Transitional forms between the three domains of life and evolutionary implications

The question as to the origin and relationship between the three domains of life is lodged in a phylogenetic impasse. The dominant paradigm is to see the three domains as separated. However, the recently characterized bacterial species have suggested continuity between the three domains. Here, we review the evidence in support of this hypothesis and evaluate the implications for and against the models of the origin of the three domains of life. The existence of intermediate steps between the three domains discards the need for fusion to explain eukaryogenesis and suggests that the last universal common ancestor was complex. We propose a scenario in which the ancestor of the current bacterial Planctomycetes, Verrucomicrobiae and Chlamydiae superphylum was related to the last archaeal and eukaryotic common ancestor, thus providing a way out of the phylogenetic impasse

Taxonomic colouring of phylogenetic trees of protein sequences

BACKGROUND: Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the species associated to those sequences. However, there is no online tool to facilitate this interpretation, for example, by automatically attaching taxonomic information to the nodes of a tree, or by interactively colouring the branches of a tree according to any combination of taxonomic divisions. This is especially problematic if the tree contains on the order of hundreds of sequences, which, given the accelerated increase in the size of the protein sequence databases, is a situation that is becoming common. RESULTS: We have developed PhyloView, a web based tool for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree. Provided that the tree contains SwissProt, SpTrembl, or GenBank protein identifiers, the tool retrieves the taxonomic information from the corresponding database. A colour picker displays a summary of the findings and allows the user to associate colours to the leaves of the tree according to any number of taxonomic partitions. Then, the colours are propagated to the branches of the tree. CONCLUSION: PhyloView can be used at . A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address

La nanochirurgie laser en biologie cellulaire

La cellule est un univers dynamique et compartimenté où interagissent une multitude de sous composants à l’échelle nanométrique. Afin d’étudier l’organisation subcellulaire, il est devenu nécessaire de posséder des outils permettant une manipulation directe extrêmement précise et non invasive. L’avènement des lasers à impulsions, dès les années 60, a conduit à la naissance de la chirurgie au laser. Aujourd’hui, la réduction des impulsions laser en dessous de la nanoseconde permet de mieux comprendre leur interaction avec les tissus biologiques et de contrôler des interventions chirurgicales à une résolution de l’ordre de quelques centaines de nanomètres. Utilisant l’ionisation de la matière par la lumière, cette nanochirurgie laser permet d’effectuer des interventions chirurgicales intracellulaires telles que la découpe de microtubules ou de fibres de tension, sans endommager les structures environnantes ou compromettre la viabilité cellulaire. Ainsi, l’utilisation de lasers à impulsions ultra-courtes, plus précis et puissants, offre une nouvelle approche pour l’étude des forces en biologie ou pour la quantification de la dynamique du cytosquelette.Since their first use in the early 60’s, pulsed lasers have become increasingly popular for their ability to ablate biological tissue. Short laser pulses allow high precision surgery for biological and medical applications with minimal invasiveness. Performing highly targeted manipulation and ablation allows experiments impossible so far in development biology, cellular biology or even assisted reproductive technologies and laser surgery has been increasingly used over the last five years to answer key questions in Biology. Recently, picosecond UV and femtosecond IR laser pulses have been used to cleave microtubules and to severe actin stress fibers in vivo with a spatial precision in the submicrometer range to study their dynamics without affecting cell viability. We review recent findings on the underlying principles of pulsed laser nanosurgery mechanisms showing how the use of ultra short laser pulses increases precision and non-invasiveness of laser surgery. We show how the understanding of the surgical process allows one to distinguish between single cell ablation in living organisms or intracellular nanosurgery in living cells and we review recent applications to the study of forces and the quantification of cytoskeleton dynamics

Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization

BACKGROUND: Compartmentalization is a key feature of eukaryotic cells, but its evolution remains poorly understood. GTPases are the oldest enzymes that use nucleotides as substrates and they participate in a wide range of cellular processes. Therefore, they are ideal tools for comparative genomic studies aimed at understanding how aspects of biological complexity such as cellular compartmentalization evolved. RESULTS: We describe the identification and characterization of a unique family of circularly permuted GTPases represented by the human orthologue of yeast Lsg1p. We placed the members of this family in the phylogenetic context of the YlqF Related GTPase (YRG) family, which are present in Eukarya, Bacteria and Archea and include the stem cell regulator Nucleostemin. To extend the computational analysis, we showed that hLsg1 is an essential GTPase predominantly located in the endoplasmic reticulum and, in some cells, in Cajal bodies in the nucleus. Comparison of localization and siRNA datasets suggests that all members of the family are essential GTPases that have increased in number as the compartmentalization of the eukaryotic cell and the ribosome biogenesis pathway have evolved. CONCLUSION: We propose a scenario, consistent with our data, for the evolution of this family: cytoplasmic components were first acquired, followed by nuclear components, and finally the mitochondrial and chloroplast elements were derived from different bacterial species, in parallel with the formation of the nucleolus and the specialization of nuclear components

085: Heart failure with preserved ejection fraction: changes in clinical parameters between acute presentation and subsequent follow-up

PurposeIn the prospective KaRen registry of heart failure with preserved ejection fraction (HFPEF), changes in clinical and biological parameters and medications were assessed between acute presentation and out-patient follow-up in stable state.MethodsThe KaRen study included patients presenting with acute heart failure (HF) according to inclusion criteria: Framingham criteria for HF, left ventricular ejection fraction > or=45% and brain natriuretic peptide (BNP)>100pg/mL or NT-proBNP>300pg/mL. Once stabilized, 4-8 weeks after the index presentation, patients returned as out-patients for repeat assessment. Changes in clinical and biological parameters and medications between inclusion and follow-up were assessed with Students t-test and Chi-square testsResults577 patients were recruited and 458 returned for the 4-8 weeks visit. 56% were women. The median [25-75pctl] age was 79 [72-84] years. Medical history included 78% hypertension, 58% atrial arrhythmia, 26% type II diabetes and 27% serum creatinin >100 micromol/l. The table provides inclusion and follow-up dataConclusionsPatients presenting with HFPEF are elderly and a majority are women, with a high rate of hypertension and atrial arrhythmias. Blood pressure is incompletely controlled. At follow-up, blood pressure and NT-proBNP were reduced, but patients remain symptomatic. Still, efforts are needed to improve symptoms in HFPEF.Table (abstract 85) – Inclusion and follow-up data.Variable Mean (IQR)NYHA I / II / III / IVSBPCreatinineNT-proBNPACEI /ARBB-blockerANTICOAGInclusion0.8 / 9.4 / 40 / 49.8%148 [130-170]93 [74-128]2433 [1272-4790]60%65%41%Follow-up13 / 62.5 / 22.2 / 2.3140 [120-150]95 [75-129]1409 [514-2641]68%67.5%51.3%p<0.00010.003<0.000

Oviductal microenvironment: role in canine oocyte maturation in vivo and in vitro

In most mammals, oocytes are ovulated at the metaphase II stage, and the meiosis inhibition is then lifted by fertilization. In bitches and other Canidae species however, oocytes are released at the prophase I stage, and another 48 to 72h are necessary for themtomature into themetaphase II stage and become fertilizable. This specificity is currently hindering the development of reproductive biotechnologies in these species. In vitro maturation rates of canine oocytes are very low, as only 10 to 30%will reach the metaphase stage after 72h in culture. In bitches, nuclear maturation occurs in the oviduct, and tubal derivatives (culture media, such as Synthetic Oviductal Fluid, oviductal explants, coculture on tubal cell layers) were used to improve the yield, but so far not very successfully. This failure may be due to the lack of data on the composition of oviductal fluid in bitches. Further studies on the oviductal microenvironment of bitches are therefore necessary, as it is probably quite different from the oviductalmicroenvironment of other females, e.g. the presence of preovulatory luteinisation in bitches only. Creating a maturation medium based on the composition of oviductal fluid could be an interesting avenue to explore to improve in vitro maturation rates.Chez la plupart des mammifères, les ovocytes sont bloqués en métaphase II au moment de l'ovulation et cette inhibition de la méiose est ensuite levée par la fécondation. Chez les chiennes et les autres femelles de canidés, les ovocytes sont libérés au stade de prophase I, et il faut encore attendre 48 à 72 heures pour qu'ils atteignent le stade de métaphase II et deviennent fécondables. Cette particularité constitue aujourd'hui un frein au développement des biotechnologies de la reproduction chez les canidés. En effet, dans les essais de maturation in vitro d'ovocytes canins, seuls 10 à 30 % des ovocytes atteignent le stade de métaphase au bout de 72 heures de culture. Chez la chienne, la maturation nucléaire se produisant dans l'oviducte, des substituts de l'oviducte (milieux de culture comme le Synthetic Oviductal Fluid, explants d'oviductes, cultures sur tapis de cellules tubaires) ont été utilisés pour les cultures d'ovocytes in vitro, afin d'en améliorer le rendement, mais sans grand succès jusqu'à maintenant. Cet échec peut être dû au manque de données sur la composition du liquide tubaire de la chienne. L'étude de ce microenvironnement prend donc tout son intérêt, celui-ci étant probablement assez différent de celui des autres femelles, ne serait-ce que par l'existence du processus de lutéinisation préovulatoire dans cette espèce. À terme, la conception d'un milieu de maturation sur la base de la composition du liquide tubaire pourrait être une voie intéressante pour augmenter les taux de maturation in vitro

Grey matter density changes of structures involved in Posttraumatic Stress Disorder (PTSD) after recovery following Eye Movement Desensitization and Reprocessing (EMDR) therapy

International audienc

Challenges and advances in optical 3D mesoscale imaging

Optical mesoscale imaging is a rapidly developing field that allows the visualisation of larger samples than is possible with standard light microscopy, and fills a gap between cell and organism resolution. It spans from advanced fluorescence imaging of micrometric cell clusters to centimetre-size complete organisms. However, with larger volume specimens, new problems arise. Imaging deeper into tissues at high resolution poses challenges ranging from optical distortions to shadowing from opaque structures. This manuscript discusses the latest developments in mesoscale imaging and highlights limitations, namely labelling, clearing, absorption, scattering, and also sample handling. We then focus on approaches that seek to turn mesoscale imaging into a more quantitative technique, analogous to quantitative tomography in medical imaging, highlighting a future role for digital and physical phantoms as well as artificial intelligence

A Holistic Approach to Marine Eco-Systems Biology

With biology becoming quantitative, systems-level studies can now be performed at spatial scales ranging from molecules to ecosystems. Biological data generated consistently across scales can be integrated with physico-chemical contextual data for a truly holistic approach, with a profound impact on our understanding of life [1]–[5]. Marine ecosystems are crucial in the regulation of Earth's biogeochemical cycles and climate [6],[7]. Yet their organization, evolution, and dynamics remain poorly understood [8],[9]. The Tara Oceans project was launched in September 2009 for a 3-year study of the global ocean ecosystem aboard the ship Tara. A unique sampling programme encompassing optical and genomic methods to describe viruses, bacteria, archaea, protists, and metazoans in their physico-chemical environment has been implemented. Starting as a grassroots initiative of a few scientists, the project has grown into a global consortium of over 100 specialists from diverse disciplines, including oceanography, microbial ecology, genomics, molecular, cellular, and systems biology, taxonomy, bioinformatics, data management, and ecosystem modeling. This multidisciplinary community aims to generate systematic, open access datasets usable for probing the morphological and molecular makeup, diversity, evolution, ecology, and global impacts of plankton on the Earth system

Open science resources for the discovery and analysis of Tara Oceans data

Le " Tara Expéditions" organise des expéditions pour étudier et comprendre l'impact des changements climatiques sur nos océans.International audienceThe Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events