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Developmental biology aims to understand how the dynamics of embryonic shapes and organ functions are encoded in linear DNA molecules. Thanks to recent progress in genomics and imaging technologies, systemic approaches are now used in parallel with small-scale studies to establish links between genomic information and phenotypes, often described at the subcellular level. Current model organism databases, however, do not integrate heterogeneous data sets at different scales into a global view of the developmental program. Here, we present a novel, generic digital system, NISEED, and its implementation, ANISEED, to ascidians, which are invertebrate chordates suitable for developmental systems biology approaches. ANISEED hosts an unprecedented combination of anatomical and molecular data on ascidian development. This includes the first detailed anatomical ontologies for these embryos, and quantitative geometrical descriptions of developing cells obtained from reconstructed three-dimensional (3D) embryos up to the gastrula stages. Fully annotated gene model sets are linked to 30,000 high-resolution spatial gene expression patterns in wild-type and experimentally manipulated conditions and to 528 experimentally validated cis-regulatory regions imported from specialized databases or extracted from 160 literature articles. This highly structured data set can be explored via a Developmental Browser, a Genome Browser, and a 3D Virtual Embryo module. We show how integration of heterogeneous data in ANISEED can provide a system-level understanding of the developmental program through the automatic inference of gene regulatory interactions, the identification of inducing signals, and the discovery and explanation of novel asymmetric divisions. [ABSTRACT FROM AUTHOR]

Resveratrol and its oligomers are biologically active compounds. This work brings new insights for the bioproduction of trans -resveratrol with three dimers, pallidol, trans -ε-viniferin, and trans -δ-viniferin, in cell suspension of Vitis labrusca . Conditions of elicitation by methyl jasmonate were optimized for the production of stilbenes using statistical design of experiment. Bio-production of stilbenes was scaled-up to 5 L and in these conditions, trans -resveratrol concentrations reached 237 mg/L, and for pallidol 114 mg/L. The comparison of different elicitation modes (different elicitors, combination with cyclodextrins or adsorbent resin) allowed to reach particularly high concentrations of target molecules: Resveratrol 6.14 g/L, pallidol 0.90 g/L, δ-viniferin 0.54 g/L, and ε-viniferin 0.50 g/L. Scale-up to 20 L-stirring-bioreactor gave similar growth rates to those observed in shake flask culture, with a high production of resveratrol (4.23 g/L) and δ-viniferin (0.76 g/L). This work provides new strategies for the production of stilbenes in plant cell suspension for biological and commercial evaluation.

Marker frequency analysis of the Escherichia coli recB mutant chromosome has revealed a deficit of DNA in a specific zone of the terminus, centred on the dif/TerC region. Using fluorescence microscopy of a marked chromosomal site, we show that the dif region is lost after replication completion, at the time of cell division, in one daughter cell only, and that the phenomenon is transmitted to progeny. Analysis by marker frequency and microscopy shows that the position of DNA loss is not defined by the replication fork merging point since it still occurs in the dif/TerC region when the replication fork trap is displaced in strains harbouring ectopic Ter sites. Terminus DNA loss in the recB mutant is also independent of dimer resolution by XerCD at dif and of Topo IV action close to dif. It occurs in the terminus region, at the point of inversion of the GC skew, which is also the point of convergence of specific sequence motifs like KOPS and Chi sites, regardless of whether the convergence of GC skew is at dif (wild-type) or a newly created sequence. In the absence of FtsK-driven DNA translocation, terminus DNA loss is less precisely targeted to the KOPS convergence sequence, but occurs at a similar frequency and follows the same pattern as in FtsK+ cells. Importantly, using ftsIts, ftsAts division mutants and cephalexin treated cells, we show that DNA loss of the dif region in the recB mutant is decreased by the inactivation of cell division. We propose that it results from septum-induced chromosome breakage, and largely contributes to the low viability of the recB mutant.

Fitness is known to have beneficial effects on brain anatomy and function. However, the understanding of mechanisms underlying immediate and long-term neurophysiological changes due to exercise is currently incomplete due to the lack of tools to investigate brain function during physical activity. In this study, we used time-domain near infrared spectroscopy (TD-NIRS) to quantify and discriminate extra-cerebral and cerebral hemoglobin concentrations and oxygen saturation ( SO 2 ) in young adults at rest and during incremental intensity exercise. In extra-cerebral tissue, an increase in deoxy-hemoglobin ( HbR ) and a decrease in SO 2 were observed while only cerebral HbR increased at high intensity exercise. Results in extra-cerebral tissue are consistent with thermoregulatory mechanisms to dissipate excess heat through skin blood flow, while cerebral changes are in agreement with cerebral blood flow ( CBF ) redistribution mechanisms to meet oxygen demand in activated regions during exercise. No significant difference was observed in oxy- ( HbO 2 ) and total hemoglobin ( HbT ). In addition HbO 2 , HbR and HbT increased with subject's peak power output (equivalent to the maximum oxygen volume consumption; VO 2 peak) supporting previous observations of increased total mass of red blood cells in trained individuals. Our results also revealed known gender differences with higher hemoglobin in men. Our approach in quantifying both extra-cerebral and cerebral absolute hemoglobin during exercise may help to better interpret past and future continuous-wave NIRS studies that are prone to extra-cerebral contamination and allow a better understanding of acute cerebral changes due to physical exercise.

Xenopus laevis is a prominent model system for studying neural development, but our understanding of the long-term temporal dynamics of neurogenesis remains incomplete. Here, we present the first continuous description of neurogenesis in X. laevis, covering the entire period of development from the specification of neural ectoderm during gastrulation to juvenile frog. We have used molecular markers to identify progenitors and neurons, short-term bromodeoxyuridine (BrdU) incorporation to map the generation of newborn neurons and dual pulse S-phase labelling to characterise changes in their cell cycle length. Our study revealed the persistence of Sox3-positive progenitor cells from the earliest stages of neural development through to the juvenile adult. Two periods of intense neuronal generation were observed, confirming the existence of primary and secondary waves of neurogenesis, punctuated by a period of quiescence before metamorphosis and culminating in another period of quiescence in the young adult. Analysis of multiple parameters indicates that neural progenitors alternate between global phases of differentiation and amplification and that, regardless of their behaviour, their cell cycle lengthens monotonically during development, at least at the population level., (© 2015. Published by The Company of Biologists Ltd.)

Ten years ago next-generation sequencing (NGS) technologies appeared on the market. During the past decade, tremendous progress has been made in terms of speed, read length, and throughput, along with a sharp reduction in per-base cost. Together, these advances democratized NGS and paved the way for the development of a large number of novel NGS applications in basic science as well as in translational research areas such as clinical diagnostics, agrigenomics, and forensic science. Here we provide an overview of the evolution of NGS and discuss the most significant improvements in sequencing technologies and library preparation protocols. We also explore the current landscape of NGS applications and provide a perspective for future developments., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

BrdU is a thymidine analog that is incorporated into DNA during the S-phase of the cell cycle. BrdU incorporation can be used to quantify the number of cells that are in S-phase in the time period that BrdU is available. Thus, BrdU incorporation is an essential method in the quantitative analysis of cell proliferation, during normal embryonic development or after experimental manipulation. It is a reliable and versatile method that can be easily combined with immunohistochemistry and in situ hybridization to relate cell proliferation with gene expression. BrdU incorporation has been used in all model organisms; here, we describe a protocol adapted for use in Xenopus embryos.

Ascidians have powerful capacities for regeneration but the underlying mechanisms are poorly understood. Here we examine oral siphon regeneration in the solitary ascidian Ciona intestinalis. Following amputation, the oral siphon rapidly reforms oral pigment organs (OPO) at its distal margin prior to slower regeneration of proximal siphon parts. The early stages of oral siphon reformation include cell proliferation and re-growth of the siphon nerves, although the neural complex (adult brain and associated organs) is not required for regeneration. Young animals reform OPO more rapidly after amputation than old animals indicating that regeneration is age dependent. UV irradiation, microcautery, and cultured siphon explant experiments indicate that OPOs are replaced as independent units based on local differentiation of progenitor cells within the siphon, rather than by cell migration from a distant source in the body. The typical pattern of eight OPOs and siphon lobes is restored with fidelity after distal amputation of the oral siphon, but as many as 16 OPOs and lobes can be reformed following proximal amputation near the siphon base. Thus, the pattern of OPO regeneration is determined by cues positioned along the proximal distal axis of the oral siphon. A model is presented in which columns of siphon tissue along the proximal-distal axis below pre-existing OPO are responsible for reproducing the normal OPO pattern during regeneration. This study reveals previously unknown principles of oral siphon and OPO regeneration that will be important for developing Ciona as a regeneration model in urochordates, which may be the closest living relatives of vertebrates., (Copyright 2010 Elsevier Inc. All rights reserved.)

Objective: The objective was to assess agreement between end-tidal carbon dioxide values measured by a handheld capnometer (Petco(2)) and values measured by a blood gas analyzer (Paco(2)) in nonintubated patients with respiratory distress in an out-of-hospital setting., Methods: This prospective study compared Petco(2) values obtained by an end-tidal capnometer (Microcap Plus; Oridion Capnography Inc, Needham, Mass) to Paco(2) values by the Bland and Altman statistical method., Results: A total of 50 patients were included. Continuous Petco(2) monitoring was easily performed in all 50 patients during ambulance transport, but blood gas analysis failed in 1 patient. Agreement between the 2 methods was poor with a bias (mean difference) between Petco(2) and Paco(2) measurements of 12 mm Hg and a precision (SD of the difference) of 8 mm Hg. The gradient between Petco(2) and Paco(2) was greater than 5 and 10 mm Hg in 41 and 25 patients, respectively., Conclusions: Petco(2) measurements poorly reflected Paco(2) values in our population of nonintubated patients with respiratory distress of various origins.

Anteroposterior patterning of the ectoderm in the invertebrate chordate Ciona intestinalis first relies on key zygotic activators, such as FoxA, and later on the coordinated responses to inducing signals from the underlying mesendoderm. Here, we focus on a mechanism of coordination of these responses by looking at the cis-regulatory logics of Ci-Rora and Ci-Rorb, which are coding for putative non-canonical transmembrane Wnt receptors, and are present in tandem along the C. intestinalis chromosome 08q. We showed that during cleavage stages, both Ci-Rora and Ci-Rorb genes are initially expressed in all blastomeres of the anterior ectoderm (a-line), as sFRP1/5 (Lamy, C., Rothbächer, U., Caillol, D., Lemaire, P., 2006. Ci-FoxA-a is the earliest zygotic determinant of the ascidian anterior ectoderm and directly activates Ci-sFRP1/5. Development 133, 2835-2844.). We then carried out a functional analysis of cis-regulatory regions and showed that both genes have elements enriched in Ci-FoxA-a binding sites. We dissected one of these early enhancers, and showed that it is directly activated by Ci-FoxA-a, as one sFRP1/5 cis-regulatory element. We also showed that although FoxA binding sites are abundant in genomes, dense clusters of these sites are found upstream from very few genes, and have a high predictive value of a-line expression. These data indicate an important role for FoxA in anterior specification, via the transcriptional regulation of target genes belonging to various signalling pathways.

Background: New, practical models of central nervous system regeneration are required and should provide molecular tools and resources. We focus here on the tunicate Ciona intestinalis, which has the capacity to regenerate nerves and a complete adult central nervous system, a capacity unusual in the chordate phylum. We investigated the timing and sequence of events during nervous system regeneration in this organism., Methodology/principal Findings: We developed techniques for reproducible ablations and for imaging live cellular events in tissue explants. Based on live observations of more than 100 regenerating animals, we subdivided the regeneration process into four stages. Regeneration was functional, as shown by the sequential recovery of reflexes that established new criteria for defining regeneration rates. We used transgenic animals and labeled nucleotide analogs to describe in detail the early cellular events at the tip of the regenerating nerves and the first appearance of the new adult ganglion anlage., Conclusions/significance: The rate of regeneration was found to be negatively correlated with adult size. New neural structures were derived from the anterior and posterior nerve endings. A blastemal structure was implicated in the formation of new neural cells. This work demonstrates that Ciona intestinalis is as a useful system for studies on regeneration of the brain, brain-associated organs and nerves.

We review the anatomical and functional features of circumventricular organs in vertebrates and their homologous neurohemal organs in invertebrates. Focusing on cyclostomes (lamprey) and urochordates (ascidians), we discuss the evolutionary origin of these organs as a function of their cell type specification and morphogenesis.

Improvements in closed-system culturing methods for marine invertebrates are important prerequisites for the generalized use of transgenic lines. We discuss here the effects of several closed-system conditions on the growth and survival of the solitary ascidian, Ciona intestinalis. In Shimoda, close to the sea, a small-tank system was used to ensure that tanks and systems were reasonably equipped, water exchange was rapid, and animals separated to minimize the risk of infection. In Gif-sur-Yvette, an inland site, we tried to determine the optimal conditions to limit handling operations, and to save artificial seawater by avoiding water pollution. A mixture of at least two types of live algae was better than any single-organism diet. With these maintenance protocols, we were able to obtain several generations of Ciona intestinalis, including several transgenic lines. Because these systems make it easier to rear Ciona intestinalis in laboratories, they increase the potentialities of this model organism for research., (Copyright 2007 Wiley-Liss, Inc.)

The objective of this study was to assess effectiveness of gum elastic bougie (GEB) in case of difficult intubation occurring in the prehospital settings. After manikin training to GEB handling, physicians were recommended to use GEB as first alternative technique in case of difficult intubation. Intubating conditions and details of patients requiring GEB-assisted laryngoscopy were recorded over 30 months. Among the 1442 extrahospital intubations performed, 41 patients (3%) required GEB. Gum elastic bougie allowed successful intubation in 33 cases (78%) and 8 patients sustained a second alternative technique. One patient was never intubated, another 1 required rescue cricothyroidotomy. Twenty-four (60%) GEB patients had associated factors for difficult intubation such as reduced or limited cervical spine mobility, morbid obesity, cervicofacial trauma, and ears, nose, and throat neoplasia. The success rate of GEB was 75% and 94%, respectively, depending on whether associated factors for difficult intubation are present or not. No adverse events associated to GEB use were noted.