Sars Seminars 2011/2012
Sars Seminar Room (222 A2) at 13:00

Date Speaker Title and Abstract
09.november Simon Henriet
Chourrout Group
Factors driving the persistence of transposable elements in the Oikopleura genome
The activity of mobile DNA has a strong influence on the evolution of genome architecture. In particular, a strong correlation is observed between the proliferation of retrotransposons and the increase in genome size. The genome of the planctonic tunicate Oikopleura dioica is extremely compact and lacks most of retrotransposons clades usually found in chordates. In contrast, Oikopleura hosts a flourishing family of LTR retrotransposons, the Tor elements, which are related to Gypsy elements from Drosophila. The Tor elements show marks of recent activity both at the sequence level and at the expression level, supporting the hypothesis that the compaction of the Oikopleura genome occurred recently, after the divergence from other urochordates. The large effective populations of Oikopleura could contribute to maintain active Tor copies in the genome, despite their potentially harmful effect on gene integrity. In addition, the presence of candidate envelope proteins (Env) raises the possibility that a large fraction of active copies are fuelled by horizontal transfer of Tor elements in the germline. To challenge this possibility, we are studying the biochemical properties of candidate Tor envelopes. In order to better understand how the genome controls the activity of mobile elements, we have started a study of the small RNA of Oikopleura and its protein partners. Our preliminary results indicate a complex repertoire of Argonaute proteins expressed at different developmental stages. We found abundant small RNA in Oikopleura tissues, and our results indicate that a fraction could be analogous to piwi-associated RNA (piRNA) involved in the control of transposable elements in other species. Our future research will aim at characterizing the biogenesis of piRNA in Oikopleura and their target RNAs.
16.november Lisbeth Olsen
Chourrout Group
Germ line development in Oikopleura dioica: Is pumilio a germ plasm marker?
23.november Elsa Denker
Jiang Group

Tubulogenesis in Ciona notochord requires the formation of bipolar cells through two discrete par3/par6/aPKC domains
Tubular structures are found in a wide variety of organs and organisms, allowing to carry fluids and cells, absorb and exchange molecules between several compartments… (Lubarsky and Krasnow, 2003). Tubulogenesis is amongst the most interesting and challenging morphogenetic processes for cell and developmental biologists, implying many changes in cell state and behavior (Baer et al., 2009, Bryant & Mostov 2008). Cell polarization is one of these critical events, because it drives the overall 3D organisation of the cell components with respect to positional cues (Tanos & Rodriguez-Boulan 2008, Bryant and Mostov 2008). Over the last decades, studies have highlighted the role of several very conserved key complexes, in particular the Par3/Par6/aPKC, that define and maintain cell polarity.

We have recently shown that Ciona notochord is a good model to study tubulogenesis, because it occurs in a structure composed of only 40 big cells, that no longer divide, only involving remodelling of cell shape and of tissue configuration, neighbour exchanges and no cell membrane rupture (Dong et al., 2009). One interesting and uncommon feature is that the tube forms from a one-cell-thick rod of cells, and that the lumen emerges at intercellular interfaces between cell. As a consequence, two luminal surfaces appear on each cell. What is the molecular basis for this polarity?

I have investigated the subcellular localization of the members of the Par complex in developping notochord cells, and have shown a strong correlation between their distribution and the specification of an apical domain where the lumen will appear, and, at the onset of lumen formation, with the formation of tight junctions around the lumen (monitored by the localization of the ZO1 marker). Conversely, usual basolateral markers such the homologues of Lethal giant larvae, Discs large and Scribble, get excluded from the apical domain and remain baso-lateral. Adherens junction markers get down-regulated from the forming apical domain and get resticted to the lateral domain. Finally, a morpholino knock-down of Par3 prevented lumen formation and the correct re-organization of polarity and junction markers.

For the first time, the mechanisms for apico-basal cell polarization have been investigated in urochordates and the same players appear to be involved again; Par3 might be a key player in junction formation, as recently reported in other models. Interstingly, the configuration of the junctions and the position of the polarity protein with respect to them is very similar to what is found in vertebrates, and the overall process is very similar to what has been described for lumen formation in cultured MDCK cells in isochoric configuration (Ferrari et al., 2008).

The major new feature, that has been not described in any other context, is that each notochord cell has two apical domains, driven by the formation of 2 discrete par3/par6/apkc patches in opposite points of the cells.

30.november Chiara Sinigaglia
Rentzsch Group
A conserved patterning system controls the development of the aboral pole of Nematostella and the anterior pole of Bilateria
07.december Jan Inge Øvrebø
Thompson Group
Regulation of multiple cell cycle variants: Revealing the function of Oikopleura dioica CDK1 paralogs
At the heart of the cell cycle lie the cyclin dependent kinases (CDKs), which control key events such as DNA replication and mitotic cell division. As their names imply the CDKs require activating subunits, the cyclins, in order to maintain kinase activity. In general the canonical cell cycle consists of four distinct phases; G1, S, G2 and M phase, but there are also other variants of the cell cycle such as meiosis, which give rise to gametes, and endoreduplication, in which cells increase their ploidy without completing cell division. Examples of multiple cell cycle variants are found in the marine urochordate Oikopleura dioica. The animal develops through rapid mitotic divisions during early development, but most cells shift to endocycles prior to metamorphosis. Studies of Oikopleura endocycling epithelial cells reveal various cell sizes and bilateral symmetry, which have been shown to be carefully controlled through G-phase length. Another fascinating example of cell cycle regulation is found in the ovary, which consists of a giant multinuclear cell containing endocycling nurse nuclei and meiotic nuclei ,seeding oocytes, all connected by a shared cytoplasm supported by an actin scaffold, whose organisation is termed a coenocyst. To better understand the underlying mechanisms of the cell cycle we have scrutinised the Oikopleura genome for cyclins and CDKs and predicted their function and annotation. This work has revealed significant amplifications of the CDK1 complement, unknown among other metazoans, as well as the cyclin B and D families. We are now focussing on understanding the spatial and temporal localization of the CDK1 paralogs, since the single CDK1 ortholog in other metazoans plays a central role in regulating cell division. CDK1 has also been reported as a prime target for downregulation when switching to endocycling in cells of other model species. O. dioica, however, appears to retain stable levels of a CDK1 paralog in both endocycling germline and somatic epithelial cells as well as mitotic cells, suggesting a modified function of this paralog. These observations are discussed in terms of what is known about regulation of endocycles in insects and mammals.
14.december Ivonne Sehring
Jiang Group
A cytokinesis-like actomyosin contractile mechanism drives cell elongation in Ciona intestinalis
Cell shape change represents a fundamental unit of morphogenesis in animal development. During embryogenesis of the simple chordate Ciona intestinalis, the elongation of individual notochord cells constitutes a crucial stage of the notochord growth, which contributes to the establishment of the larval body plan. Here we show that a constriction forming at the equator of each notochord cell harbors a cytokinesis-like actomyosin network that is essential for cell elongation. The network includes phosphorylated myosin regulatory light chain, α-actinin, cofilin, tropomyosin, and talin. Cortical flow contributes to the assembly of the actomyosin ring. Similar to cytokinetic cells, membrane blebs that represent local contractions form at the basal cortex next to the equator and participate in force generation. We present a model in which the cooperation of bleb-type contractions and equatorial actomyosin ring-based constriction promote cell elongation. Disruptions of α-actinin and cofilin activities in the contractile ring prevent notochord cell elongation. Our results demonstrate that a cytokinesis-like contractile mechanism is co-opted in a completely different developmental scenario to achieve cell shape change instead of cell division.

Christmas Break

18.january Anne Zakrzewski
Hausen Group
Molecular characterization of chaetae formation in Annelida and other Lophotrochozoa
Unraveling the ancestral design of lophotrochozoan animals and tracing their evolutionary history is still challenging due to the high morphological diversity within this group, which hampers the identification of homologous features between subtaxa. In this study I aim for an integrative comparison of chitinous bristle-like chaetae found in Brachiopoda, Myzostomida and Annelida, whose homology has been controversially discussed for a long time and is of high systematic relevance. For this purpose we complement structural investigations with molecular characterization of cell types involved in chaetogenesis in Platynereis dumerilii, Myzostoma cirriferum and Macandrevia cranium. By the combination of transmission electron microscopy, immunohistochemistry, and in situ-hybridization I obtained a broad repertoire of genes in P. dumerilii including effector genes and several genes of hitherto unknown function, which in larvae and juvenils are all exclusively expressed by the chaetal sac cells. Based on transcriptome sequencing, I identified orthologous genes in M. cirriferum and M. cranium, which likewise are specifically expressed by chaetae forming cells. The data provide new and intriguing insights in the mechanism of chaetae formation and chitin secretion in lophotrochozoan animals. Additionally, I obtained strong evidence for the homology of chaetae in annelids and myzostomids and that clearly supports recent molecular systematic studies placing myzostomids back into the annelids. Ongoing investigations in M. cranium likewise point towards a similar molecular machinery underlying chaetogenesis. This approach introduces a new comparative level that helps to clarify the question when chaetae evolved within the Lophotrochozoa.
25.january Lucas Leclère
Rentzsch Group
Evolution of Wnt pathway components and primary body axis:
insights from the aboral pole of Nematostella vectensis

In cnidarians the primary body axis runs from the oral opening to the aboral pole, where in some anthozoans, like Nematostella vectensis, an apical sense organ develops. Molecular and morphological data suggest that the oral pole of cnidarians is homologous to the posterior pole of bilaterians. Notably, they both correspond to the activation domain of the Wnt signaling pathway during early embryogenesis, a signaling pathway involved in the formation of both cnidarian (oral-aboral) and bilaterian (anterior-posterior) primary axes. In bilaterians, inhibitors of the Wnt pathway (SFRP –Secreted Frizzled Related Protein and Dickkopf) in addition to frizzled receptors are expressed at the anterior pole, opposite to the Wnt domain. Activation of the Wnt pathway at one pole of the embryo and inhibition at the other seem to be conserved features of bilaterians and has a major role in defining the primary axis of the body. We question if a similar system can be found in non-bilaterian animals. We analyzed evolution of these signaling molecules using phylogenetic methods and performed functional analyses in Nematostella vectensis. We found expression of the Wnt pathway inhibitor SFRP1/2/5 and the Wnt receptor frizzled5/8 at the aboral pole during early embryogenesis. Injection of antisense morpholinos directed against these aborally expressed Wnt pathway components shows that SFRP1/2/5 and Frizzled5/8 act downstream of FGF signaling and are involved in the patterning of the aboral pole and formation of the ciliated apical organ. These data reveal similarities in the patterning system of the aboral pole of cnidarians and the anterior pole of bilaterians, involving inhibitors of the Wnt pathway, and regulators of the FGF signalling.
01.february Wei Deng
Ci-Slc26a&alpha is essential for lumen expansion during Ciona intestilanis notochord tubulogenesis
Recent progresses have been made in understanding the common design principles and underlining molecular networks of biological tube morphogenesis, while the details of how these molecules function is not well known. SLC26 family sulfate transporters are responsible for epithelial anion transport and physiology, but their role in tubulogenesis has not been addressed. In this work, we used morpholino knockdown, rescue experiments, electrophysiology, together with mutation assays, to study the role of Ci-Slc26aα in notochord tubulogenesis, a newly established model system in Ciona intestinalis embryos. Our results suggest that Ci-Slc26aα is essential for notochord lumen formation and expansion, but not for apical/luminal membrane formation and lumen connection. We show that Ci-Slc26aα behaved as an anion exchanger, exchanging sulfate, oxalate and bicarbonate for chloride in equal molar ratio, however, the bivalent/monovalent anion exchange is dispensable for in vivo function of Ci-Slc26aα. Our work reveals the consequence and relationship of several key processes in lumen formation, and establishes an in vivo assay to study the molecular basis of the transport properties of SLC26 family transporters.
08.february Marcin Adamski
Genomes and transcriptomes of two Calcaronean sponges reveal unprecedented complexity of developmental signaling in basal metazoa andallow for quantification of gene expression in development and regeneratio
15.february Sven Leininger
Axial patterning in the calcareous sponge Sycon ciliatu
22.february Markus Bause
Rentzsch Group
Molecular analysis of the development of the apical organ in the sea anemone Nematostella vectensis
29.february Gunasekaran Subramaniam
Growth and developmental arrest in Oikopleura dioica: TOR signalling and cyclin D variants
Caloric intake and growth are tightly coupled processes. Studies have shown that TOR (Target of Rapamycin) signalling, a nutritional signalling pathway is coupled to growth and lifespan by regulating cell division and protein synthesis. In rapidly growing cells, high TOR activity culminates in increased protein translation and subsequently results in a high percentage of unfolded or misfolded protein, endoplasmic reticulum stress and massive production of free radicals which are responsible for damage to DNA, proteins and membranes, thus causing senescence or ageing.
Conversely, reduction of TOR activity by Dietary Restriction (DR) confers extended lifespan and protection from many age related diseases. Studies in yeast, C. elegans, drosophila and mouse have also shown that DR inhibits TOR signalling. Thus TOR signalling plays an important role in growth and longevity of cells in organisms. In the current study we exploit Oikopleura dioica, as a model organism to study the effect of TOR signalling on growth and lifespan since it has a rapid growth and short life span (6days at 160 C)
Growth in Oikopluera dioica is rapid due to extensive recourse to endoreduplication during its short life cycle leading to polyploidy in cells. The present study explores the influence of TOR signalling on growth and lifespan in Oikopleura dioica. In this study, blocking TOR signalling in Oikopleura using rapamycin, or growing them under Dietary Restriction revealed that the growth arrest is due to endocycling arrest. On the contrary, inhibition of TOR signalling in the mitotic germ nuclei rendered them unaffected, allowing them to continue proliferation without entering meiosis and thus prolonging lifespan. Surprisingly, our findings showed that the survival MAPK pathways ERK1/2 and p38-MSK1 are activated in germ nuclei, during dietary restriction.
Interestingly, a study with Cyclin Dependent Kinase (CDK) inhibitor p27, in the somatic cells and germ line suggests that TOR signalling regulates p27. Inhibiting TOR signalling resulted in increased nuclear localisation of p27 in the somatic cells leading to cell cycle arrest whereas p27 was excluded from the mitotic germ nuclei, which continued to proliferate even when TOR signalling was inhibited. Additionally, increased mRNA and protein levels of Cyclin Db splice variant β, a G1 regulator, during DR, suggests that Cyclin Db-β is instrumental as a cell cycle regulator during this inhibition. Further analysis revealed that Cyclin Db-β colocalized with p27 in the germ line cytoplasm perhaps indicating it’s role in regulating p27 in mitotic germ nuclei when TOR signalling is inhibited. Co-immunoprecipitation studies with CDK6 showed that an inhibitory phosphorylation mark of tyrosine 24 on CDK6 binds to Cyclin Db-β only and not the other Cyclin D variants suggesting that this CDK6 phosphorylation may play a major role in p27 sequestration in germ line.
Additionally, the presence of AP1, a MAPK (ERK1/2 and p38) effector, binding sites in the promoter of Cyclin Db and interaction of tyrosine phospho form of CDK 6 with Cyclin Db-β and p27, lead us to hypothesize that in the absence of TOR signalling by DR, MAPK pathway is activated leading to increased Cyclin Db-β production. This increased Cyclin Db-β interacts with the tyrosine phosphorylated form CDK6, which then sequesters p27 in the cytoplasm and prevents cell cycle arrest in germ line.
Further characterization of the molecules downstream of TOR, and survival signalling of ERK1/2 and p38 signalling with emphasis on effectors of the G1-S transition and regulation of CDK6 phosphorylation will help to increase our understanding of TOR mediated regulation of somatic endoreduplication, oogenesis and prolongation of life span in Oikopleura dioica.
07.march Sabrina Schiemann
Hejnol Group
Gastrulation and germ layer formation in the bdelloid rotifer Adineta vaga"
14.march Sofia Fortunato
Genome-wide analysis of developmental transcription factors in Sycon ciliatum. Part 2: Sox and Homeobox genes
Sponges are likely the earliest branching multicellular animals, and represent a key phylum for evolutionary developmental studies. Recently, genome analysis of the demosponge Amphimedon queeslandica demonstrated presence and developmental expression of most Eumetazoan transcription factors (TF) classes. However, it appears that the number of TFs is significantly lower in Amphimedon than in Cnidarians and Bilaterians, in agreement with the notion that the developmental inventory of genes increased during evolution. To expand the understanding of sponge development and genome evolution, developmental transcription factors should be identified in other groups of sponges. The genome of the calcareous sponge Sycon ciliatum reveals that the number of TFs in Sycon is larger than in Amphimedon with some gene families represented by twice or three times more genes, while other families (e.g, Paired) reduced in Sycon. In situ hybridization analysis demonstrates that Sox and homeobox genes are dynamically expressed during S. ciliatum embryogenesis, and in adult tissues, in patterns consistent with roles in cell differentiation and body plan patterning. Our findings highlight the differences between the two sponge lineages and underscore the necessity to analyze additional sponge genomes to reveal the evolutionary history of the developmental toolkit.
Gemma Richards
Analysis of SoxB2 in Nematostella provides further evidence of conserved neurogenic processes in the Eumetazoa
28.march Aina Børve
The Anteroposterior and Dorsoventral Patterning of the Adult Nervous System of  Meara stichopi.

Easter Break

18.april Jean-Marie Bouquet
Phenotypic plasticity of Oikopleura dioica in response to ocean acidification
02.may Pavla Navratilova
Analysis of histone modification patterns in Oikopleura dioica
Posttranslational histone modification is a key mechanism influencing chromosome condensation changes through cell cycle, chromatin dynamics during transcription, replication and DNA repair. This epigenetic information can be passed or re-established, but in a flexible way during cell divisions which also enables differentiation. We preclude the epigenome variability caused by mitosis and differentiation by using Oikopleura dioica gonads for genome-wide histone modification profiling. Most of the female gonad nuclei are not proliferating but are transcriptionally active endocycling nuclei. Distributions of 12 histone modifications in single-histone resolution inform us about organization and some unique features of the Oikopleura supercompact epigenome and also its conservation to vertebrates and invertebrates.
09.may Kevin Pang
Evolution of sensory systems: Chemoreception in Mnemiopsis leidyi and nervous system development in Priapulus caudatus.
16.may Chema Martín-Durán
Gut evolution in bilaterians: endomesoderm development in Priapulus caudatus (Priapulida) and Prostheceraeus vittatus (Platyhelminthes)
30.may Matteo Ugolini
07.june Joe Ryan
15.june Oliver Vöcking
20.june Bruno Vellutini
27.june Jana Mikhaleva

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