Integral presentation of Experimental Results and Bioinformatic Analyses on _Ciona_ _intestinalis_ Proteins

For the aim of facilitating biologists to find new knowledge through the comprehensive proteomic and transcriptomic data of _Ciona intestinalis_, we have been developing an intuitive and integral view of experimental and bioinformatic results for each protein, which, unlike on human proteins, was incomplete for _Ciona_ proteins. In the presentation, we integrated in a view the experimental results of 2D-PAGE analyses done at Shimoda Marine Research Center, University of Tsukuba, 3D-view of expressions (3DPL) done by Hotta _et al_., and cross-references with JGI version 1 and ENSEMBL. A total of 1,673 entries of 2D-PAGE and 57 of 3DPL are currently contained in CIPRO database. The information is summarized in a single page for a protein. Together with BLAST results, comparative genomics, expression profiles, domain search results, localization, phylogeny etc., we provide biologists the highly integrated view amongst the existing databases, which facilitates to understand the protein. For example, the 2D-PAGE and the microarray results of the same protein are sometimes different, which implies the spatial or temporal gaps of the expressions between the mRNA and the protein. Besides, two functionalities are implemented. One is an improved 2D-PAGE viewer, which provides the compact view of spots and experimental information, and another is peptide fragment mass search functionality as improved PerMS algorithm by Hozumi _et al_., by enabling detection of seven kinds of modifications and suspected contaminants

A generalized linear model for decomposing cis-regulatory, parent-of-origin, and maternal effects on allele-specific gene expression

Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis-regulatory mutations. Here we propose a simple method to decompose cis-regulatory (i.e., allelic genotype, AG), genomic imprinting (i.e., parent-of-origin, PO), and maternal (i.e., maternal genotype, MG) effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the efficiency of method using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seq data. Consistent with previous studies, we found little evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified dozens and hundreds of mouse genes with significant PO and MG effects, respectively. Interestingly, a similar number of genes with significant PO effect were detect in mouse TSCs and livers, whereas more genes with significant MG effect were observed in livers. Further application of this method will clarify how these three effects influence gene expression levels in different tissues and developmental stages, and provide novel insight into the evolution of gene expression regulation.Comment: 27 pages, 3 figures, 2 tabl

Incorporating Community Annotation Interfaces into the CIPRO2.5 Database with Comprehensible Sketches to Support Quick Annotations of Proteome Data.

User annotation or comment interfaces are now widely used in several web sites such as journals, news, weblogs and Wikipedia. However, there are only a few biological databases with annotation interfaces. The _Ciona_ _intestinalis_ protein database (CIPRO) was created in order to provide integrated proteome data especially for experimental biologists. The current database contains 89,673 unique sequences covering all the known and predicted gene models. Typical tasks include which gene models are reliable and which function is plausible. The human-curated annotation is most important for the meaningful database.
Here we incorporate three new functions into the CIPRO2.5 database (http://cipro.ibio.jp/2.5/), providing enriched resources for the users. First, a community annotation interface as web forms and a user comment editor with rating its comment were added. Second, the web pages were specifically designed to compact for quickly understood overviews. For example, cytolocalization was automatically provided by a color-depicted cell image based on the intensity instead of the numeric values of raw data. The expression data of EST, microarray and 2D-PAGE were integrated as one chart. In addition to these data, the images of transmembrane prediction, domain and motif search, and the OMIM ortholog on the chromosome map were included in each protein page. The last, even the BLAST and PMF search were added to combined fields in the retrieval system.
As a result, a total of 11,134 pages were annotated by our community. Furthermore, 2,186 comments were added to the database. Those annotated data are freely accessible at the CIPRO2.5 web site

Complete Fracture-Dislocation of the Thoracolumbar Spine with No Critical Neurological Deficit : A Case Report

Fractures at the thoracolumbar junction are the most common spinal column fractures. Among type C fractures in the Arbeitsgemeinschaft für Osteosynthesefragen Spine Classification, cases with complete fracture-dislocations of the spinal column often result in a critical neurological deficit despite surgical treatment. We present a case of an 18-year-old man who had a complete fracture-dislocation of the T12 vertebral body and multiple injuries following high-energy trauma but no critical neurological deficits. Because of active bleeding in the left thoracic cavity, the patient underwent open reduction of the T12 vertebral body and anterior spinal fusion of the T11-L1 vertebral bodies via an anterior approach between the T9 and T10 ribs within 24 h of the accident. Four months postoperatively, the patient could ambulate independently, with a slight disturbance of light touch. At 6 months postoperatively, plain computed tomography scans showed bony union of the T12 vertebral body. We postulated two reasons for the absence of critical neurological dysfunction : (1) spontaneous spinal canal sparing because of the fracture of the right superior articular process in the L1 vertebral body and (2) fracture morphology, that is, a rotational fracture with mild to moderately strong shearing stress to the dura mater

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

CIPK23 regulates blue light-dependent stomatal opening in Arabidopsis thaliana

Phototropins (phot1 and phot2) are plant blue light receptor kinases that function to mediate phototropism, chloroplast movement, leaf flattening, and stomatal opening in Arabidopsis. Considerable progress has been made in understanding the mechanisms associated with phototropin receptor activation by light. However, the identities of phototropin signaling components are less well understood by comparison. In this study, we specifically searched for protein kinases that interact with phototropins by using an in vitro screening method (AlphaScreen) to profile interactions against an Arabidopsis protein kinase library. We found that CBL‐interacting protein kinase 23 (CIPK23) interacts with both phot1 and phot2. Although these interactions were verified by in vitro pull‐down and in vivo bimolecular fluorescence complementation assays, CIPK23 was not phosphorylated by phot1, as least in vitro. Mutants lacking CIPK23 were found to exhibit impaired stomatal opening in response to blue light but no deficits in other phototropin‐mediated responses. We further found that blue light activation of inward‐rectifying K+ (K+in) channels was impaired in the guard cells of cipk23 mutants, whereas activation of the plasma membrane H+‐ATPase was not. The blue light activation of K+in channels was also impaired in the mutant of BLUS1, which is one of the phototropin substrates in guard cells. We therefore conclude that CIPK23 promotes stomatal opening through activation of K+in channels most likely in concert with BLUS1, but through a mechanism other than activation of the H+‐ATPase. The role of CIPK23 as a newly identified component of phototropin signaling in stomatal guard cells is discussed