furrow across the developing retina.
doi:10.4161/fly.27691
PMCID: PMC3974893  PMID: 24406336
extramacrochaetae; Hedgehog; Drosophila; Suppressor of Fused; morphogenetic furrow
8.  Bi-functional cross-linking reagents efficiently capture protein-DNA complexes in Drosophila embryos 
Fly  2013;8(1):43-51.
Chromatin immunoprecipitation (ChIP) is widely used for mapping DNA-protein interactions across eukaryotic genomes in cells, tissues or even whole organisms. Critical to this procedure is the efficient cross-linking of chromatin-associated proteins to DNA sequences that are in close proximity. Since the mid-nineties formaldehyde fixation has been the method of choice. However, some protein-DNA complexes cannot be successfully captured for ChIP using formaldehyde. One such formaldehyde refractory complex is the developmentally regulated insulator factor, Elba. Here we describe a new embryo fixation procedure using the bi-functional cross-linking reagents DSG (disuccinimidyl glutarate) and DSP (dithiobis[succinimidyl propionate). We show that unlike standard formaldehyde fixation protocols, it is possible to capture Elba association with insulator elements in 2–5 h embryos using this new cross-linking procedure. We show that this new cross-linking procedure can also be applied to localize nuclear proteins that are amenable to ChIP using standard formaldehyde cross-linking protocols, and that in the cases tested the enrichment was generally superior to that achieved using formaldehyde cross-linking.
doi:10.4161/fly.26805
PMCID: PMC3974894  PMID: 24135698
chromatin immunoprecipitation; ChIP; formadelhyde; bi-functional cross-linkers; insulators; DSG DSP; DNA binding; Elba; Insensitive
9.  A strategy for generation and balancing of autosome: Y chromosome translocations 
Fly  2014;8(1):58-62.
We describe a method for generation and maintenance of translocations that move large autosomal segments onto the Y chromosome. Using this strategy we produced (2;Y) translocations that relocate between 1.5 and 4.8 Mb of the 2nd chromosome.. All translocations were easily balanced over a male-specific lethal 1 (msl-1) mutant chromosome. Both halves of the translocation carry visible markers, as well as P-element ends that enable molecular confirmation. Halves of these translocations can be separated to produce offspring with duplications and with lethal second chromosome deficiencies . Such large deficiencies are otherwise tedious to generate and maintain.
doi:10.4161/fly.27814
PMCID: PMC3974896  PMID: 24646827
Drosophila melanogaster; chromosome translocations; deficiencies; Y chromosome
10.  Multiple roles of Nrf2-Keap1 signaling 
Fly  2013;8(1):7-12.
Xenobiotic and oxidative responses protect cells from external and internal toxicities. Nrf2 and Keap1 are central factors that mediate these responses, and are closely related with many human diseases. In a recent study, we revealed novel developmental function and regulatory mechanism of Nrf2 and Keap1 by investigating their Drosophila homolog CncC and dKeap1. We found that CncC and dKeap1 control metamorphosis through regulations of ecdysone biosynthetic genes and ecdysone response genes in different tissues. CncC and dKeap1 cooperatively activate these developmental genes, in contrast to their conserved antagonizing effect to xenobiotic response transcription. In addition, interactions between CncC and Ras signaling in metamorphosis and in transcriptional regulation were established. Here I discuss the implications that place these classic xenobiotic response factors into a broader network that potentially control development and oncogenesis using mechanisms other than those mediating xenobiotic response.
doi:10.4161/fly.27007
PMCID: PMC3974897  PMID: 24406335
xenobiotic response; development; transcriptional regulation; Nrf2/CncC; Keap1/dKeap1; steroid hormone; cancer
11.  Small RNAs tackle large viruses: RNA interference-based antiviral defense against DNA viruses in insects 
Fly  2013;7(4):216-223.
The antiviral RNA interference (RNAi) pathway processes viral double-stranded RNA (dsRNA) into viral small interfering RNAs (vsiRNA) that guide the recognition and cleavage of complementary viral target RNAs. In RNA virus infections, viral replication intermediates, dsRNA genomes or viral structured RNAs have been implicated as Dicer-2 substrates. In a recent publication, we demonstrated that a double-stranded DNA virus, Invertebrate iridescent virus 6, is a target of the Drosophila RNAi machinery, and we proposed that overlapping converging transcripts base pair to form the dsRNA substrates for vsiRNA biogenesis. Here, we discuss the role of RNAi in antiviral defense to DNA viruses in Drosophila and other invertebrate model systems.
doi:10.4161/fly.25708
PMCID: PMC3896492  PMID: 23974177
RNA silencing; small RNA profiling; small silencing RNA; next-generation sequencing; Dicer; Argonaute; Drosophila; insect immunity; antiviral immunity; Iridoviridae
12.  All together now 
Fly  2013;7(4):224-228.
Maintenance of genomic stability during eukaryotic cell division relies on the Spindle Assembly Checkpoint (SAC), which has evolved as a surveillance mechanism that monitors kinetochore-microtubule attachment and prevents APC/C-mediated mitotic exit until all chromosomes are properly attached to the mitotic spindle. Reversible protein phosphorylation has long been accredited as a regulatory mechanism of the SAC. Nevertheless, knowledge of how several mitotic kinases act in concert within the signaling pathway to orchestrate SAC function is still emerging. In a recent study, we undertook a comprehensive dissection of the hierarchical framework controlling SAC function in Drosophila cells. We found that Polo lies at the top of the SAC pathway promoting the efficient recruitment of Mps1 to unattached kinetochores. This renders Mps1 fully active to control BubR1 phosphorylation that generates the 3F3/2 phosphoepitope at tensionless kinetochores. We have proposed that Polo is required for SAC function and that the molecular outcome of Mps1-dependent 3F3/2 formation is to promote the association of Cdc20 with BubR1 allowing proper kinetochore recruitment of Cdc20 and efficient assembly of the Mitotic Checkpoint Complex (MCC) required for a sustained SAC response.
doi:10.4161/fly.26231
PMCID: PMC3896493  PMID: 23989224
Aurora B; Polo; Mps1; BubR1; Cdc20; mitosis; spindle assembly checkpoint; phosphoregulation
13.  Modeling Huntington disease in Drosophila 
Fly  2013;7(4):229-236.
Huntington disease (HD) is an inherited neurodegenerative disorder caused by a polyglutamine (polyQ) expansion in the huntingtin (Htt) gene. Despite years of research, there is no treatment that extends life for patients with the disorder. Similarly, little is known about which cellular pathways that are altered by pathogenic Huntingtin (Htt) protein expression are correlated with neuronal loss. As part of a longstanding effort to gain insights into HD pathology, we have been studying the protein in the context of the fruitfly Drosophila melanogaster. We generated transgenic HD models in Drosophila by engineering flies that carry a 12-exon fragment of the human Htt gene with or without the toxic trinucleotide repeat expansion. We also created variants with a monomeric red fluorescent protein (mRFP) tag fused to Htt that allows in vivo imaging of Htt protein localization and aggregation. While wild-type Htt remains diffuse throughout the cytoplasm of cells, pathogenic Htt forms insoluble aggregates that accumulate in neuronal soma and axons. Aggregates can physically block transport of numerous organelles along the axon. We have also observed that aggregates are formed quickly, within just a few hours of mutant Htt expression. To explore mechanisms of neurodegeneration in our HD model, we performed in vivo and in vitro screens to search for modifiers of viability and pathogenic Htt aggregation. Our results identified several novel candidates for HD therapeutics that can now be tested in mammalian models of HD. Furthermore, these experiments have highlighted the complex relationship between aggregates and toxicity that exists in HD.
doi:10.4161/fly.26279
PMCID: PMC3896494  PMID: 24022020
Huntington disease; polyglutamine; Drosophila; aggregates; axonal transport
14.  Parasitoid wasp virulence 
Fly  2013;7(4):242-248.
In nature, larvae of the fruit fly Drosophila melanogaster are commonly infected by parasitoid wasps. Following infection, flies mount an immune response termed cellular encapsulation in which fly immune cells form a multilayered capsule that covers and kills the wasp egg. Parasitoids have thus evolved virulence factors to suppress cellular encapsulation. To uncover the molecular mechanisms underlying the antiwasp response, we and others have begun identifying and functionally characterizing these virulence factors. Our recent work on the Drosophila parasitoid Ganaspis sp.1 has demonstrated that a virulence factor encoding a SERCA-type calcium pump plays an important role in Ganaspis sp.1 virulence. This venom SERCA antagonizes fly immune cell calcium signaling and thereby prevents the activation of the encapsulation response. In this way, the study of wasp virulence factors has revealed a novel aspect of fly immunity, namely a role for calcium signaling in fly immune cell activation, which is conserved with human immunity, again illustrating the marked conservation between fly and mammalian immune responses. Our findings demonstrate that the cellular encapsulation response can serve as a model of immune cell function and can also provide valuable insight into basic cell biological processes.
doi:10.4161/fly.26484
PMCID: PMC3896496  PMID: 24088661
Drosophila; Ganaspis; SERCA; calcium; encapsulation; immunity; parasitoid
15.  Effete, an E2 ubiquitin-conjugating enzyme with multiple roles in Drosophila development and chromatin organization 
Fly  2013;7(4):256-262.
The Drosophila effete gene encodes an extremely conserved class I E2 ubiquitin-conjugating enzyme. Growing evidence indicates that Eff is involved in many cellular processes including eye development, maintenance of female germline stem cells, and regulation of apoptosis. Eff is also a major component of Drosophila chromatin and it is particularly enriched in chromatin with repressive properties. In addition, Eff is required for telomere protection and to prevent telomere fusion. Consistent with its multiple roles in chromatin maintenance, Eff is also one of the rare factors that modulate both telomere-induced and heterochromatin-induced position effect variegation.
doi:10.4161/fly.26567
PMCID: PMC3896498  PMID: 24088712
effete; UbcD1; TPE; PEV; chromatin organization; E2 enzyme
16.  Variation of NimC1 expression in Drosophila stocks and transgenic strains 
Fly  2013;7(4):263-266.
The NimC1 molecule has been described as a phagocytosis receptor, and is being used as a marker for professional phagocytes, the plasmatocytes, in Drosophila melanogaster. In studies including tumor-biology, developmental biology, and cell mediated immunity, monoclonal antibodies (P1a and P1b) to the NimC1 antigen are used. As we observed that these antibodies did not react with plasmatocytes of several strains and genetic combinations, a molecular analysis was performed on the structure of the nimC1 gene. In these strains we found 2 deletions and an insertion within the nimC1 gene, which may result in the production of a truncated NimC1 protein. The NimC1 positivity was regained by recombining the mutation with a wild-type allele or by using nimC1 mutant lines under heterozygous conditions. By means of these procedures or using the recombined stock, NimC1 can be used as a marker for phagocytic cells in the majority of the possible genetic backgrounds.
doi:10.4161/fly.25654
PMCID: PMC3896499  PMID: 23899817
innate immunity; Drosophila; plasmatocyte; phagocytosis receptor; marker
17.  Mutations in palmitoyl-protein thioesterase 1 alter exocytosis and endocytosis at synapses in Drosophila larvae 
Fly  2013;7(4):267-279.
Infantile-onset neuronal ceroid lipofuscinosis (INCL) is a severe pediatric neurodegenerative disorder produced by mutations in the gene encoding palmitoyl-protein thioesterase 1 (Ppt1). This enzyme is responsible for the removal of a palmitate group from its substrate proteins, which may include presynaptic proteins like SNAP-25, cysteine string protein (CSP), dynamin, and synaptotagmin. The fruit fly, Drosophila melanogaster, has been a powerful model system for studying the functions of these proteins and the molecular basis of neurological disorders like the NCLs. Genetic modifier screens and tracer uptake studies in Ppt1 mutant larval garland cells have suggested that Ppt1 plays a role in endocytic trafficking. We have extended this analysis to examine the involvement of Ppt1 in synaptic function at the Drosophila larval neuromuscular junction (NMJ). Mutations in Ppt1 genetically interact with temperature sensitive mutations in the Drosophila dynamin gene shibire, accelerating the paralytic behavior of shibire mutants at 27 °C. Electrophysiological work in NMJs of Ppt1-deficient larvae has revealed an increase in miniature excitatory junctional potentials (EJPs) and a significant depression of evoked EJPs in response to repetitive (10 hz) stimulation. Endocytosis was further examined in Ppt1-mutant larvae using FM1–43 uptake assays, demonstrating a significant decrease in FM1–43 uptake at the mutant NMJs. Finally, Ppt1-deficient and Ppt1 point mutant larvae display defects in locomotion that are consistent with alterations in synaptic function. Taken together, our genetic, cellular, and electrophysiological analyses suggest a direct role for Ppt1 in synaptic vesicle exo- and endocytosis at motor nerve terminals of the Drosophila NMJ.
doi:10.4161/fly.26630
PMCID: PMC3896500  PMID: 24091420
Drosophila; infantile neuronal ceroid lipofuscinosis; Batten disease; palmitoyl-protein thioesterase-1; synaptic vesicle cycling; endocytosis; exocytosis
18.  Localized serine protease activity and the establishment of Drosophila embryonic dorsoventral polarity 
Fly  2013;7(3):161-167.
Drosophila embryo dorsoventral polarity is established by a maternally encoded signal transduction pathway in which three sequentially acting serine proteases, Gastrulation Defective, Snake and Easter, generate the ligand that activates the Toll receptor on the ventral side of the embryo. The spatial regulation of this pathway depends upon ventrally restricted expression of the Pipe sulfotransferase in the ovarian follicle during egg formation. Several recent observations have advanced our understanding of the mechanism regulating the spatially restricted activation of Toll. First, several protein components of the vitelline membrane layer of the eggshell have been determined to be targets of Pipe-mediated sulfation. Second, the processing of Easter by Snake has been identified as the first Pipe-dependent, ventrally-restricted processing event in the pathway. Finally, Gastrulation Defective has been shown to undergo Pipe-dependent, ventral localization within the perivitelline space and to facilitate Snake-mediated processing of Easter. Together, these observations suggest that Gastrulation Defective, localized on the interior ventral surface of the eggshell in association with Pipe-sulfated eggshell proteins, recruits and mediates an interaction between Snake and Easter. This event leads to ventrally-restricted processing and activation of Easter and consequently, localized formation of the Toll ligand, and Toll activation.
doi:10.4161/fly.25141
PMCID: PMC4049848  PMID: 24047959
Drosophila; Easter; Gastrulation Defective; Pipe; Snake; Spätzle; Toll; dorsal-ventral; follicle; perivitelline; sulfation; sulfonation
19.  Smaug 
Fly  2013;7(3):142-145.
Drosophila Smaug is a sequence-specific RNA-binding protein that can repress the translation and induce the degradation of target mRNAs in the early Drosophila embryo. Our recent work has uncovered a new mechanism of Smaug-mediated translational repression whereby it interacts with and recruits the Argonaute 1 (Ago1) protein to an mRNA. Argonaute proteins are typically recruited to mRNAs through an associated small RNA, such as a microRNA (miRNA). Surprisingly, we found that Smaug is able to recruit Ago1 to an mRNA in a miRNA-independent manner. This work suggests that other RNA-binding proteins are likely to employ a similar mechanism of miRNA-independent Ago recruitment to control mRNA expression. Our work also adds yet another mechanism to the list that Smaug can use to regulate its targets and here we discuss some of the issues that are raised by Smaug’s multi-functional nature.
doi:10.4161/fly.24336
PMCID: PMC4049845  PMID: 23519205
Smaug; Argonaute; nanos; Drosophila; embryo; translational control
20.  Building a synapse 
Fly  2013;7(3):146-152.
L-glutamate is the primary neurotransmitter at excitatory synapses in the vertebrate CNS and at arthropod neuromuscular junctions (NMJs). However, the molecular mechanisms that trigger the recruitment of glutamate receptors at the onset of synaptogenesis and promote their stabilization at postsynaptic densities remain poorly understood. We have reported the discovery of a novel, evolutionary conserved molecule, Neto, essential for clustering of ionotropic glutamate receptors (iGluRs) at Drosophila NMJ. Neto is the first auxiliary subunit described in Drosophila and is the only non-channel subunit absolutely required for functional iGluRs. Here we review the role of Drosophila Neto in synapse assembly, its similarities with other Neto proteins and a new perspective on how glutamatergic synapses are physically assembled and stabilized.
doi:10.4161/fly.24413
PMCID: PMC4049846  PMID: 23680998
glutamatergic synapses; synapse assembly; glutamate receptors; Drosophila; neuromuscular junction; auxiliary subunits
21.  UpSET-ing the balance 
Fly  2013;7(3):153-160.
Appropriate gene expression relies on the sophisticated interplay between genetic and epigenetic factors. Histone acetylation and an open chromatin configuration are key features of transcribed regions and are mainly present around active promoters. Our recent identification of the SET-domain containing protein UpSET established a new functional link between the modulation of open chromatin features and active recruitment of well-known co-repressors in metazoans. Structurally, the SET domain of UpSET resembles H3K4 and H3K36 methyltransferases; however, it is does not confer histone methyltransferase activity. Rather than methylating histones to regulate gene expression like other SET domain-containing proteins, UpSET fine-tunes transcription by modulating the chromatin structure around active promoters resulting in suppression of expression of off-target genes or nearby repetitive elements. Chromatin modulation by UpSET occurs in part through its interaction with histone deacetylases. Here, we discuss the different scenarios in which UpSET could play key roles in modulating gene expression.
doi:10.4161/fly.24732
PMCID: PMC4049847  PMID: 23649046
UpSET; Rpd3; Sin3A; Set3C; Mixed Lineage Leukemia protein 5; histone acetylation; chromatin accessibility
22.  Genetic decay of balancer chromosomes in Drosophila melanogaster 
Fly  2013;7(3):184-186.
Theoretical considerations predict that balancer chromosomes in Drosophila melanogaster should accumulate numerous deleterious mutations with time. We counted the number of recessive lethal mutations on two balancer chromosomes from the In(2LR)SM1/In(2LR)Pm strain maintained in our lab, after making the balancers heterozygous with deficiencies from second-chromosome Kyoto Deficiency kit strains. We detected 10 recessive lethal mutations in the balancer In(2LR)Pm, which is consistent with the mutation rate estimated previously. However, we detected only three mutations, a significantly smaller number, in the balancer In(2LR)SM1, although this may be an artifact. In conclusion, we observed genetic decay over an estimable timescale by using balancers with historical records. Thus, balancers of any strain may have accumulated many unidentified recessive lethal mutations.
doi:10.4161/fly.24466
PMCID: PMC4049851  PMID: 23648996
inversion; mutation rate; recessive lethal; recombination; balancer chromosomes; Drosophila melanogaster
23.  An automated climbing apparatus to measure chemotherapy-induced neurotoxicity in Drosophila melanogaster 
Fly  2013;7(3):187-192.
We have developed a novel model system in Drosophila melanogaster to study chemotherapy-induced neurotoxicity in adult flies. Neurological deficits were measured using a manual geotactic climbing assay. The manual assay is commonly used; however, it is laborious, time-consuming, subject to human error and limited to observing one sample at a time. We have designed and built a new automated fly-counting apparatus that uses a “video capture-particle counting technology” to automatically measure 10 samples at a time, with 20 flies per sample. Climbing behavior was assessed manually, as in our previous studies, and with the automated apparatus within the same experiment yielding statistically similar results. Both climbing endpoints as well as the climbing rate can be measured in the apparatus, giving the assay more versatility than the manual assay. Automation of our climbing assay reduces variability, increases productivity and enables high throughput drug screens for neurotoxicity.
doi:10.4161/fly.24789
PMCID: PMC4049852  PMID: 23695893
automated; Drosophila; geotactic; climbing; neurotoxicity; apparatus; chemotherapy; cisplatin
24.  A method for reversible drug delivery to internal tissues of Drosophila embryos 
Fly  2013;7(3):193-203.
Drosophila melanogaster is a powerful model organism to elucidate basic cellular mechanisms of development. Indeed, much of our understanding of genetic pathways comes from work in Drosophila. However, mutations in many critical genes cause early embryonic lethality; thus, it is difficult to study the role of proteins that are required for early fundamental processes during later embryonic stages. We have therefore developed a method to reversibly deliver drugs to internal tissues of stage 15–16 Drosophila embryos using a 1:1 combination of D-limonene and heptane (LH). Specifically, delivery of Nocodazole was shown to be effective as evidenced by the significant decrease in microtubule density seen in muscle cells. Following complete depolymerization of the microtubule cytoskeleton, removing the Nocodazole and washing for 10 min was sufficient for the microtubule network to be re-established, indicating that drug delivery is reversible. Additionally, the morphology of LH-treated embryos resembled that of untreated controls, and embryo viability post-treatment with LH was significantly increased compared with previously reported permeabilization techniques. These advances in embryo permeabilization provide a means to disrupt protein function in vivo with high temporally specificity, bypassing the complications associated with genetic disruptions as they relate to the study of late-stage developmental mechanisms.
doi:10.4161/fly.25438
PMCID: PMC4049853  PMID: 23846179
Drosophila; embryo; Chorion; permeabilization; drug delivery
25.  Density dynamics of diverse Spiroplasma strains naturally infecting different species of Drosophila 
Fly  2013;7(3):204-210.
Facultative heritable bacterial endosymbionts can have dramatic effects on their hosts, ranging from mutualistic to parasitic. Within-host bacterial endosymbiont density plays a critical role in maintenance of a symbiotic relationship, as it can affect levels of vertical transmission and expression of phenotypic effects, both of which influence the infection prevalence in host populations. Species of genus Drosophila are infected with Spiroplasma, whose characterized phenotypic effects range from that of a male-killing reproductive parasite to beneficial defensive endosymbiont. For many strains of Spiroplasma infecting at least 17 species of Drosophila, however, the phenotypic effects are obscure. The infection prevalence of these Spiroplasma vary within and among Drosophila species, and little is known about the within-host density dynamics of these diverse strains. To characterize the patterns of Spiroplasma density variation among Drosophila we used quantitative PCR to assess bacterial titer at various life stages of three species of Drosophila naturally-infected with two different types of Spiroplasma. For naturally infected Drosophila species we found that non-male-killing infections had consistently lower densities than the male-killing infection. The patterns of Spiroplasma titer change during aging varied among Drosophila species infected with different Spiroplasma strains. Bacterial density varied within and among populations of Drosophila, with individuals from the population with the highest prevalence of infection having the highest density. This density variation underscores the complex interaction of Spiroplasma strain and host genetic background in determining endosymbiont density.
doi:10.4161/fly.25469
PMCID: PMC4049854  PMID: 23846301
Spiroplasma; Drosophila; vertically-transmitted endosymbiont; endosymbiont density

Results 1-25 (123)