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Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.

In recent years, the concept of autonomous navigation systems has gained substantial significance, with the potential to change the traditional concept of autonomous navigation. The presented numerical simulation investigates the feasibility of a ship's autonomous navigation system through a laser communication infrastructure handled by a two-degrees-of-freedom (DoFs) acquisition, tracking and pointing (ATP) system able to enable ship–satellite data transmission. The methodology introduced presents the geometrical and kinematic delineation of the model, coupled with the implemented control system, aimed at assessing the pointing accuracy. The minimum requested pointing accuracy is 100 µrad and the analysis highlights the need of using methodologies to reduce the pointing error. Two approaches are investigated to examine a possible improvement of the system, and results show that the pointing phase is influenced less by ship motions and more by errors that occur during the satellite's positioning and the ship motion acquisition process. A trade-off in choosing parameters to improve the system's accuracy leads to a satellite's first targeting time of 0.25 s alongside the probability of hitting the target once every 0.0013 s. The reliability of the system is evaluated through a brief sizing of the optical electromechanical component of the system using the trade-off parameters chosen to improve the pointing phase accuracy. [ABSTRACT FROM AUTHOR]

In tunicates, several species in the Molgulidae family have convergently lost the tailed, swimming larval body plan, including the morphogenesis of the notochord, a major chordate-defining trait. Through the comparison of tailless M. occulta and a close relative, the tailed species M. oculata , we show that notochord-specific expression of the Collagen Type I/II Alpha (Col1/2a) gene appears to have been lost specifically in the tailless species. Using CRISPR/Cas9-mediated mutagenesis in the tailed laboratory model tunicate Ciona robusta , we demonstrate that Col1/2a plays a crucial role in the convergent extension of notochord cells during tail elongation. Our results suggest that the expression of Col1/2a in the notochord, although necessary for its morphogenesis in tailed species, is dispensable for tailless species. This loss is likely a result of the accumulation of cis -regulatory mutations in the absence of purifying selective pressure. More importantly, the gene itself is not lost, likely due to its roles in other developmental processes, including during the adult stage. Our study further confirms the Molgulidae as an interesting family in which to study the evolutionary loss of tissue-specific expression of indispensable genes. [ABSTRACT FROM AUTHOR]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2009.02.007 Byline: Matthew P. Dunn, Anna Di Gregorio Keywords: Ciona; Brachyury; Notochord; Muscle; Ascidian; Leprecan; T-box; Tbx6; Prolyl 3-hydroxylase; cis-Regulation Abbreviations: AP, anterior-posterior; bp, base pair(s); CNS, central nervous system; ER, endoplasmic reticulum; EST, expressed sequence tag; GFP, green fluorescent protein; GST, glutathione S-transferase; kb, kilobase(s), or 1000 base pairs; PCR, polymerase chain reaction; RFP, red fluorescent protein; wt, wild-type Abstract: In Ciona intestinalis, leprecan was identified as a target of the notochord-specific transcription factor Ciona Brachyury (Ci-Bra) (Takahashi, H., Hotta, K., Erives, A., Di Gregorio, A., Zeller, R.W., Levine, M., Satoh, N., 1999. Brachyury downstream notochord differentiation in the ascidian embryo. Genes Dev. 13, 1519-1523). By screening [approximately equal to]14 kb of the Ci-leprecan locus for cis-regulatory activity, we have identified a 581-bp minimal notochord-specific cis-regulatory module (CRM) whose activity depends upon T-box binding sites located at the 3'-end of its sequence. These sites are specifically bound in vitro by a GST-Ci-Bra fusion protein, and mutations that abolish binding in vitro result in loss or decrease of regulatory activity in vivo. Serial deletions of the 581-bp notochord CRM revealed that this sequence is also able to direct expression in muscle cells through the same T-box sites that are utilized by Ci-Bra in the notochord, which are also bound in vitro by the muscle-specific T-box activators Ci-Tbx6b and Ci-Tbx6c. Additionally, we created plasmids aimed to interfere with the function of Ci-leprecan and categorized the resulting phenotypes, which consist of variable dislocations of notochord cells along the anterior-posterior axis. Together, these observations provide mechanistic insights generally applicable to T-box transcription factors and their target sequences, as well as a first set of clues on the function of Leprecan in early chordate development. Author Affiliation: Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, Box 60, New York, NY 10065, USA Article History: Received 22 September 2008; Revised 21 January 2009; Accepted 3 February 2009

We present evidence that notochord and muscle differentiation are crucial for morphogenesis of the ascidian tail. We developed a novel approach for embryological manipulation of the developing larval tissues using a simple method to introduce DNA into Ciona intestinalis and the several available tissue-specific promoters. With such promoters, we misexpressed the Xenopus homeobox gene bix in notochord or muscle of Ciona embryos as a means of interfering with development of these tissues. Ciona embryos expressing bix in the notochord from the 64-cell stage develop into larvae with very short tails, in which the notochord precursors fail to intercalate and differentiate. Larvae with mosaic expression of bix have intermediate phenotypes, in which a partial notochord is formed by the precursor cells that did not receive the transgene while the precursors that express the transgene cluster together and fail to undergo any of the cell-shape changes associated with notochord differentiation. Muscle cells adjacent to differentiated notochord cells are properly patterned, while those next to the notochord precursor cells transformed by bix exhibit various patterning defects. In these embryos, the neural tube extends in the tail to form a nerve cord, while the endodermal strand fails to enter the tail region. Similarly, expression of bix in muscle progenitors impairs differentiation of muscle cells, and as a result, notochord cells fail to undergo normal extension movements. Hence, these larvae have a shorter tail, due to a block in the elongation of the notochord. Taken together, these observations suggest that tail formation in ascidian larvae requires not only signaling from notochord to muscle cells, but also a 'retrograde' signal from muscle cells to notochord. Key Words: Ciona intestinalis; ascidian; notochord; muscle; endodermal strand; bix.

Recent research reveals that developmental aspects of ascidian larva and vetebrate tadpole demonstrate similarities at evolutionary and molecular levels. Data indicate that same genes are preferentially expressed in both ascidian and vetebrate notochord and nervous systems.

Downstream notochord differentiation by Brachyury in the ascidian embryo has been studied. Brachyury is essential for notochord differentiation in vertebrates and in the ascidian tadpole, which has the most simplified chordate body design. The misexpression of the Brachyury gene (Ci-Bra) of Ciona intestinalis, an ascidian, is enough to transform endoderm into notochord. Subtractive hybridization screens were conducted to identify potential Brachyury target genes induced on Ci-Bra misexpression. The potential Ci-Bra downstream genes seem to encode a broad spectrum of divergent proteins associated with notochord formation.