Kouki Yonezawa

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 The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated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.

Proteomic profiling reveals compartment‐specific, novel functions of ascidian sperm proteins

In this study, we performed extensive proteomic analysis of sperm from the ascidian Ciona intestinalis. Sperm were fractionated into heads and flagella, followed by further separation into Triton X‐100‐soluble and ‐insoluble fractions. Proteins from each fraction and whole sperm were separated by isoelectric focusing using two different pH ranges, followed by SDS–PAGE at two different polyacrylamide concentrations. In total, 1,294 protein spots representing 304 non‐redundant proteins were identified by mass spectrometry (MALDI‐TOF). On comparison of the proteins in each fraction, we were able to identify the proteins specific to different sperm compartments. Further comparison with the testis proteome allowed the pairing of proteins with sperm‐specific functions. Together with information on gene expression in developing embryos and adult tissues, these results provide insight into novel cellular and functional aspects of sperm proteins, such as distinct localization of actin isoforms, novel Ca2+‐binding proteins in axonemes, localization of testis‐specific serine/threonine kinase, and the presence of G‐protein coupled signaling and ubiquitin pathway in sperm flagella. Mol. Reprod. Dev. 78:529–549, 2011.

The orthogonal CNN problem

The online CNN problem had no known competitive algorithms for a long time. Sitters, Stougie and de Paepe showed that there exists a competitive online algorithm for this problem. However, both their algorithm and analysis are quite complicated, and above all, their upper bound for the competitive ratio is 105. In this paper, we examine why this problem seems so difficult. To this end we introduce a nontrivial restriction, orthogonality, against this problem and show that it decreases the competitive ratio dramatically, down to at most 9.

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

CIPRO database (http://cipro.ibio.jp/2.5) is an integrated protein database for a tunicate species Ciona intestinalis that is part of the Urochordata. Although CIPRO provides proteomic and transcriptomic data on 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 human evolution. Furthermore, C. intestinalis has been one of the favorites of developmental biologists; therefore, a lot of amount of accumulated knowledge on its development, morphology, in addition to the recent genome sequence and gene expression data exists. The CIPRO database aims to collect published data and to present unique information, including the unpublished transcriptomic and proteomic data and human curated annotation, for the use of researchers in biology and bioinformatics. The current database contains 89,673 unique sequences covering all the proteins from all the gene models on this species; the number was reduced to 70,493 by similarity clustering. Of these sequences, more than 5,000 proteins are manually annotated based on the large-scale transcriptomic, proteomic and bioinformatic data. Those annotations can be subjected to be qualification by rating, curation, and comments by named and anonymous users through the web site of CIPRO database. Unique features of CIPRO database include: (i) Original experimental data Unpublished experimental data, including 2D-PAGE with the identified protein spots by protein mass fingerprint (PMF) MS analysis, expressions or localizations of protein and RNA across developmental stages and tissues, altogether summarized in a single chart for the comparison among status and methods. RNA expressions are observed by microarray and EST. Each protein is linked to an independent Ascidian Proteome Database summarizing large-scale MS-based proteomic analyses. (ii) Whole Ciona intestinalis proteome database Proteins across gene models are presented: all protein models derived from published gene models are incorporated, including Kyoto model (KG), KH (successor of KG model), PROCITS, JGIs versions 1 and 2, and Ensembl (version 58.2) are incorporated. Identical sequences across gene models are shown. (iii) Original comprehensive user-friendly interfaces Bioinformatic analyses and prediction results are summarized in pictures for grasp at a glance: homology search, cytolocalization, secondary structure prediction combined with modification sites, such include phosphorylation and three-dimensional structures. (iv) Comparative analysis data for disease association Comparison with human genome: map location of human homologues is graphically shown with associated disease information. Comparative data for other model organisms are also included. (v) Community-wide curation capability opened to users To facilitate progressive improvement of annotation by visited users, users can place additional annotation for the protein name and/or comments, which will be subjected to rating by the followed data viewers. To aid curation by wide community, information for literature and essence of matched motif patterns and other related protein information are shown with the links. (vi) Useful search facilities Various search methods are provided including blast homology, free text, partial sequence, protein mass fragment, and cross item searches.

Online Chasing Problems for Regular n-Gons

We consider a server location problem with only one server to move. If each request must be served on the exact position, there is no choice for the online player and the problem is trivial. In this paper we assume that a request is given as a region and that the service can be done anywhere inside the region. Namely, for each request an online algorithm chooses an arbitrary point in the region and moves the server there. Our main result shows that if the region is a regular n-gon, the competitive ratio of the greedy algorithm is 1/sin pi/2n for odd n and 1/sin pi/n for even n. Especially for a square region, the greedy algorithm turns out to be optimal.