Imagerie

@article{garrett_identification_2009,

title = {Identification and analysis of serpin-family genes by homology and synteny across the 12 sequenced Drosophilid genomes},

author = {Matthew Garrett and Ane Fullaondo and Laurent Troxler and Gos Micklem and David Gubb},

doi = {10.1186/1471-2164-10-489},

issn = {1471-2164},

year  = {2009},

date = {2009-01-01},

journal = {BMC Genomics},

volume = {10},

pages = {489},

abstract = {BACKGROUND: The Drosophila melanogaster genome contains 29 serpin genes, 12 as single transcripts and 17 within 6 gene clusters. Many of these serpins have a conserved "hinge" motif characteristic of active proteinase inhibitors. However, a substantial proportion (42%) lacks this motif and represents non-inhibitory serpin-fold proteins of unknown function. Currently, it is not known whether orthologous, inhibitory serpin genes retain the same target proteinase specificity within the Drosophilid lineage, nor whether they give rise to non-inhibitory serpin-fold proteins or other, more diverged, proteins. RESULTS: We collated 188 orthologues to the D. melanogaster serpins from the other 11 Drosophilid genomes and used synteny to find further family members, raising the total to 226, or 71% of the number of orthologues expected assuming complete conservation across all 12 Drosophilid species. In general the sequence constraints on the serpin-fold itself are loose. The critical Reactive Centre Loop (RCL) sequence, including the target proteinase cleavage site, is strongly conserved in inhibitory serpins, although there are 3 exceptional sets of orthologues in which the evolutionary constraints are looser. Conversely, the RCL of non-inhibitory serpin orthologues is less conserved, with 3 exceptions that presumably bind to conserved partner molecules. We derive a consensus hinge motif, for Drosophilid inhibitory serpins, which differs somewhat from that of the vertebrate consensus. Three gene clusters appear to have originated in the melanogaster subgroup, Spn28D, Spn77B and Spn88E, each containing one inhibitory serpin orthologue that is present in all Drosophilids. In addition, the Spn100A transcript appears to represent a novel serpin-derived fold. CONCLUSION: In general, inhibitory serpins rarely change their range of proteinase targets, except by a duplication/divergence mechanism. Non-inhibitory serpins appear to derive from inhibitory serpins, but not the reverse. The conservation of different family members varied widely across the 12 sequenced Drosophilid genomes. An approach considering synteny as well as homology was important to find the largest set of orthologues.},

keywords = {Animals, bioinformatic, Comparative Genomic Hybridization, Conserved Sequence, DNA, Drosophilidae, Evolution, Genome, Insect, Molecular, Multigene Family, Sequence Alignment, Sequence Analysis, Serpins, Synteny},

pubstate = {published},

tppubtype = {article}

}

@article{cronin_genome-wide_2009b,

title = {Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection},

author = {Shane J F Cronin and Nadine T Nehme and Stefanie Limmer and Samuel Liegeois and Andrew J Pospisilik and Daniel Schramek and Andreas Leibbrandt and Ricardo Matos de Simoes and Susanne Gruber and Urszula Puc and Ingo Ebersberger and Tamara Zoranovic and Gregory G Neely and Arndt von Haeseler and Dominique Ferrandon and Josef M Penninger},

doi = {10.1126/science.1173164},

issn = {1095-9203},

year  = {2009},

date = {2009-01-01},

journal = {Science},

volume = {325},

number = {5938},

pages = {340--343},

abstract = {Innate immunity represents the first line of defense in animals. We report a genome-wide in vivo Drosophila RNA interference screen to uncover genes involved in susceptibility or resistance to intestinal infection with the bacterium Serratia marcescens. We first employed whole-organism gene suppression, followed by tissue-specific silencing in gut epithelium or hemocytes to identify several hundred genes involved in intestinal antibacterial immunity. Among the pathways identified, we showed that the JAK-STAT signaling pathway controls host defense in the gut by regulating stem cell proliferation and thus epithelial cell homeostasis. Therefore, we revealed multiple genes involved in antibacterial defense and the regulation of innate immunity.},

keywords = {*Genome, *RNA Interference, Animal, Animals, Cell Proliferation, Drosophila melanogaster/*genetics/immunology/*microbiology, Drosophila Proteins/genetics/metabolism, Epithelial Cells, Epithelial Cells/cytology/physiology, ferrandon, Genetically Modified, Genome, Hemocytes, Hemocytes/immunology/metabolism/microbiology, Homeostasis, Immunity, Innate, Innate/*genetics, Insect, Intestinal Mucosa, Intestinal Mucosa/cytology/immunology/metabolism/microbiology, Janus Kinases, Janus Kinases/genetics/metabolism, M3i, Models, RNA Interference, Serratia Infections, Serratia Infections/genetics/*immunology/microbiology, Serratia marcescens, Serratia marcescens/*immunology/physiology, Signal Transduction, STAT Transcription Factors, STAT Transcription Factors/genetics/metabolism, Stem Cells, Stem Cells/cytology/physiology},

pubstate = {published},

tppubtype = {article}

}

@article{wang-sattler_mosaic_2007,

title = {Mosaic genome architecture of the Anopheles gambiae species complex},

author = {Rui Wang-Sattler and Stephanie A Blandin and Ye Ning and Claudia Blass and Guimogo Dolo and Yeya T Touré and Alessandra delle Torre and Gregory C Lanzaro and Lars M Steinmetz and Fotis C Kafatos and Liangbiao Zheng},

doi = {10.1371/journal.pone.0001249},

issn = {1932-6203},

year  = {2007},

date = {2007-01-01},

journal = {PLoS ONE},

volume = {2},

number = {11},

pages = {e1249},

abstract = {BACKGROUND: Attempts over the last three decades to reconstruct the phylogenetic history of the Anopheles gambiae species complex have been important for developing better strategies to control malaria transmission. METHODOLOGY: We used fingerprint genotyping data from 414 field-collected female mosquitoes at 42 microsatellite loci to infer the evolutionary relationships of four species in the A. gambiae complex, the two major malaria vectors A. gambiae sensu stricto (A. gambiae s.s.) and A. arabiensis, as well as two minor vectors, A. merus and A. melas. PRINCIPAL FINDINGS: We identify six taxonomic units, including a clear separation of West and East Africa A. gambiae s.s. S molecular forms. We show that the phylogenetic relationships vary widely between different genomic regions, thus demonstrating the mosaic nature of the genome of these species. The two major malaria vectors are closely related and closer to A. merus than to A. melas at the genome-wide level, which is also true if only autosomes are considered. However, within the Xag inversion region of the X chromosome, the M and two S molecular forms are most similar to A. merus. Near the X centromere, outside the Xag region, the two S forms are highly dissimilar to the other taxa. Furthermore, our data suggest that the centromeric region of chromosome 3 is a strong discriminator between the major and minor malaria vectors. CONCLUSIONS: Although further studies are needed to elucidate the basis of the phylogenetic variation among the different regions of the genome, the preponderance of sympatric admixtures among taxa strongly favor introgression of different genomic regions between species, rather than lineage sorting of ancestral polymorphism, as a possible mechanism.},

keywords = {Animals, Anopheles gambiae, Artificial, Bacterial, Biological Evolution, blandin, Chromosomes, Female, Genetic Markers, Genetic Variation, Genome, M3i, Microsatellite Repeats, Mosaicism},

pubstate = {published},

tppubtype = {article}

}

@article{evans_immune_2006,

title = {Immune pathways and defence mechanisms in honey bees Apis mellifera},

author = {J D Evans and K Aronstein and Y P Chen and Charles Hetru and Jean-Luc Imler and H Jiang and M Kanost and G J Thompson and Z Zou and D Hultmark},

doi = {10.1111/j.1365-2583.2006.00682.x},

issn = {0962-1075},

year  = {2006},

date = {2006-10-01},

journal = {Insect Molecular Biology},

volume = {15},

number = {5},

pages = {645--656},

abstract = {Social insects are able to mount both group-level and individual defences against pathogens. Here we focus on individual defences, by presenting a genome-wide analysis of immunity in a social insect, the honey bee Apis mellifera. We present honey bee models for each of four signalling pathways associated with immunity, identifying plausible orthologues for nearly all predicted pathway members. When compared to the sequenced Drosophila and Anopheles genomes, honey bees possess roughly one-third as many genes in 17 gene families implicated in insect immunity. We suggest that an implied reduction in immune flexibility in bees reflects either the strength of social barriers to disease, or a tendency for bees to be attacked by a limited set of highly coevolved pathogens.},

keywords = {Animals, Bees, Carrier Proteins, Genome, imler, Immunity, Insect, Janus Kinases, M3i, Multigene Family, Serine Endopeptidases, Signal Transduction, STAT Transcription Factors, Toll-Like Receptors},

pubstate = {published},

tppubtype = {article}

}

@article{irving_new_2005,

title = {New insights into Drosophila larval haemocyte functions through genome-wide analysis},

author = {Phil Irving and Jean-Michel Ubeda and Daniel Doucet and Laurent Troxler and Marie Lagueux and Daniel Zachary and Jules A Hoffmann and Charles Hetru and Marie Meister},

doi = {10.1111/j.1462-5822.2004.00462.x},

issn = {1462-5814},

year  = {2005},

date = {2005-03-01},

journal = {Cell. Microbiol.},

volume = {7},

number = {3},

pages = {335--350},

abstract = {Drosophila blood cells or haemocytes comprise three cell lineages, plasmatocytes, crystal cells and lamellocytes, involved in immune functions such as phagocytosis, melanisation and encapsulation. Transcriptional profiling of activities of distinct haemocyte populations and from naive or infected larvae, was performed to find genes contributing to haemocyte functions. Of the 13 000 genes represented on the microarray, over 2500 exhibited significantly enriched transcription in haemocytes. Among these were genes encoding integrins, peptidoglycan recognition proteins (PGRPs), scavenger receptors, lectins, cell adhesion molecules and serine proteases. One relevant outcome of this analysis was the gain of new insights into the lamellocyte encapsulation process. We showed that lamellocytes require betaPS integrin for encapsulation and that they transcribe one prophenoloxidase gene enabling them to produce the enzyme necessary for melanisation of the capsule. A second compelling observation was that following infection, the gene encoding the cytokine Spatzle was uniquely upregulated in haemocytes and not the fat body. This shows that Drosophila haemocytes produce a signal molecule ready to be activated through cleavage after pathogen recognition, informing distant tissues of infection.},

keywords = {Animals, bioinformatic, Catechol Oxidase, Cell Lineage, Enzyme Precursors, Escherichia coli, Fat Body, Gene Expression Profiling, Genome, Hemocytes, hoffmann, Integrin alpha Chains, Integrins, Larva, M3i, Micrococcus luteus},

pubstate = {published},

tppubtype = {article}

}

@article{royet_sensing_2005,

title = {Sensing and signaling during infection in Drosophila},

author = {Julien Royet and Jean-Marc Reichhart and Jules A Hoffmann},

doi = {10.1016/j.coi.2004.12.002},

issn = {0952-7915},

year  = {2005},

date = {2005-02-01},

journal = {Curr. Opin. Immunol.},

volume = {17},

number = {1},

pages = {11--17},

abstract = {Most of the progress in dissecting the Drosophila antimicrobial response over the past decade has centered around intracellular signaling pathways in immune response tissues and expression of genes encoding antimicrobial peptide genes. The past few years, however, have witnessed significant advances in our understanding of the recognition of microbial invaders and subsequent activation of signaling cascades. In particular, the roles of peptidoglycan recognition proteins, which have known homologues in mammals, have been recognized and examined at the structural and functional levels.},

keywords = {Animals, Antimicrobial Cationic Peptides, Bacterial Infections, Gene Expression Regulation, Genome, hoffmann, Immunity, Innate, M3i, reichhart, Signal Transduction},

pubstate = {published},

tppubtype = {article}

}

@article{bilak_toll_2003,

title = {Toll and Toll-like receptors in Drosophila},

author = {Hana Bilak and S Tauszig-Delamasure and Jean-Luc Imler},

doi = {10.1042/},

issn = {0300-5127},

year  = {2003},

date = {2003-06-01},

journal = {Biochemical Society Transactions},

volume = {31},

number = {Pt 3},

pages = {648--651},

abstract = {The Drosophila Toll receptor controls the immune response to Gram-positive bacteria and fungi by activating a signalling pathway partially conserved throughout evolution. The Drosophila genome encodes eight additional Toll-related receptors, most of which appear to carry out developmental rather than immune functions. One exception may be Toll-9, which shares structural and functional similarities with mammalian TLRs.},

keywords = {Animals, Biological Evolution, Cell Surface, Fungi, Genome, Gram-Negative Bacteria, Gram-Positive Bacteria, imler, M3i, Membrane Glycoproteins, Receptors, Toll-Like Receptor 5, Toll-Like Receptors},

pubstate = {published},

tppubtype = {article}

}

@article{christophides_immunity-related_2002,

title = {Immunity-related genes and gene families in Anopheles gambiae},

author = {George K Christophides and Evgeny Zdobnov and Carolina Barillas-Mury and Ewan Birney and Stephanie A Blandin and Claudia Blass and Paul T Brey and Frank H Collins and Alberto Danielli and George Dimopoulos and Charles Hetru and Ngo T Hoa and Jules A Hoffmann and Stefan M Kanzok and Ivica Letunic and Elena A Levashina and Thanasis G Loukeris and Gareth Lycett and Stephan Meister and Kristin Michel and Luis F Moita and Hans-Michael Müller and Mike A Osta and Susan M Paskewitz and Jean-Marc Reichhart and Andrey Rzhetsky and Laurent Troxler and Kenneth D Vernick and Dina Vlachou and Jennifer Volz and Christian von Mering and Jiannong Xu and Liangbiao Zheng and Peer Bork and Fotis C Kafatos},

url = {http://www.ncbi.nlm.nih.gov/pubmed/12364793},

doi = {10.1126/science.1077136},

issn = {1095-9203},

year  = {2002},

date = {2002-10-01},

journal = {Science},

volume = {298},

number = {5591},

pages = {159--165},

abstract = {We have identified 242 Anopheles gambiae genes from 18 gene families implicated in innate immunity and have detected marked diversification relative to Drosophila melanogaster. Immune-related gene families involved in recognition, signal modulation, and effector systems show a marked deficit of orthologs and excessive gene expansions, possibly reflecting selection pressures from different pathogens encountered in these insects' very different life-styles. In contrast, the multifunctional Toll signal transduction pathway is substantially conserved, presumably because of counterselection for developmental stability. Representative expression profiles confirm that sequence diversification is accompanied by specific responses to different immune challenges. Alternative RNA splicing may also contribute to expansion of the immune repertoire.},

keywords = {Alternative Splicing, Animals, Anopheles, Apoptosis, bacteria, bioinformatic, blandin, Catechol Oxidase, Computational Biology, Enzyme Precursors, Gene Expression Regulation, Genes, Genetic, Genome, hoffmann, Immunity, Innate, Insect, Insect Proteins, M3i, Multigene Family, Peptides, Phylogeny, Plasmodium, Protein Structure, reichhart, Selection, Serine Endopeptidases, Serpins, Signal Transduction, Tertiary},

pubstate = {published},

tppubtype = {article}

}

@article{irving_genome-wide_2001,

title = {A genome-wide analysis of immune responses in Drosophila},

author = {Phil Irving and Laurent Troxler and Timothy S Heuer and Marcia Belvin and Casey Kopczynski and Jean-Marc Reichhart and Jules A Hoffmann and Charles Hetru},

doi = {10.1073/pnas.261573998},

issn = {0027-8424},

year  = {2001},

date = {2001-12-01},

journal = {Proc. Natl. Acad. Sci. U.S.A.},

volume = {98},

number = {26},

pages = {15119--15124},

abstract = {Oligonucleotide DNA microarrays were used for a genome-wide analysis of immune-challenged Drosophila infected with Gram-positive or Gram-negative bacteria, or with fungi. Aside from the expression of an established set of immune defense genes, a significant number of previously unseen immune-induced genes were found. Genes of particular interest include corin- and Stubble-like genes, both of which have a type II transmembrane domain; easter- and snake-like genes, which may fulfil the roles of easter and snake in the Toll pathway; and a masquerade-like gene, potentially involved in enzyme regulation. The microarray data has also helped to greatly reduce the number of target genes in large gene groups, such as the proteases, helping to direct the choices for future mutant studies. Many of the up-regulated genes fit into the current conceptual framework of host defense, whereas others, including the substantial number of genes with unknown functions, offer new avenues for research.},

keywords = {Animals, bioinformatic, Gene Expression Regulation, Genome, Gram-Negative Bacteria, hoffmann, M3i, Male, Oligonucleotide Array Sequence Analysis, reichhart, Signal Transduction},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3' LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition},

author = { T. Heyman and B. Agoutin and S. Friant and F. X. Wilhelm and M. L. Wilhelm},

year  = {1995},

date = {1995-01-01},

journal = {J Mol Biol},

volume = {253},

number = {2},

pages = {291-303},

abstract = {Long terminal repeat elements and retroviruses require primers for initiation of minus and plus-strand DNA synthesis by reverse transcriptase. Here we demonstrate genetically that plus-strand DNA synthesis of the yeast Ty1 element is initiated at two sites located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the pol gene in the integrase coding sequence (PPT2). A consequence of the presence of two PPTs is that Ty1 plus-strand DNA exists as segments at some time during replication. Three fragments have been identified: the plus-strand strong-stop DNA initiated at PPT1, a downstream fragment initiated at PPT2 and an upstream fragment spanning the 5'-terminal part of Ty1 and a portion of the TyB gene. Characterization of the 3' ends of the plus-strand DNA fragments reveals (1) that the upstream fragment is elongated beyond PPT2 creating a plus-strand overlap and (2) that the majority of plus-strand strong-stop DNA fragments bear a copy of the minus-strand primer binding site in agreement with the accepted model of retroviral genomic RNA reverse transcription. The two polypurine tracts, PPT1 and PPT2, have an identical sequence GGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition.},

note = {0022-2836 

Journal Article},

keywords = {*DNA, *Genes, *Repetitive, *Retroelements, Acid, Base, C/analysis, cerevisiae/genetics/*virology, Chain, Cloning, Data, DNA, Fungal, Fungal/biosynthesis, Genes, Genetic, Genome, Gov't, Mapping, Molecular, Non-U.S., Nucleic, pol, Poly, Polymerase, Primers, Reaction, Replication, Restriction, Saccharomyces, Sequence, Sequences, Support, Transcription, Viral, Viral/*biosynthesis},

pubstate = {published},

tppubtype = {article}

}