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 The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated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

Menadione 処理した Candida albicans ROS 生産機構の解析

Menadione shows anti Condida activity by promoting ROS production. However, the ROS production mechanism has not been clarifield. Thus, in this study, we studied thr relation between anti Candida activity of menadione and ROS production. Menadione inhibited the growth of C. albicans BWP17 strain, the growth of C. albicans JM02 strain was not inhibited. ROS production in C. albicans BWP17 strain was enhanced by addition of menadione. The ROS production in C. albicans JM02 strain was also enhanced by menadione, however, the amount of ROS was lower than that in menadione untreated C. albicans BWP17 strain. NDH51 is 51-kDa subunit of NADH dehydrogenase complex I, and C. albicans JM02 strain is deficient in NDH51 strain. Rotenone, an NADH dehydrogenase complex I inhibitor, decreased the menadione sensitivity of the C. albicans BWP17 strain, indicating that NDH51 related to the menadione sensitivity of C. albicans. The expression of NDH51 mRNA was increased by menadione in C. albicans BWP17 strain. These results indicated that menadion inhibited the growthe of C. albicans by stimulating the ROS production system though activation of NDH51 in C. albicans

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

N-アセチルノイラミン酸によるCandida albicans形態変化の制御について

Candida albicans is a dimorphic fungus and generally grows in hyphal form in RPMI1640 medium. However, addition of N-acetylneuraminic acid inhibited the hyphal growth. The expression of CGR1 mRNA in C. albicans was inhibited by addition of N-acetylneuraminic acid. Diltiazem, a calcium channel blocker, inhibited the yeast to hyphal transformation in C. albicans as well as addition of N-acetylneuraminic acid. These results indicated that inhibition of hyphal growth of C. albicans by N-acetylneuraminic acid was mediated by interruption of CGR1 mRNA expression

菌密度変化に伴うCandida albicansの増殖時形態変化メカニズムの解析

Candida albicans generally grows in hyphal form in RPMI-1640 medium. However, transformation of hyphal form to yeast form is observed by increasing of the cell density in RPMI-1640 medium. Intracellular Ca^ was increased in yeast growth condition (high cell density condition) compared with that of hyphal growth condition. The expression of CGR1 mRNA was inhibited in the yeast growth condition. These results indicated that the transformation of C. albicans was mediated by Ca^-dependent stimulation system, and the system was regulated by CGR1 expression

pH変化によるCandida albicans形態変化シグナルの解析

Candida albicans generally grows in hyphal form in RPMI-1640 medium. However, transformation of hyphal form to yeast form is inhibited by declining pH in RPMI-1640 medium and low pH enhance the yeast like forming. The expressions of RAS1, EFG1, ALS1 and CYR1 mRNA in low pH conditions are significantly decreased compared with that of neutral pH conditions. These results suggested that the transformation of C. albicans may be regulated by pH-dependent stimulation system, and the system was regulated by RAS1 expression

Low replicative fitness of neuraminidase inhibitor-resistant H7N9 avian influenza a virus with R292K substitution in neuraminidase in cynomolgus macaques compared with I222T substitution.

Human cases of H7N9 influenza A virus infection have been increasing since 2013. The first choice of treatment for influenza is neuraminidase (NA) inhibitors (NAIs), but there is a concern that NAI-resistant viruses are selected in the presence of NAIs. In our previous study, an H7N9 virus carrying AA substitution of threonine (T) for isoleucine (I) at residue 222 in NA (NA222T, N2 numbering) and an H7N9 virus carrying AA substitution of lysine (K) for arginine (R) at residue 292 in NA (NA292K, N2 numbering) were found in different macaques that had been infected with A/Anhui/1/2013 (H7N9) and treated with NAIs. In the present study, the variant with NA292K showed not only resistance to NAIs but also lower replication activity in MDCK cells than did the virus with wild-type NA, whereas the variant with NA222T, which was less resistant to NAIs, showed replication activity similar to that of the wild-type virus. Next, we examined the pathogenicity of these H7N9 NAI-resistant viruses in macaques. The variants caused clinical signs similar to those caused by the wild-type virus with similar replication potency. However, the virus with NA292K was replaced within 7 days by that with NA292R (same as the wild-type) in nasal samples from macaques infected with the virus with NA292K, i.e. the so-called revertant (wild-type virus) became dominant in the population in the absence of an NAI. These results suggest that the clinical signs observed in macaques infected with the NA292K virus are caused by the NA292K virus and the NA292R virus and that the virus with NA292K may not replicate continuously in the upper respiratory tract of patients without treatment as effectively as the wild-type virus

Relationships Among Tweets Related to Radiation: Visualization Using Co-Occurring Networks

Background: After the Fukushima Daiichi nuclear accident on March 11, 2011, interest in, and fear of, radiation increased among citizens. When such accidents occur, appropriate risk communication must provided by the government. It is therefore necessary to understand the fears of citizens in the days after such accidents.\nObjective: This study aimed to identify the progression of people’s concerns, specifically fear, from a study of radiation-related tweets in the days after the Fukushima Daiichi nuclear accident.\nMethods: From approximately 1.5 million tweets in Japanese including any of the phrases “radiation” (放射線), “radioactivity” (放射能), and “radioactive substance” (放射性物質) sent March 11-17, 2011, we extracted tweets that expressed fear. We then performed a morphological analysis on the extracted tweets. Citizens’ fears were visualized by creating co-occurrence networks using co-occurrence degrees showing relationship strength. Moreover, we calculated the Jaccard coefficient, which is one of the co-occurrence indices for expressing the strength of the relationship between morphemes when creating networks.\nResults: From the visualization of the co-occurrence networks, we found high citizen interest in “nuclear power plant” on March 11 and 12, “health” on March 12 and 13, “medium” on March 13 and 14, and “economy” on March 15. On March 16 and 17, citizens’ interest changed to “lack of goods in the afflicted area.” In each co-occurrence network, trending topics, citizens’ fears, and opinions to the government were extracted.\nConclusions: This study used Twitter to understand changes in the concerns of Japanese citizens during the week after the Fukushima Daiichi nuclear accident, with a focus specifically on citizens’ fears. We found that immediately after the accident, the interest in the accident itself was high, and then interest shifted to concerns affecting life, such as health and economy, as the week progressed. Clarifying citizens’ fears and the dissemination of information through mass media and social media can add to improved risk communication in the future