Table of Contents

Volume 6, Issue 2

  April/May/June 2012

  Pages 69 - 131

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 Issue Catalogue (MARC XML)

EDITOR'S PREVIEW

Open Access Article

In this issue of Fly

Barbara P. Rattner
Pages 69 - 70
http://dx.doi.org/10.4161/fly.20456
Full Text | PDF




BRIEF COMMUNICATION

Open Access Article

The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions

Nuno A. Fonseca, Cristina P. Vieira, Christian Schlötterer and Jorge Vieira
Pages 71 - 74
http://dx.doi.org/10.4161/fly.19423
Abstract | Full Text | PDF

Chromosomal inversions can originate from breakage and repair by non-homologous end-joining. Nevertheless, they can also originate from ectopic recombination between transposable elements located on the same chromosome inserted in opposite orientations. Here, we show that a MITE element (DAIBAM), previously involved in the origin of one Drosophila americana polymorphic inversion, is also involved in the origin of one fixed inversion between D. virilis and D. americana and another D. americana polymorphic inversion. Therefore, DAIBAM is responsible for at least 20% of the chromosomal rearrangements that are observed within and between species of the virilis phylad (D. virilis, D. lummei, D. novamexicana and D. americana), having thus played a significant role in the chromosomal evolution of this group of closely related species.




METHODS AND TECHNICAL ADVANCES

Open Access Article

An improved method for nematode infection assays in Drosophila larvae

Pavel Dobes, Zhi Wang, Robert Markus, Ulrich Theopold and Pavel Hyrsl
Pages 75 - 79
http://dx.doi.org/10.4161/fly.19553
Abstract | Full Text | PDF

The infective juveniles (IJs) of entomopathogenic nematodes (EPNs) seek out host insects and release their symbiotic bacteria into their body cavity causing septicaemia, which eventually leads to host death. The interaction between EPNs and their hosts are only partially understood, in particular the host immune responses appears to involve pathways other than phagocytosis and the canonical transcriptional induction pathways. These pathways are genetically tractable and include for example clotting factors and lipid mediators. The aim of this study was to optimize the nematode infections in Drosophila melanogaster larvae, a well-studied and genetically tractable model organism. Here we show that two nematode species namely Steinernema feltiae and Heterorhabditis bacteriophora display different infectivity toward Drosophila larvae with the latter being less pathogenic. The effects of supporting media and IJ dosage on the mortality of the hosts were assessed and optimized. Using optimum conditions, a faster and efficient setup for nematode infections was developed. This newly established infection model in Drosophila larvae will be applicable in large scale screens aimed at identifying novel genes/pathways involved in innate immune responses.




RESEARCH PAPERS

Open Access Article

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w¹¹¹⁸; iso-2; iso-3

Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J. Land, Xiangyi Lu and Douglas M. Ruden
Pages 80 - 92
http://dx.doi.org/10.4161/fly.19695
Abstract | Full Text | PDF

We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted.

Here the use of SnpEff is illustrated by annotating ~356,660 candidate SNPs in ~117 Mb unique sequences, representing a substitution rate of ~1/305 nucleotides, between the Drosophila melanogaster w¹¹¹⁸; iso-2; iso-3 strain and the reference y¹; cn¹ bw¹ sp¹ strain. We show that ~15,842 SNPs are synonymous and ~4,467 SNPs are non-synonymous (N/S ~0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in the 5′UTR. We found, as expected, that the SNP frequency is proportional to the recombination frequency (i.e., highest in the middle of chromosome arms). We also found that start-gain or stop-lost SNPs in Drosophila melanogaster often result in additions of N-terminal or C-terminal amino acids that are conserved in other Drosophila species. It appears that the 5′ and 3′ UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus.

As genome sequencing is becoming inexpensive and routine, SnpEff enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.

Open Access Article

H3S10 phosphorylation by the JIL-1 kinase regulates H3K9 dimethylation and gene expression at the white locus in Drosophila

Chao Wang, Weili Cai, Yeran Li, Jack Girton, Jørgen Johansen and Kristen M. Johansen
Pages 93 - 97
http://dx.doi.org/10.4161/fly.20029
Abstract | Full Text | PDF

The JIL-1 kinase is a multidomain protein that localizes specifically to euchromatin interband regions of polytene chromosomes and is the kinase responsible for histone H3S10 phosphorylation at interphase. Genetic interaction assays have suggested that the function of the epigenetic histone H3S10ph mark is to antagonize heterochromatization by participating in a dynamic balance between factors promoting repression and activation of gene expression as measured by position-effect variegation (PEV) assays. Interestingly, JIL-1 loss-of-function alleles can act either as an enhancer or indirectly as a suppressor of w^m4 PEV depending on the precise levels of JIL-1 kinase activity. In this study, we have explored the relationship between PEV and the relative levels of the H3S10ph and H3K9me2 marks at the white gene in both wild-type and w^m4 backgrounds by ChIP analysis. Our results indicate that H3K9me2 levels at the white gene directly correlate with its level of expression and that H3K9me2 levels in turn are regulated by H3S10 phosphorylation.

Open Access Article

The wild side of life: Drosophila reproduction in nature

Therese A. Markow, Stephen Beall and Sergio Castrezana
Pages 98 - 101
http://dx.doi.org/10.4161/fly.19552
Abstract | Full Text | PDF

Drosophila species vary in the rates at which females remate and the number of sperm they receive in the laboratory. In species such as D. melanogaster and D. pseudoobscura, in which females receive thousands of sperm and remate infrequently compared with species such as D. hydei and D. nigrospiracula, where females receive only a few hundred sperm and remate many times in a day, wild caught females should produce far more progeny. We tested this prediction by collecting, directly from nature, females of six species whose remating rates and number of sperm received vary from high to low and assessing the proportion of females with sperm and the number of progeny females produce. Over 95% of D. pseudoobscura and D. melanogaster females were inseminated while far fewer of the other species contained any sperm. In addition, D, pseudoobscura females produced progeny for over two weeks, D. melanogaster for over a week, while D. hydei and D. nigrospiracula females ran out of sperm after 1–2 d. These observations suggest extreme sperm limitation in these latter species.




EXTRA VIEWS

Open Access Article

desat1: A Swiss army knife for pheromonal communication and reproduction?

François Bousquet and Jean-François Ferveur
Pages 102 - 107
http://dx.doi.org/10.4161/fly.19554
Abstract | Full Text | PDF

The desat1 gene possesses an extraordinary—maybe unique—feature in the control of sensory communication systems: it codes for the two principal and complementary aspects—the emission and the reception—of Drosophila sex pheromones. These two complex aspects depend on separate genetic control indicating that desat1 pleiotropically acts on pheromonal communication. This gene also control other characters either related to reproduction and to osmoregulation. Such a functional pleiotropy may be related to the molecular structure of desat1 gene which combines a highly conserved coding region with fast evolving regulatory regions: It produces at least five transcripts all giving rise to the ∆9-desaturase enzyme.

Open Access Article

Stem cell aging and plasticity in the Drosophila nervous system

Hakima Flici and Angela Giangrande
Pages 108 - 112
http://dx.doi.org/10.4161/fly.19797
Abstract | Full Text | PDF

The majority of neural stem cells (NSCs) are considered as very plastic precursors that, in vitro, can divide indefinitely or differentiate into neurons or glia under specific conditions. However, in vivo, these cells actively proliferate during development, and later enter quiescence or apoptosis. This raises the issue as to whether stem cells keep their plastic behavior throughout their life, which may impact their therapeutic potential in regenerative medicine. Using the Gcm/Glide (for Glial cell missing/Glial cell deficient) transcription factor, which is able to trigger a complete and stable fate conversion into glia when ectopically expressed, we recently reported that the plasticity of Drosophila NSCs, commonly called neuroblasts (NBs), is age-dependent. When challenged with Gcm/Glide, newborn NBs are more easily converted into glia than old ones. Furthermore, the few old NBs that can be converted frequently generate cells with a stable (NB/glia) intermediate identity, a phenotype characteristic of cancer cells. We here discuss the concept of aging in NSC fate conversion and speculate on how our findings impact the ongoing debate concerning NSC plasticity.

Open Access Article

Mitochondria-driven cell elongation mechanism for competing sperms

Tatsuhiko Noguchi, Michiko Koizumi and Shigeo Hayashi
Pages 113 - 116
http://dx.doi.org/10.4161/fly.19862
Abstract | Full Text | PDF

Sexual competition has selected a number of extreme phenotypes like the tail ornament of peacock male. Sperm tail of Drosophilidae elongate up to 6 cm as a result of evolutionary selection for reproductive fitness among competing sperms. Sperm elongation takes place post meiotically and can proceed in the absence of an axoneme. Here, we used primary cultures of elongating spermatids of D. melanogaster to demonstrate that sperm elongation is driven by interdependent extension of giant mitochondria and microtubule array that is formed around the mitochondrial surface. This work established that, in addition to functioning as an energy source, mitochondria can serve as internal skeleton for shaping cell morphology.

Open Access Article

Drosophila eye color mutants as therapeutic tools for Huntington disease

Edward W. Green, Susanna Campesan, Carlo Breda, Korrapati V. Sathyasaikumar, Paul J. Muchowski, Robert Schwarcz, Charalambos P. Kyriacou and Flaviano Giorgini
Pages 117 - 120
http://dx.doi.org/10.4161/fly.19999
Abstract | Full Text | PDF

Huntington disease (HD) is a fatal inherited neurodegenerative disorder caused by a polyglutamine expansion in the huntingtin protein (htt). A pathological hallmark of the disease is the loss of a specific population of striatal neurons, and considerable attention has been paid to the role of the kynurenine pathway (KP) of tryptophan (TRP) degradation in this process. The KP contains three neuroactive metabolites: 3-hydroxykynurenine (3-HK), quinolinic acid (QUIN), and kynurenic acid (KYNA). 3-HK and QUIN are neurotoxic, and are increased in the brains of early stage HD patients, as well as in yeast and mouse models of HD. Conversely, KYNA is neuroprotective and has been shown to be decreased in HD patient brains. We recently used a Drosophila model of HD to measure the neuroprotective effect of genetic and pharmacological inhibition of kynurenine monoxygenase (KMO)—the enzyme catalyzing the formation of 3-HK at a pivotal branch point in the KP. We found that KMO inhibition in Drosophila robustly attenuated neurodegeneration, and that this neuroprotection was correlated with reduced levels of 3-HK relative to KYNA. Importantly, we showed that KP metabolites are causative in this process, as 3-HK and KYNA feeding experiments modulated neurodegeneration. We also found that genetic inhibition of the upstream KP enzyme tryptophan-2,3-dioxygenase (TDO) was neuroprotective in flies. Here, we extend these results by reporting that genetic impairment of KMO or TDO is protective against the eclosion defect in HD model fruit flies. Our results provide further support for the possibility of therapeutic KP interventions in HD.

Open Access Article

Characterizing gene movements between chromosomes in Drosophila

Mira V. Han
Pages 121 - 125
http://dx.doi.org/10.4161/fly.20144
Abstract | Full Text | PDF

Genes occasionally change their location in the genome through inter-chromosomal duplication and loss. These changes happen as mistakes during recombination or through retrotransposition. In Han and Hahn 2011,¹ we surveyed the genomes of ten Drosophila species, to identify and characterize the gene transposition events in the history of these species. In the paper, we showed that the rate of gene transposition in Drosophila is higher than previously appreciated. To understand the process of gene transposition, we examined the sequences, locations, and functions of the transposed genes. Based on the elevated rate of sequence evolution in transposed genes and the frequent movements near the centromeres and telomeres, we could not reject the hypothesis that these are mutations fixed through relaxed selection. But, by examining the functions of transposed genes more carefully, we found that genes with male-specific functions and genes with female-specific functions move in opposite directions involving the X chromosome. We also found an over-representation of chromosome related functions among the transposed genes. These observations suggest the possibility of particular selection pressures contributing to gene transpositions in Drosophila.

Open Access Article

Hipk proteins dually regulate Wnt/Wingless signal transduction

Esther M. Verheyen, Sharan Swarup and Wendy Lee
Pages 126 - 131
http://dx.doi.org/10.4161/fly.20143
Abstract | Full Text | PDF

The Wnt/Wingless (Wg) pathway is an evolutionarily conserved signaling system that is used reiteratively, both spatially and temporally, to control the development of multicellular animals. The stability of cytoplasmic β-catenin/Armadillo, the transcriptional effector of the pathway, is controlled by sequential N-terminal phosphorylation and ubiquitination that targets it for proteasome-mediated degradation. Orthologous members of the Homeodomain-interacting protein kinase family from Drosophila to vertebrates have been implicated in the regulation of Wnt/Wingless signaling. In Drosophila, as a consequence of Hipk activity, cells accumulate stabilized Armadillo that directs the expression of Wg-specific target genes. Hipk promotes the stabilization of Armadillo by inhibiting its ubiquitination (and hence subsequent degradation) by the SCF^Slimb E3 ubiquitin ligase complex. Vertebrate Hipk2 impedes β-catenin ubiquitination to promote its stability and the Wnt signal in a mechanism that is functionally conserved. Moreover, we describe here that Hipk proteins have a role independent of their effect on β-catenin/Armadillo stability to enhance Wnt/Wingless signaling.