Publications
FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Authors: Lasierra MAR, Fernández-Guerrero M, Delisle L, Yakushiji-Kaminatsui N, Darbellay F, Pérez-Gómez R, Duboule D
The developing vertebrate limb has long proved as an excellent system for studying the mechanisms involved in pattern formation and morphogenesis and more recently in transcriptional regulation and morphological evolution. To elucidate the stage-specific expression profiles of the components of the developing limb, we have generated the temporal transcriptome of the limb progenitors and of the overlying ectoderm separately. Our study has uncovered a collinear activation of Hoxc genes in the limb ectoderm that we have validated by in situ hybridization. However, while members of the HoxA and HoxD clusters show complex and dynamic patterns of expression during limb development that correlate with the morphology of the different limb segments, no specific function for the HoxC or HoxB clusters has been identified ( 1 - 3 ). To investigate the function of Hoxc genes in the limb ectoderm, we have reexamined the HoxC cluster null mice. Remarkably, and despite exhibiting normal terminal phalanges, these mice didn't form claws (anonychia). Morphological and immunohistochemical analysis identified a failure in the differentiation of the main components of the nail/claw organ. To unravel the transcriptional regulation of Hoxc genes in the limb ectoderm, we used the ATACseq technique. Using this approach, we identified two putative regulatory regions which activity was tested in mouse transgenic enhancer assays. It is currently considered that Hox genes have played a key role in the evolution of morphological traits, probably associated with changes in their regulatory landscapes ( 4 ). Given that the form and size of the distal limb integumentary organ (nail, claw or hoof) correlates with that of the distal phalanx and that the development of hooves was a major innovation in the evolution of a cursorial lifestyle, we are also exploring the possible implication of Hoxc genes in the nail/claw/hoof transition. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Eyes of the Deep-sea Floor: The Integrative Taxonomy of the Foraminiferal Genus Vanhoeffenella.
2018
Protist
Authors: Voltski I, Gooday AJ, Pawlowski J
Vanhoeffenella is a common deep-sea monothalamous foraminifer, some species of which have a unique eye-like test morphology. Owing to its world-wide distribution, it has been recorded numerous times since the "heroic age" of the deep-sea exploration in the early 20th century. So far, only 4 species have been described, and no attempts have been made to estimate the real diversity of this peculiar genus. Over the last fifteen years, we have collected specimens of Vanhoeffenella from various deep-sea areas, providing the basis for an integrative taxonomy and biogeography of this genus. Here, we clarify the phylogenetic position of Vanhoeffenella and give an account of its diversity in the Atlantic, Arctic and Southern Oceans (the Weddell Sea) as revealed by genetic marker (SSU rDNA) and morphology. Our study shows that Vanhoeffenella branches within Clade F of monothalamids and incorporates at least 10 putative species. Some could be distinguished by either morphological or molecular features, but only the integrative taxonomic approach provides a robust way to assess their diversity. We examine the new material of the type species (V. gaussi Rhumbler), redescribe the poorly-known V. oculus Earland and describe formally a fifth species, V. dilatata sp. nov.
Molecular Biology
Authors: Gauthier J., Gayral P., Le Ru B. P., Jancek S., Dupas S., Kaiser L., Gyapay G. and Herniou E. A.
The African parasitoid wasp Cotesia sesamiae is a generalist species structured in locally adapted populations showing differences in host range. The recent discovery of Cotesia typhae, a specialist, sister species to C. sesamiae, provides a good framework to study the genetic determinants of parasitoid host range. To investigate the genomic bases of divergence between these populations and species, we used a targeted sequencing approach on 24 samples. We targeted the bracovirus genomic region encoding virulence genes involved in the interaction with the lepidopteran hosts of the wasps. High sequencing coverage was obtained for all samples, allowing the study of genetic variation between wasp populations and species. By combining population genetic estimations, such as nucleotide diversity (π), relative differentiation (FST) and absolute divergence (dxy), with branch‐site dN/dS measures, we identified six of 98 bracovirus genes showing significant divergence and evidence of positive selection. These genes, belonging to different gene families, are potentially involved in host adaptation and in the specialization process. Fine‐scale analyses of genetic variation also revealed mutations and large deletions in certain genes inducing pseudogenization and loss of function. The image emerging from these results is that adaptation mediated by bracovirus genes happens through selection of particularly adaptive alleles and loss of nonadaptive genes. These results highlight the central role of the bracovirus in the molecular interactions between the wasps and their hosts and in the evolutionary processes of specialization.
Rescue of an aggressive female sexual courtship in mice by CRISPR/Cas9 secondary mutation in vivo.
2018
BMC research notes
Authors: Zakany J, Duboule D
We had previously reported a mouse line carrying the Atypical female courtship (HoxD) allele, where an ectopic accumulation of Hoxd10 transcripts was observed in a sparse population of cells in the adult isocortex, as a result of a partial deletion of the HoxD gene cluster. Female mice carrying this allele displayed an exacerbated paracopulatory behavior, culminating in a severe mutilation of the studs' external genitals. To unequivocally demonstrate that this intriguing phenotype was indeed caused by an illegitimate function of the HOXD10 protein, we use CRISPR/Cas9 technology to induce a microdeletion into the homeobox of the Hoxd10 gene in cis with the HoxDallele.
BMC evolutionary biology
Authors: Liberti J, Baer B, Boomsma JJ
Promiscuous mating and sperm competition often induce arms races between the sexes with detrimental outcomes for females. However, ants with multiply-inseminated queens have only a single time-window for sperm competition and queens are predicted to gain control over the outcome of sperm storage quickly. The seminal fluid of Acromyrmex leaf-cutting ants reduces the viability of rival sperm, but how confrontations between unrelated ejaculates affect sperm storage remains unknown.
PLoS biology
Authors: Thomson SA, Pyle RL, Ahyong ST, Alonso-Zarazaga M, Ammirati J, Araya JF, Ascher JS, Audisio TL, Azevedo-Santos VM, Bailly N, Baker WJ, Balke M, Barclay MVL, Barrett RL, Benine RC, Bickerstaff JRM, Bouchard P, Bour R, Bourgoin T, Boyko CB, Breure ASH, Brothers DJ, Byng JW, Campbell D, Ceríaco LMP, Cernák I, Cerretti P, Chang CH, Cho S, Copus JM, Costello MJ, Cseh A, Csuzdi C, Culham A, D'Elía G, d'Udekem d'Acoz C, Daneliya ME, Dekker R, Dickinson EC, Dickinson TA, van Dijk PP, Dijkstra KB, Dima B, Dmitriev DA, Duistermaat L, Dumbacher JP, Eiserhardt WL, Ekrem T, Evenhuis NL, Faille A, Fernández-Triana JL, Fiesler E, Fishbein M, Fordham BG, Freitas AVL, Friol NR, Fritz U, Frøslev T, Funk VA, Gaimari SD, Garbino GST, Garraffoni ARS, Geml J, Gill AC, Gray A, Grazziotin FG, Greenslade P, Gutiérrez EE, Harvey MS, Hazevoet CJ, He K, He X, Helfer S, Helgen KM, van Heteren AH, Hita Garcia F, Holstein N, Horváth MK, Hovenkamp PH, Hwang WS, Hyvönen J, Islam MB, Iverson JB, Ivie MA, Jaafar Z, Jackson MD, Jayat JP, Johnson NF, Kaiser H, Klitgård BB, Knapp DG, Kojima JI, Kõljalg U, Kontschán J, Krell FT, Krisai-Greilhuber I, Kullander S, Latella L, Lattke JE, Lencioni V, Lewis GP, Lhano MG, Lujan NK, Luksenburg JA, Mariaux J, Marinho-Filho J, Marshall CJ, Mate JF, McDonough MM, Michel E, Miranda VFO, Mitroiu MD, Molinari J, Monks S, Moore AJ, Moratelli R, Murányi D, Nakano T, Nikolaeva S, Noyes J, Ohl M, Oleas NH, Orrell T, Páll-Gergely B, Pape T, Papp V, Parenti LR, Patterson D, Pavlinov IY, Pine RH, Poczai P, Prado J, Prathapan D, Rabeler RK, Randall JE, Rheindt FE, Rhodin AGJ, Rodríguez SM, Rogers DC, Roque FO, Rowe KC, Ruedas LA, Salazar-Bravo J, Salvador RB, Sangster G, Sarmiento CE, Schigel DS, Schmidt S, Schueler FW, Segers H, Snow N, Souza-Dias PGB, Stals R, Stenroos S, Stone RD, Sturm CF, Štys P, Teta P, Thomas DC, Timm RM, Tindall BJ, Todd JA, Triebel D, Valdecasas AG, Vizzini A, Vorontsova MS, de Vos JM, Wagner P, Watling L, Weakley A, Welter-Schultes F, Whitmore D, Wilding N, Will K, Williams J, Wilson K, Winston JE, Wüster W, Yanega D, Yeates DK, Zaher H, Zhang G, Zhang ZQ, Zhou HZ
Fish and Fisheries
Authors: Guinot, G. & Cavin, L.
Fishes are characterized by their capacity to occupy all aquatic environments and by their amazing range of size and morphology. While it is known that habitat influenced the diversity dynamics of fish clades, studies on environmental colonization events through the evolutionary history of ray-finned fishes have yielded conflicting results as to the origin of modern clades and preferential directions of shifts. The effects of habitat over morphological evolution such as body size remain poorly known in vertebrates. However, body size evolution is more frequently addressed in terms of variation through time and numerous studies have demonstrated that successive taxa within a clade tend to increase in size through time (Cope's or Depéret's rule). We use phylogenetic comparative methods on a genus-level actinopterygian super-tree based on extant and fossil data covering the Late Jurassic-Paleogene interval. Results indicate marine ancestry for freshwater lineages and a dominance of colonizations from marine clades towards other habitats. Similar trends in environment occupancy among different ray-finned clades are explored. Three main trends affecting non-closely-related clades are recognized: (i) the freshwater invaders, (ii) the predominantly marine dwellers and (iii) the environmentally labile fishes. Habitat effects on body size evolution are not statistically supported, but most actinopterygian subclades originate from small-sized ancestors and tend to increase in size in the course of their evolutionary history. This trend is clear for lineages restricted for long periods of time in the same environments, either marine or freshwater, but it is not observed in environmentally labile fish lineages.
PLoS genetics
Authors: Tas D, Stickley L, Miozzo F, Koch R, Loncle N, Sabado V, Gnägi B, Nagoshi E
Forkhead box (FOXO) proteins are evolutionarily conserved, stress-responsive transcription factors (TFs) that can promote or counteract cell death. Mutations in FOXO genes are implicated in numerous pathologies, including age-dependent neurodegenerative disorders, such as Parkinson's disease (PD). However, the complex regulation and downstream mechanisms of FOXOs present a challenge in understanding their roles in the pathogenesis of PD. Here, we investigate the involvement of FOXO in the death of dopaminergic (DA) neurons, the key pathological feature of PD, in Drosophila. We show that dFOXO null mutants exhibit a selective loss of DA neurons in the subgroup crucial for locomotion, the protocerebral anterior medial (PAM) cluster, during development as well as in adulthood. PAM neuron-targeted adult-restricted knockdown demonstrates that dFOXO in adult PAM neurons tissue-autonomously promotes neuronal survival during aging. We further show that dFOXO and the bHLH-TF 48-related-2 (FER2) act in parallel to protect PAM neurons from different forms of cellular stress. Remarkably, however, dFOXO and FER2 share common downstream processes leading to the regulation of autophagy and mitochondrial morphology. Thus, overexpression of one can rescue the loss of function of the other. These results indicate a role of dFOXO in neuroprotection and highlight the notion that multiple genetic and environmental factors interact to increase the risk of DA neuron degeneration and the development of PD.
Journal of Biogeography
Authors: Martinez PA, Pia MV, Bahechar IA, Molina WF, Bidau CJ, Montoya-Burgos JI.
Understanding the mechanisms that drive phenotypic divergence along climatic gradients is a long-standing goal of biogeography. To fulfil this objective, we tested if neutral and/or adaptive effects drive phenotypic diversification. We quantified the effects of neutral evolution and natural selection on morphological variability of a well-suited mammalian species, the fox, Lycalopex culpaeus.
Nature Communications
Authors: De Simone A, Spahr A, Busso C, Gönczy P
Microtubule asters must be positioned precisely within cells. How forces generated by molecular motors such as dynein are integrated in space and time to enable such positioning remains unclear. In particular, whereas aster movements depend on the drag caused by cytoplasm viscosity, in vivo drag measurements are lacking, precluding a thorough understanding of the mechanisms governing aster positioning. Here, we investigate this fundamental question during the migration of asters and pronuclei in C. elegans zygotes, a process essential for the mixing of parental genomes. Detailed quantification of these movements using the female pronucleus as an in vivo probe establish that the drag coefficient of the male-asters complex is approximately five times that of the female pronucleus. Further analysis of embryos lacking cortical dynein, the connection between asters and male pronucleus, or the male pronucleus altogether, uncovers the balance of dynein-driven forces that accurately position microtubule asters in C. elegans zygotes.
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