CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality

The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includes original large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite of developmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and gene expression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequences, but for higher usability it covers 89 683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10 000 proteins have been manually annotated. Furthermore, to establish a community-supported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http://cipro.ibio.jp/2.5

CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments

CIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata. Although the CIPRO database deals with proteomic and transcriptomic data of a single species, the animal is considered unique in the evolutionary tree, representing a possible origin of the vertebrates and is a good model for understanding chordate evolution, including that of humans. Furthermore, C. intestinalis has been one of the favorites of developmental biologists; there exists a huge amount of accumulated knowledge on its development and morphology, in addition to the recent genome sequence and gene expression data. The CIPRO database is aimed at not only collecting published data, but also presenting unique information, including the unpublished transcriptomic and proteomic data and human curated annotation, for the use by researchers in broad research fields of biology and bioinformatics

Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations

An improved assembly of the Ciona intestinalis genome reveals that it contains non-canonical introns and that about 20% of Ciona genes reside in operons

Clinical outcomes of Najuta thoracic stent graft system for arch aneurysms

ObjectivesWe aimed to elucidate the perioperative and short-term clinical outcomes of the Najuta thoracic stent graft system with fenestrations for supra-aortic vessels.MethodsWe retrospectively investigated the perioperative and short-term clinical outcomes of 20 patients treated for arch or distal arch aneurysms using the Najuta thoracic stent graft system during the period from May 2019 to February 2023.ResultsThe technical success rate of the Najuta thoracic stent graft system was 95%. Of the 20 patients, 17 patients (85.0%) underwent concomitant extra-anatomical supra-aortic bypass. Postoperative CT revealed type Ia (n = 2) and type II (n = 3) endoleaks which disappeared on follow-up. The postoperative complications were stroke (n = 2, 10.0%), paraplegia (n = 1, 5.0%), and paraparesis (n = 1, 5.0%). In a very old patient, a blood transfusion was performed from the common iliac artery using the retroperitoneal approach. There were no aorta-related complications such as retrograde type A dissection or distal stent graft–induced new entry.ConclusionsWe treated arch or distal arch thoracic aneurysms by inserting a tube-type stent graft as a scaffold on the peripheral site and placing the Najuta thoracic stent graft on the proximal site. By extending the landing zone to Zone 0 and using a low radial force, which is a feature of the Najuta thoracic stent graft system, postoperative bird-beak and aorta-related complications were avoided. The treatment of arch and distal arch aortic aneurysms using the Najuta thoracic stent graft system showed acceptable perioperative and short-term clinical outcomes. Thoracic endovascular aortic repair using the Najuta thoracic stent graft system may be a potential treatment option for arch and distal arch aortic aneurysms, warranting further studies

Sustained heterozygosity across a self-incompatibility locus in an inbred ascidian.

Because self-incompatibility loci are maintained heterozygous and recombination within self-incompatibility loci would be disadvantageous, self-incompatibility loci are thought to contribute to structural and functional differentiation of chromosomes. Although the hermaphrodite chordate, Ciona intestinalis, has two self-incompatibility genes, this incompatibility system is incomplete and self-fertilization occurs under laboratory conditions. Here, we established an inbred strain of C. intestinalis by repeated self-fertilization. Decoding genome sequences of sibling animals of this strain identified a 2.4-Mbheterozygous region on chromosome 7. A self-incompatibility gene, Themis-B, was encoded within this region. This observation implied that this self-incompatibility locus and the linkage disequilibrium of its flanking region contribute to the formation of the 2.4-Mb heterozygous region, probably through recombination suppression. We showed that different individuals in natural populations had different numbers and different combinations of Themis-B variants, and that the rate of self-fertilization varied among these animals. Our result explains why self-fertilization occurs under laboratory conditions. It also supports the concept that the Themis-B locus is preferentially retained heterozygous in the inbred line and contributes to the formation of the 2.4-Mb heterozygous region. High structural variations might suppress recombination, and this long heterozygous region might represent a preliminary stage of structural differentiation of chromosomes