ABSTRACT. Ribosomal DNA (rDNA) sequences have been shown to be very useful for identification of microbial eukaryotes. Usually, complete or long partial sequences of the rDNA genes are analysed. However, the development of new massive sequencing technologies producing a large amount of relatively short sequences raises the question about the minimum length of rDNA fragments necessary for species distinction in environmental sampling. To answer this question, we compared six variable regions of the small subunit (SSU) rDNA of foraminifera, known to have rapidly evolving ribosomal genes. For each region, we analysed (1) the sequence divergence between and within foraminiferal morphospecies, (2) the intraspecific polymorphism, and (3) the ability of each region to recognize the phylotypes inferred from analysis of a longer fragment. Our results show that although the variable regions differ considerably between taxonomic groups, most of them perform very well as species identifiers. Taking into account different analyses, the expansion segment of Helix 37 appears to be the best candidate for barcoding foraminifera. We propose that this relatively short region, averaging 50-60 nt in length, could be an ideal barcode for identification of foraminifera in environmental samples using massive sequencing approach. Department of Zoology and Animal Biology, University of Geneva, CH-1211 Geneva 4,,Switzerland. Pawlowski, J.,Lecroq, B. 2010-02-02T12:16:09+01:00 502 10.1111/j.1550-7408.2009.00468.x J Eukaryot Microbiol JEU468 2010-01-01 20113377 false J Eukaryot Microbiol. 2010 Jan 22. 2010-02-02T12:16:09+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/20113377 48 Vasomotion consists in cyclic arterial diameter variations induced by synchronous contractions and relaxations of smooth muscle cells (SMCs). However, the arteries do not contract simultaneously on macroscopic distances and a propagation of the contraction can be observed. In the present study, our aim was to investigate this propagation. We stimulated endothelium-denuded rat mesenteric arterial strips with phenylephrine (PE) to obtain vasomotion and observed that the contraction waves are linked to intercellular calcium waves. A velocity of about 100 mum/s was measured for the two kinds of waves. To investigate the calcium wave propagation mechanisms, we used a method allowing a PE stimulation of a small area of the strip. No calcium propagation could be induced by this local stimulation when the strip was in its resting state. However, if a low PE concentration was added on the whole strip, local PE stimulations induced calcium waves spreading over finite distances. The calcium wave velocity induced by local stimulation was identical to the velocity observed during vasomotion. This suggests that the propagation mechanisms are similar in the two cases. Using inhibitors of gap junctions and of voltage operated calcium channels, we showed that the locally induced calcium propagation likely depends on the propagation of the SMCs depolarization. Finally, we proposed a model of the propagation mechanisms underlying these intercellular calcium waves. Key words: Conducted vasomotor response, Smooth muscle cell, Rat mesenteric artery. Swiss Federal Institute of Technology. Seppey, D.,Sauser, R.,Koenigsberger, M.,Beny, J. L.,Meister, J. J. 2009-12-10T10:27:27+01:00 500 10.1152/ajpheart.00281.2009 Am J Physiol Heart Circ Physiol 00281.2009 2009-12-01 19966061 false Am J Physiol Heart Circ Physiol. 2009 Dec 4. 2009-12-10T10:27:27+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19966061 14 The enigmatic Semimorula liquescens E.F. Haskins, McGuin. & C.S. Berry has been isolated repeatedly from dried infructescences of Lythrum salicaria collected from Seattle and Kirkland, Washington. Detailed developmental, morphological and ultrastructural studies suggested that it represents a taxon within Mycetozoa, closely allied with Myxogastria (Myxomycetes) but with unique characteristics. Phylogeny based on two genes places it with confidence in family Echinosteliidae. This species differs from a typical Echinostelium in the way spores germinate and in the lack of a stalked sporophore, the latter being a secondary loss. Semimorula liquescens therefore might be a useful negative model to search for genes inducing stalk formation during sporulation. University of Oxford, Department of Zoology, South Parks Road, Oxford OX1 3PS,,United Kingdom. afiore-donno6@infomaniak.ch Fiore-Donno, A. M.,Haskins, E. F.,Pawlowski, J.,Cavalier-Smith, T. 2009-11-27T14:56:42+01:00 499 6 Mycologia 773-776 2009-11-01 19927743 false Mycologia. 2009 Nov-Dec;101(6):773-6. 2009-11-27T14:56:42+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19927743 48 101 Temporal and spatial control of Hox gene expression is essential for correct patterning of many animals. In both Drosophila and vertebrates, Polycomb and Trithorax group complexes control the maintenance of Hox gene expression in appropriate domains. In vertebrates, dynamic changes in chromatin modifications are also observed during the sequential activation of Hox genes in the embryo, suggesting that progressive epigenetic modifications could regulate collinear gene activation. National Research Centre 'Frontiers in Genetics', Department of Zoology and,Animal Biology, University of Geneva, Sciences III, Geneva. Soshnikova, N.,Duboule, D. 2009-11-26T10:02:03+01:00 498 8 Epigenetics 10132 2009-11-01 19923920 false Epigenetics. 2009 Nov 21;4(8). 2009-11-26T10:02:03+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19923920 17 4 Spumochlamys perforata n. sp. and Spumochlamys bryora n. sp. were isolated and described from dry epiphytic moss. The morphology and ultrastructure of both species clearly demonstrate that they belong to the genus Spumochlamys (family Microchlamyiidae). They differ from its only described member, Spumochlamys iliensis (as well as from species of Microchlamys), in the relief of the dorsal surface of the test, revealed by scanning electron microscopy, which can represent a good characteristic for species identification. They also differ in the structure of the dorsal part of the test wall (especially S. perforata). Small subunit ribosomal DNA-based molecular phylogenetic analyses show that Spumochlamys is a deeply branching lineage of the Arcellinida, without any close affinities. Actin gene sequence analysis places this genus within the Tubulinea, close to two other arcellinid lineages but without forming a monophyletic group with them. These data together strongly suggest that the lack of resolution in the arcellinid molecular phylogenies is due to serious undersampling of taxa, a limited number of sequence data, and high divergence rates in most of the species. Research Group Protozoology, Institute of Biology/Zoology, Free University of,Berlin, Konigin-Luise-Strasse 1-3, 14195 Berlin, Germany. aak@ak14261.spb.edu Kudryavtsev, A.,Pawlowski, J.,Hausmann, K. 2009-11-17T16:50:54+01:00 497 10.1111/j.1550-7408.2009.00430.x 6 J Eukaryot Microbiol 495-503 JEU430 2009-11-01 19883438 false J Eukaryot Microbiol. 2009 Nov-Dec;56(6):495-503. 2009-11-17T16:50:54+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19883438 48 56 Departement d'herpetologie et d'ichtyologie, Museum d'histoire naturelle, 1 route,de Malagnou, C.P. 6434, CH-1211 Geneve 6, Switzerland; Departement de zoologie et,de biologie animale, Universite de Geneve, Sciences III, 30 quai E. Ansermet,,CH-1211 Geneve 4, Switzerland. Covain, R.,Dray, S.,Fisch-Muller, S.,Montoya-Burgos, J. I. 2009-11-17T16:49:06+01:00 496 10.1016/j.ympev.2009.10.036 Mol Phylogenet Evol S1055-7903(09)00445-X 2009-11-01 19895892 false Mol Phylogenet Evol. 2009 Nov 3. 2009-11-17T16:49:06+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19895892 47 Morphological identification of naked lobose amoebae has always been a problem, hence the development of reliable molecular tools for species distinction is a priority for amoebae systematics. Previous studies based on SSU rDNA sequences provided a backbone for the phylogeny of Amoebozoa but were of little help for the species distinctions in this group. On one hand, the SSU rDNA sequences were rather conserved between closely related species; on the other hand, the intra-strain polymorphism of the SSU gene obscured species identification. In the present study, a 3' fragment of the SSU, a complete ITS1-5.8S-ITS2 block and a 5' fragment of COI gene were cloned and sequenced for six Vannella morphospecies, of which V. simplex was represented by six different isolates. SSU rDNA and ITS were found to be inappropriate for species differentiation, while distinctive and homogenous COI sequences were obtained for each well-defined morphospecies. Moreover, a number of distinct COI genotypes have been identified among V. simplex isolates. This suggests that COI may be a good candidate for DNA barcoding of amoebae, but further studies are necessary to confirm the accurateness of the COI gene as a barcode in other gymnamoebae, and to understand the taxonomic meaning of COI variations. Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS,,Tikhoretsky ave. 4, 194064 St. Petersburg, Russia. Nassonova, E.,Smirnov, A.,Fahrni, J.,Pawlowski, J. 2009-10-26T09:32:16+01:00 495 10.1016/j.protis.2009.07.003 Protist S1434-4610(09)00055-8 2009-10-01 19819756 false Protist. 2009 Oct 9. 2009-10-26T09:32:16+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19819756 48 Histone chaperones are involved in a variety of chromatin transactions. By a proteomics survey, we identified the interaction networks of histone chaperones ASF1, CAF1, HIRA, and NAP1. Here, we analyzed the cooperation of H3/H4 chaperone ASF1 and H2A/H2B chaperone NAP1 with two closely related silencing complexes: LAF and RLAF. NAP1 binds RPD3 and LID-associated factors (RLAF) comprising histone deacetylase RPD3, histone H3K4 demethylase LID/KDM5, SIN3A, PF1, EMSY, and MRG15. ASF1 binds LAF, a similar complex lacking RPD3. ASF1 and NAP1 link, respectively, LAF and RLAF to the DNA-binding Su(H)/Hairless complex, which targets the E(spl) NOTCH-regulated genes. ASF1 facilitates gene-selective removal of the H3K4me3 mark by LAF but has no effect on H3 deacetylation. NAP1 directs high nucleosome density near E(spl) control elements and mediates both H3 deacetylation and H3K4me3 demethylation by RLAF. We conclude that histone chaperones ASF1 and NAP1 differentially modulate local chromatin structure during gene-selective silencing. Department of Biochemistry, Center for Biomedical Genetics, Erasmus University,Medical Center, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands. Moshkin, Y. M.,Kan, T. W.,Goodfellow, H.,Bezstarosti, K.,Maeda, R. K.,Pilyugin, M.,Karch, F.,Bray, S. J.,Demmers, J. A.,Verrijzer, C. P. 2009-10-02T16:03:07+02:00 494 10.1016/j.molcel.2009.07.020 6 Mol Cell 782-793 S1097-2765(09)00516-4 2009-09-01 19782028 false Mol Cell. 2009 Sep 25;35(6):782-93. 2009-10-02T16:03:07+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19782028 19 35 Decapitated Hydra regenerate their heads via morphallaxis, i.e., without significant contributions made by cell proliferation or interstitial stem cells. Indeed, Hydra depleted of interstitial stem cells regenerate robustly, and Wnt3 from epithelial cells triggers head regeneration. However, we find a different mechanism controlling regeneration after midgastric bisection in animals equipped with both epithelial and interstitial cell lineages. In this context, we see rapid induction of apoptosis and Wnt3 secretion among interstitial cells at the head- (but not foot-) regenerating site. Apoptosis is both necessary and sufficient to induce Wnt3 production and head regeneration, even at ectopic sites. Further, we identify a zone of proliferation beneath the apoptotic zone, reminiscent of proliferative blastemas in regenerating limbs and of compensatory proliferation induced by dying cells in Drosophila imaginal discs. We propose that different types of injuries induce distinct cellular modes of Hydra head regeneration, which nonetheless converge on a central effector, Wnt3. Department of Zoology and Animal Biology, University of Geneva, 30 Quai Ernest,Ansermet, CH-1211 Geneva 4, Switzerland. Chera, S.,Ghila, L.,Dobretz, K.,Wenger, Y.,Bauer, C.,Buzgariu, W.,Martinou, J. C.,Galliot, B. 2009-08-19T16:30:31+02:00 493 10.1016/j.devcel.2009.07.014 2 Dev Cell 279-289 S1534-5807(09)00298-6 2009-08-01 19686688 true Dev Cell. 2009 Aug;17(2):279-89. 2009-08-19T16:30:31+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19686688 35 17 Stalks and loricae of chrysomonads were studied by fluorescence microscopy employing Calcoflor White-Evans blue (CW-Eb) staining, and by uranyl acetate staining of dried, whole mount preparations for electron microscopy. These structures were composed of microfibrils ~4nm in diameter embedded in a matrix. The organization of the loricae of Poterioochromonas malhamenesis, "Amimonas minuta", Poterioochromonas stipitata and Ochromonas gloeopara showed a similar structural plan, consisting of a foot, stalk and cup region that together resemble a wine glass. CW-Eb-stained, microfibrillar stalks were identified also in Paraphysomonas vestita, Anthophysa vegetans and "Felimonas flocculans". These results suggest that CW-Eb-stained structures composed of microfibrils ~4nm in diameter may be more common in chrysomonads than previously recognized. In cultures, these structures participate in the formation of cell aggregates and attachment of cells to substrates, and thus may be of ecological importance. Additionally, non-siliceous, CW-Eb-stained cysts were identified for the first time in P. malhamensis. Department of Zoology and Animal Biology, University of Geneva, Sciences III, 30 ,Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland. Peck, R. K. 2009-08-17T11:06:47+02:00 492 10.1016/j.protis.2009.07.002 Protist S1434-4610(09)00053-4 2009-08-01 19674932 false Protist. 2009 Aug 10. 2009-08-17T11:06:47+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19674932 49 A new species of Leptomyxida, named Rhizamoeba neglecta was found during studies of the amoeba fauna of the inner Lake Leshevoe located at Valamo archipelago (The Lake Ladoga, North-Western Russia). Light-microscopical and ultrastructural studies indicated that it represents a new species of Leptomyxida. The partial 18S rDNA sequence of this amoeba is very similar to that of Leptomyxa reticulata.. These organisms, however, are very different in LM morphology and biology. Organisms assigned to the genus Rhizamoeba do not form a single clade in the 18S rDNA tree. This may indicate that the genus is an artificial grouping or that a number of studied strains were misidentified. The phylogeny and the systematics of leptomyxids require further investigation. Department of Invertebrate Zoology, Faculty of Biology and Soil Sciences, St.,Petersburg State University, Universitetskaja nab. 7/9, 199034 St. Petersburg,,Russia. Smirnov, A.,Nassonova, E.,Fahrni, J.,Pawlowski, J. 2009-08-05T15:10:43+02:00 490 10.1016/j.ejop.2009.04.002 Eur J Protistol S0932-4739(09)00030-3 2009-08-01 19651498 false Eur J Protistol. 2009 Aug 1. 2009-08-05T15:10:43+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19651498 48 During vertebrate development, the temporal control of Hox gene transcriptional activation follows the genomic order of the genes within the Hox clusters. Although it is recognized that this "Hox clock" serves to coordinate body patterning, the underlying mechanism remains elusive. We have shown that successive Hox gene activation in the mouse embryo is closely associated with a directional transition in chromatin status, as judged by the dynamic progression of transcription-competent modifications: Increases in activation marks correspond to decreases in repressive marks. Furthermore, using a mouse in which a Hox cluster was split into two pieces, we document the necessity to maintain a clustered organization to properly implement this process. These results suggest that chromatin modifications are important parameters in the temporal regulation of this gene family. National Research Centre Frontiers in Genetics, Department of Zoology and Animal ,Biology, University of Geneva, Sciences III, Quai Ernest-Ansermet 30, 1211 Geneva,4, Switzerland. Soshnikova, N.,Duboule, D. 2009-06-08T15:01:19+02:00 487 10.1126/science.1171468 5932 Science 1320-1323 324/5932/1320 2009-06-01 19498168 false Science. 2009 Jun 5;324(5932):1320-1323. 2009-06-08T15:01:19+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19498168 17 324 New perspectives on the origin of neurogenesis emerged with the identification of genes encoding post-synaptic proteins as well as many "neurogenic" regulators as the NK, Six, Pax, bHLH proteins in the Demosponge genome, a species that might differentiate sensory cells but no neurons. However, poriferans seem to miss some key regulators of the neurogenic circuitry as the Hox/paraHox and Otx-like gene families. Moreover as a general feature, many gene families encoding evolutionarily-conserved signaling proteins and transcription factors were submitted to a wave of gene duplication in the last common eumetazoan ancestor, after Porifera divergence. In contrast gene duplications in the last common bilaterian ancestor, Urbilateria, are limited, except for the bHLH Atonal-class. Hence Cnidaria share with Bilateria a large number of genetic tools. The expression and functional analyses currently available suggest a neurogenic function for numerous orthologs in developing or adult cnidarians where neurogenesis takes place continuously. As an example, in the Hydra polyp, the Clytia medusa and the Acropora coral, the Gsx/cnox2/Anthox-2 ParaHox gene likely supports neurogenesis. Also neurons and nematocytes (mechano-sensory cells) share in hydrozoans a common stem cell and several regulatory genes indicating that they can be considered as sister cells. Performed in anthozoan and medusozoan species, these studies should tell us more about the way(s) evolution hazards achieved the transition from epithelial to neuronal cell fate, and about the robustness of the genetic circuitry that allowed neuro-muscular transmission to arise and be maintained across evolution. Department of Zoology and Animal Biology, Faculty of Science, University of,Geneva, Sciences III, 30 quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland. Galliot, B.,Quiquand, M.,Ghila, L.,de Rosa, R.,Miljkovic-Licina, M.,Chera, S. 2009-05-26T17:58:30+02:00 484 10.1016/j.ydbio.2009.05.563 Dev Biol S0012-1606(09)00875-6 2009-05-01 19465018 false Dev Biol. 2009 May 21. 2009-05-26T17:58:30+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19465018 52 The Hydra polyp provides a powerful model system to investigate the regulation of cell survival and cell death in homeostasis and regeneration as Hydra survive weeks without feeding and regenerates any missing part after bisection. Induction of autophagy during starvation is the main surviving strategy in Hydra as autophagic vacuoles form in most myoepithelial cells after several days. When the autophagic process is inhibited, animal survival is actually rapidly jeopardized. An appropriate regulation of autophagy is also essential during regeneration as Hydra RNAi knocked-down for the serine protease inhibitor Kazal-type (SPINK) gene Kazal1, exhibit a massive autophagy after amputation that rapidly compromises cell and animal survival. This excessive autophagy phenotype actually mimics that observed in the mammalian pancreas when SPINK genes are mutated, highlighting the paradigmatic value of the Hydra model system for deciphering pathological processes. Interestingly autophagy during starvation predominantly affects ectodermal epithelial cells and lead to cell survival whereas Kazal1(RNAi)-induced autophagy is restricted to endodermal digestive cells that rapidly undergo cell death. This indicates that distinct regulations that remain to be identified, are at work in these two contexts. Cnidarian express orthologs for most components of the autophagy and TOR pathways suggesting evolutionarily-conserved roles during starvation. Department of Zoology and Animal Biology, Faculty of Sciences, University of,Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland. Chera, S.,Buzgariu, W.,Ghila, L.,Galliot, B. 2009-05-05T07:47:15+02:00 481 10.1016/j.bbamcr.2009.03.010 BBA Molecular Cell Research S0167-4889(09)00082-2 2009-04-01 19362111 true Biochim Biophys Acta. 2009 Apr 9. 2009-05-27T15:28:27+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19362111 35 in press Mammals rely heavily on olfaction to interact adequately with each other and with their environment. They make use of seven-transmembrane G-protein-coupled receptors to identify odorants and pheromones. These receptors are present on dendrites of olfactory sensory neurons located in the main olfactory or vomeronasal sensory epithelia, and pertain to the odorant, trace amine-associated receptor and vomeronasal type 1 (ref. 4) or 2 (refs 5-7) receptor superfamilies. Whether these four sensor classes represent the complete olfactory molecular repertoire used by mammals to make sense of the outside world is unknown. Here we report the expression of formyl peptide receptor-related genes by vomeronasal sensory neurons, in multiple mammalian species. Similar to the four known olfactory receptor gene classes, these genes encode seven-transmembrane proteins, and are characterized by monogenic transcription and a punctate expression pattern in the sensory neuroepithelium. In vitro expression of mouse formyl peptide receptor-like 1, 3, 4, 6 and 7 provides sensitivity to disease/inflammation-related ligands. Establishing an in situ approach that combines whole-mount vomeronasal preparations with dendritic calcium imaging in the intact neuroepithelium, we show neuronal responses to the same molecules, which therefore represent a new class of vomeronasal agonists. Taken together, these results suggest that formyl peptide receptor-like proteins have an olfactory function associated with the identification of pathogens, or of pathogenic states. [1] Department of Zoology and Animal Biology, and National Center of Competence,'Frontiers in Genetics', University of Geneva, 1205 Geneva, Switzerland [2] These,authors contributed equally to this work. Riviere, S.,Challet, L.,Fluegge, D.,Spehr, M.,Rodriguez, I. 2009-04-27T09:14:34+02:00 471 10.1038/nature08029 Nature nature08029 2009-04-01 19387439 true Nature. 2009 Apr 22. 2009-08-01T08:56:59+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19387439 50 One of the earliest morphogenetic processes in the development of many animals is epiboly. In the zebrafish, epiboly ensues when the animally localized blastoderm cells spread, thin over, and enclose the vegetally localized yolk. Only a few factors are known to function in this fundamental process. We identified a maternal-effect mutant, betty boop (bbp), which displays a novel defect in epiboly, wherein the blastoderm margin constricts dramatically, precisely when half of the yolk cell is covered by the blastoderm, causing the yolk cell to burst. Whole-blastoderm transplants and mRNA microinjection rescue demonstrate that Bbp functions in the yolk cell to regulate epiboly. We positionally cloned the maternal-effect bbp mutant gene and identified it as the zebrafish homolog of the serine-threonine kinase Mitogen Activated Protein Kinase Activated Protein Kinase 2, or MAPKAPK2, which was not previously known to function in embryonic development. We show that the regulation of MAPKAPK2 is conserved and p38 MAP kinase functions upstream of MAPKAPK2 in regulating epiboly in the zebrafish embryo. Dramatic alterations in calcium dynamics, together with the massive marginal constrictive force observed in bbp mutants, indicate precocious constriction of an F-actin network within the yolk cell, which first forms at 50% epiboly and regulates epiboly progression. We show that MAPKAPK2 activity and its regulator p38 MAPK function in the yolk cell to regulate the process of epiboly, identifying a new pathway regulating this cell movement process. We postulate that a p38 MAPKAPK2 kinase cascade modulates the activity of F-actin at the yolk cell margin circumference allowing the gradual closure of the blastopore as epiboly progresses. Department of Cell and Developmental Biology, University of Pennsylvania School,of Medicine, Philadelphia, Pennsylvania, United States of America. Holloway, B. A.,Gomez de la Torre Canny, S.,Ye, Y.,Slusarski, D. C.,Freisinger, C. M.,Dosch, R.,Chou, M. M.,Wagner, D. S.,Mullins, M. C. 2009-03-14T21:19:08+01:00 463 10.1371/journal.pgen.1000413 3 PLoS Genet e1000413 2009-03-01 19282986 false PLoS Genet. 2009 Mar;5(3):e1000413. Epub 2009 Mar 13. 2009-03-14T21:19:08+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19282986 46 5 During development of the vertebrate body axis, Hox genes are transcribed sequentially, in both time and space, following their relative positions within their genomic clusters. Analyses of animal genomes support the idea that Hox gene clustering is essential for coordinating the various times of gene activations. However, the eventual collinear ordering of the gene specific transcript domains in space does not always require genomic clustering. We analyzed these complex regulatory relationships by using mutant alleles at the mouse HoxD locus, including one that splits the cluster into two pieces. We show that both positive and negative regulatory influences, located on either side of the cluster, control an early phase of collinear expression in the trunk. Interestingly, this early phase does not systematically impact upon the subsequent expression patterns along the main body axis, indicating that the mechanism underlying temporal collinearity is distinct from those acting during the second phase. We discuss the potential functions and evolutionary origins of these mechanisms, as well as their relationship with similar processes at work during limb development. National Research Centre "Frontiers in Genetics", Department of Zoology and,Animal Biology, University of Geneva, Sciences III, Geneva, Switzerland. Tschopp, P.,Tarchini, B.,Spitz, F.,Zakany, J.,Duboule, D. 2009-03-08T19:58:26+01:00 457 10.1371/journal.pgen.1000398 3 PLoS Genet e1000398 2009-03-01 19266017 false PLoS Genet. 2009 Mar;5(3):e1000398. Epub 2009 Mar 6. 2009-03-08T19:58:26+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19266017 17 5 Rotifers of Class Bdelloidea are remarkable in having evolved for millions of years, apparently without males and meiosis. In addition, they are unusually resistant to desiccation and ionizing radiation and are able to repair hundreds of radiation-induced DNA double-strand breaks per genome with little effect on viability or reproduction. Because specific histone H2A variants are involved in DSB repair and certain meiotic processes in other eukaryotes, we investigated the histone H2A genes and proteins of two bdelloid species. Genomic libraries were built and probed to identify histone H2A genes in Adineta vaga and Philodina roseola, species representing two different bdelloid families. The expressed H2A proteins were visualized on SDS-PAGE gels and identified by tandem mass spectrometry. We find that neither the core histone H2A, present in nearly all other eukaryotes, nor the H2AX variant, a ubiquitous component of the eukaryotic DSB repair machinery, are present in bdelloid rotifers. Instead, they are replaced by unusual histone H2A variants of higher mass. In contrast, a species of rotifer belonging to the facultatively sexual, desiccation- and radiation-intolerant sister class of bdelloid rotifers, the monogononts, contains a canonical core histone H2A and appears to lack the bdelloid H2A variant genes. Applying phylogenetic tools, we demonstrate that the bdelloid-specific H2A variants arose as distinct lineages from canonical H2A separate from those leading to the H2AX and H2AZ variants. The replacement of core H2A and H2AX in bdelloid rotifers by previously uncharacterized H2A variants with extended carboxy-terminal tails is further evidence for evolutionary diversity within this class of histone H2A genes and may represent adaptation to unusual features specific to bdelloid rotifers. Department of Biology, University of Namur, Namur, Belgium. Van Doninck, K.,Mandigo, M. L.,Hur, J. H.,Wang, P.,Guglielmini, J.,Milinkovitch, M. C.,Lane, W. S.,Meselson, M. 2009-03-07T15:08:14+01:00 456 10.1371/journal.pgen.1000401 3 PLoS Genet e1000401 2009-03-01 19266019 false PLoS Genet. 2009 Mar;5(3):e1000401. Epub 2009 Mar 6. 2009-03-07T15:08:14+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19266019 327 5 In many animals, gamete formation during embryogenesis is specified by maternal cytoplasmic determinants termed germ plasm [1, 2]. During oogenesis, germ plasm forms a distinct cellular structure such as pole plasm in Drosophila or the Balbiani body, an aggregate of organelles also found in mammals [3-10]. However, in vertebrates, the key regulators of germ plasm assembly are largely unknown. Here, we show that, at the beginning of zebrafish oogenesis, the germ plasm defect in bucky ball (buc) mutants precedes the loss of polarity, indicating that Buc primarily controls Balbiani body formation. Moreover, we molecularly identify the buc gene, which is exclusively expressed in the ovary with a novel, dynamic mRNA localization pattern first detectable within the Balbiani body. We find that a Buc-GFP fusion localizes to the Balbiani body during oogenesis and with the germ plasm during early embryogenesis, consistent with a role in germ plasm formation. Interestingly, overexpression of buc seems to generate ectopic germ cells in the zebrafish embryo. Because we discovered buc homologs in many vertebrate genomes, including mammals, these results identify buc as the first gene necessary and sufficient for germ plasm organization in vertebrates. Department of Zoology, University of Geneva, 1211 Geneva 4, Switzerland. Bontems, F.,Stein, A.,Marlow, F.,Lyautey, J.,Gupta, T.,Mullins, M. C.,Dosch, R. 2009-03-03T14:55:11+01:00 454 10.1016/j.cub.2009.01.038 Curr Biol S0960-9822(09)00610-1 2009-02-01 19249209 false Curr Biol. 2009 Feb 25. 2009-03-03T14:55:11+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19249209 46 Hox genes control many aspects of embryonic development in metazoans. Previous analyses of this gene family revealed a surprising diversity in terms of gene number and organization between various animal species. In vertebrates, Hox genes are grouped into tightly organized clusters, claimed to be devoid of repetitive sequences. Here, we report the genomic organization of the four Hox loci present in the green anole lizard and show that they have massively accumulated retrotransposons, leading to gene clusters larger in size when compared to other vertebrates. In addition, similar repeats are present in many other development-related gene-containing regions, also thought to be refractory to such repetitive elements. Transposable elements are major sources of genetic variations, including alterations of gene expression, and hence this situation, so far unique among vertebrates, may have been associated with the evolution of the spectacular realm of morphological variations in the body plans of Squamata. Finally, sequence alignments highlight some divergent evolution in highly conserved DNA regions between vertebrate Hox clusters, which may coincide with the emergence of mammalian-specific features. National Research Center "Frontiers in Genetics," Department of Zoology and,Animal Biology, University of Geneva, 1211 Geneva 4, Switzerland; Di-Poi, N.,Montoya-Burgos, J. I.,Duboule, D. 2009-02-21T17:38:49+01:00 450 10.1101/gr.087932.108 Genome Res gr.087932.108 2009-02-01 19228589 false Genome Res. 2009 Feb 18. 2009-02-21T17:38:49+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19228589 47 ABSTRACT: A recent study in BMC Evolutionary Biology shows that many of the open reading frames in mammalian Hox genes are more conserved than expected on the basis of their protein sequence. The presence of highly conserved DNA elements is thus not confined to the noncoding DNA in neighboring regions but clearly overlaps with coding sequences. These findings support an emerging view that gene regulatory and coding sequences are likely to be more intermingled than once believed. National Research Centre 'Frontiers in Genetics', Department of Zoology and,Animal Biology, University of Geneva, Sciences III, Quai Ernest-Ansermet 30, 1211,Geneva 4, Switzerland. Denis.Duboule@unige.ch. Woltering, J. M.,Duboule, D. 2009-02-20T16:32:46+01:00 448 10.1186/jbiol116 2 J Biol 17 jbiol116 2009-02-01 19226447 false J Biol. 2009 Feb 6;8(2):17. 2009-02-20T16:32:46+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19226447 17 8 Sensory coding strategies within vertebrates involve the expression of a limited number of receptor types per sensory cell. In mice, each vomeronasal sensory neuron transcribes monoallelically a single V1R pheromone receptor gene, chosen from a large V1R repertoire. The nature of the signals leading to this strict receptor expression is unknown, but is apparently based on a negative feedback mechanism initiated by the transcription of the first randomly chosen functional V1R gene. We show, in vivo, that the genetic replacement of the V1rb2 pheromone receptor coding sequence by an unrelated one from the odorant receptor gene M71 maintains gene exclusion. The expression of this exogenous odorant receptor in vomeronasal neurons does not trigger the transcription of odorant receptor-associated signalling molecules. These results strongly suggest that despite the different odorant and vomeronasal receptor expression sites, function and transduction cascades, a common mechanism is used by these chemoreceptors to regulate their transcription. Department of Zoology and Animal Biology, and NCCR 'Frontiers in Genetics',,University of Geneva, 30 Quai Ernest Ansermet, 1204 Geneva, Switzerland. Capello, L.,Roppolo, D.,Jungo, V. P.,Feinstein, P.,Rodriguez, I. 2009-02-10T15:50:54+01:00 445 10.1111/j.1460-9568.2009.06630.x Eur J Neurosci EJN6630 2009-02-01 19200072 false Eur J Neurosci. 2009 Feb 6. 2009-02-10T15:50:54+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19200072 50 In vertebrates, face and throat structures, such as jaw, hyoid and thyroid cartilages develop from a rostrocaudal metameric series of pharyngeal arches, colonized by cranial neural crest cells (NCCs). Colinear Hox gene expression patterns underlie arch specific morphologies, with the exception of the first (mandibular) arch, which is devoid of any Hox gene activity. We have previously shown that the first and second (hyoid) arches share a common, Hox-free, patterning program. However, whether or not more posterior pharyngeal arch neural crest derivatives are also patterned on the top of the same ground-state remained an unanswered question. Here, we show that the simultaneous inactivation of all Hoxa cluster genes in NCCs leads to multiple jaw and first arch-like structures, partially replacing second, third and fourth arch derivatives, suggesting that rostral and caudal arches share the same mandibular arch-like ground patterning program. The additional inactivation of the Hoxd cluster did not significantly enhance such a homeotic phenotype, thus indicating a preponderant role of Hoxa genes in patterning skeletogenic NCCs. Moreover, we found that Hoxa2 and Hoxa3 act synergistically to pattern third and fourth arch derivatives. These results provide insights into how facial and throat structures are assembled during development, and have implications for the evolution of the pharyngeal region of the vertebrate head. Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/ULP, ,UMR 7104, Strasbourg, France. Minoux, M.,Antonarakis, G. S.,Kmita, M.,Duboule, D.,Rijli, F. M. 2009-01-27T16:45:06+01:00 440 10.1242/dev.028621 4 Development 637-645 136/4/637 2009-02-01 19168678 false Development. 2009 Feb;136(4):637-45. 2009-01-27T16:45:06+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19168678 17 136 In early October 2008, researchers from diverse backgrounds gathered at an EMBO conference entitled ;The Molecular and Cellular Basis of Regeneration and Tissue Repair' to discuss the basic biology of regeneration. Topics included cell plasticity in regenerative and developmental contexts, and the link between wound healing and regeneration. The meeting also highlighted the progress made in identifying the molecular networks that underlie regeneration in a variety of model systems. Center for Regenerative Therapies in Dresden (CRTD Germany. Tanaka, E.,Galliot, B. 2009-01-16T10:15:06+01:00 434 10.1242/dev.031682 3 Development 349-353 136/3/349 2009-02-01 19141666 false Development. 2009 Feb;136(3):349-53. 2009-01-16T10:15:06+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19141666 35 136 AIM: Exogenous ATP elicits a delayed calcium-independent K(+) current on freshly isolated mouse thoracic aorta myocytes. We investigated the receptor, the intracellular pathway and the nature of this current. METHODS: The patch-clamp technique was used to record ATP-elicited delayed K(+) current in freshly dissociated myocytes. RESULTS: ATP-elicited delayed K(+) current was not inhibited by a 'cocktail' of K(+) channel blockers (4-AP, TEA, apamin, charybdotoxin, glibenclamide). The amplitude of the delayed K(+) current decreased after the reduction of extracellular pH from 7.4 to 6.5. These two characteristics suggest that this current could be carried by the TASK subfamily of 'twin-pore potassium channels' (K2P). Purinergic agonists including dATP, but not ADP, activated the delayed K(+) current, indicating that P2Y(11) is the likely receptor involved in its activation. The PKC activator phorbol ester 12,13-didecanoate stimulated this current. In addition, the PKC inhibitor Go 6850 partially inhibited it. Real-time quantitative PCR showed that the genes encoding TASK-1 and TASK-2 are expressed. CONCLUSION: Our results indicate that blocker cocktail-insensitive delayed K(+) current in freshly dissociated aortic myocytes is probably carried by the TASK subfamily of twin-pore channels. Department of Zoology and Animal Biology, University of Geneva, Sciences III,,Geneva, Switzerland. Hayoz, S.,Bychkov, R.,Serir, K.,Docquier, M.,Beny, J. L. 2008-08-02T09:50:08+02:00 363 10.1111/j.1748-1716.2008.01884.x 2 Acta Physiol (Oxf) 247-258 APS1884 2009-02-01 18616685 false Acta Physiol (Oxf). 2009 Feb;195(2):247-58. Epub 2008 Jul 30. 2009-01-20T21:12:51+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/18616685 14 195 In his 1978 seminal paper, Ed Lewis described a series of mutations that affect the segmental identities of the segments forming the posterior two-thirds of the Drosophila body plan. In each class of mutations, particular segments developed like copies of a more-anterior segment. Genetic mapping of the different classes of mutations led to the discovery that their arrangement along the chromosome paralleled the body segments they affect along the anteroposterior axis of the fly. As all these mutations mapped to the same cytological location, he named this chromosomal locus after its founding mutation. Thus the first homeotic gene (Hox) cluster became known as the bithorax complex (BX-C). Even before the sequencing of the BX-C, the fact that these similar mutations grouped together in a cluster, lead Ed Lewis to propose that the homeotic genes arose through a gene duplication mechanism and that these clusters would be conserved through evolution. With the identification of the homeobox in the early 1980s, Lewis' first prediction was confirmed. The two cloned Drosophila homeotic genes, Antennapedia and Ultrabithorax, were indeed related genes. Using the homeobox as an entry point, homologous genes have since been cloned in many other species. Today, Hox clusters have been discovered in almost all metazoan phyla, confirming Lewis' second prediction. Remarkably, these homologous Hox genes are also arranged in clusters with their order within each cluster reflecting the anterior boundary of their domain of expression along the anterior-posterior axis of the animal. This correlation between the genomic organization and the activity along the anteroposterior body axis is known as the principle of "colinearity." The description of the BX-C inspired decades of developmental and evolutionary biology. And although this first Hox cluster led to the identification of many important features common to all Hox gene clusters, it now turns out that the fly Hox clusters are rather exceptional when compared with the Hox clusters of other animals. In this chapter, we will review the history and salient features of bithorax molecular genetics, in part, emphasizing its unique features relative to the other Hox clusters. Maeda, R. K.,Karch, F. 2009-08-05T15:12:03+02:00 491 10.1016/S0070-2153(09)88001-0 Curr Top Dev Biol 1-33 S0070-2153(09)88001-0 2009-01-01 19651300 false Curr Top Dev Biol. 2009;88C:1-33. 2009-08-05T15:12:03+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19651300 19 88C Denis Duboule is one of the most influential and highly-cited scientists in developmental biology. Born in Geneva in 1955, he holds dual Swiss and French nationality. His undergraduate studies in biology at the University of Geneva included research on mouse embryology. He later learned molecular techniques in the laboratory of Pierre Chambon, becoming a major player in characterising the newly-discovered vertebrate Hox genes. He helped discover their genomic clustering, realising that they had arisen by trans duplication. With Gaunt and Sharpe, he proposed that vertebrate Hox clusters might show spatial colinearity, and subsequently extended this concept to the timing of gene activation (temporal colinearity). Along with the Krumlauf laboratory, he reported the structural and functional conservation of the homeotic systems in flies and vertebrates. His lab was the first to describe nested patterns of Hox gene expression in the developing mouse limb, and later showed that digit-associated Hoxd gene expression was lacking in zebrafish paired fin development. His concept of phylotypic progression helps explain major evolutionary developmental phenomena in terms of Hox gene regulatory networks. His research helped reveal that the genital tubercle may, like the limb, be patterned by Hox genes. His lab developed targeted meiotic recombination (TAMERE), using it to make profound advances in our understanding of Hox gene regulation. Remote enhancers linked to digit patterning have been uncovered, together with a likely mechanism for colinearity. Denis lives in Geneva with his wife Brigitte Galliot, also a scientist, with their four children. Duboule, D. 2009-07-02T15:29:14+02:00 489 10.1387/ijdb.072558mr 5-6 Int J Dev Biol 717-723 072558mr 2009-01-01 19557678 false Int J Dev Biol. 2009;53(5-6):717-23. 2009-07-02T15:29:14+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19557678 17 53 Hox and ParaHox (H/P) genes belong to evolutionary-sister clusters that arose through duplication of a ProtoHOX cluster early in animal evolution. In contrast to bilaterians, cnidarians express, beside PG1, PG2 and Gsx orthologs, numerous Hox-related genes with unclear origin. We characterized from marine hydrozoans three novel Hox-related genes expressed at medusa and polyp stages, which include a Pdx/Xlox ParaHox ortholog induced one day later than Gsx during embryonic development. To reconstruct H/P genes' early evolution, we performed multiple systematic comparative phylogenetic analyses, which identified derived sequences that blur the phylogenetic picture, recorded dramatically different evolutionary rates between ParaHox and Hox in cnidarians and showed the unexpected grouping of [Gsx-Pdx/Xlox-PG2-PG3] families in a single metagroup distinct from PG1. We propose a novel more parsimonious evolutionary scenario whereby H/P genes originated from a [Gsx-Pdx/Xlox-PG2-PG3]-related ProtoHox gene, the <<posterior>> and <<anterior>> H/P genes appearing secondarily. The ProtoHOX cluster would have contained the three Gsx/PG2, Pdx/PG3, Cdx/PG9 paralogs and produced through tandem duplication the primordial HOX and ParaHOX clusters in the Cnidaria-Bilateria ancestor. The stronger constraint on cnidarian ParaHox genes suggests that the primary function of pre-bilaterian H/P genes was to drive cellular evolutionary novelties such as neurogenesis rather than axis specification. Department of Zoology and Animal Biology, University of Geneva, Switzerland. Quiquand, M.,Yanze, N.,Schmich, J.,Schmid, V.,Galliot, B.,Piraino, S. 2009-04-27T09:12:40+02:00 469 10.1016/j.ydbio.2009.01.022 Dev Biol 173-187 S0012-1606(09)00062-1 2009-01-01 19389364 true Dev Biol. 2009 Jan 26. 2009-06-09T10:35:14+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19389364 35 328 The amoebae and amoeboid protists form a large and diverse assemblage of eukaryotes characterized by various types of pseudopodia. For convenience, the traditional morphology-based classification grouped them together in a macrotaxon named Sarcodina. Molecular phylogenies contributed to the dismantlement of this assemblage, placing the majority of sarcodinids into two new supergroups: Amoebozoa and Rhizaria. In this review, we describe the taxonomic composition of both supergroups and present their small subunit rDNA-based phylogeny. We comment on the advantages and weaknesses of these phylogenies and emphasize the necessity of taxon-rich multigene datasets to resolve phylogenetic relationships within Amoebozoa and Rhizaria. We show the importance of environmental sequencing as a way of increasing taxon sampling in these supergroups. Finally, we highlight the interest of Amoebozoa and Rhizaria for understanding eukaryotic evolution and suggest that resolving their phylogenies will be among the main challenges for future phylogenomic analyses. Department of Zoology and Animal Biology, University of Geneva, Geneva,,Switzerland. jan.pawlowski@zoo.unige.ch Pawlowski, J.,Burki, F. 2009-04-06T09:01:05+02:00 464 10.1111/j.1550-7408.2008.00379.x 1 J Eukaryot Microbiol 16-25 JEU379 2009-01-01 19335771 false J Eukaryot Microbiol. 2009 Jan-Feb;56(1):16-25. 2009-04-06T09:01:05+02:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19335771 48 56 Abstract Neotropical freshwater fishes have reached an unrivalled diversity, organized into several areas of endemism, yet the underlying processes are still largely unknown. The topographical and ecological characteristics of the Guyanas Region make it an ideal area of endemism in which to investigate the forces that have shaped this great diversity. This region is thought to be inhabited by species descending from Amazonian ancestors, which would have used two documented routes that, however, hardly explain the entrance of species adapted to running waters. Here, we investigate the evolutionary history of Pseudancistrus brevispinis, a catfish endemic to this region and exclusively found in running waters, thus making it an ideal model for investigating colonization routes and dispersal in such habitats. Our analyses, based on mitochondrial and nuclear markers, revealed an unexpected diversity consisting of six monophyletic lineages within P. brevispinis, showing a disjoint distribution pattern. The lineages endemic to Guyanas coastal rivers form a monophyletic group that originated via an ancestral colonization event from the Amazon basin. Evidence given favours a colonization pathway through river capture between an Amazonian tributary and the Upper Maroni River. Population genetic analyses of the most widespread species indicate that subsequent dispersal among Guyanas coastal rivers occurred principally by temporary connections between adjacent rivers during periods of lower sea level, yet instances of dispersal via interbasin river captures are not excluded. During high sea level intervals, the isolated populations would have diverged leading to the observed allopatric species. This evolutionary process is named the sea level fluctuation (SLF) hypothesis of diversification. Department of Zoology and Animal Biology, University of Geneva, 30 Quai Ernest,Ansermet, 1211 Geneva 4, Switzerland. Cardoso, Y. P.,Montoya-Burgos, J. I. 2009-02-13T09:13:53+01:00 447 10.1111/j.1365-294X.2008.04068.x Mol Ecol MEC4068 2009-01-01 19207251 false Mol Ecol. 2009 Jan 29. 2009-02-13T09:13:53+01:00 http://www.ncbi.nlm.nih.gov:80/pubmed/19207251 47