Increased Expression and Protein Divergence in Duplicate Genes Is Associated with Morphological Diversification

The differentiation of both gene expression and protein function is thought to be important as a mechanism of the functionalization of duplicate genes. However, it has not been addressed whether expression or protein divergence of duplicate genes is greater in those genes that have undergone functionalization compared with those that have not. We examined a total of 492 paralogous gene pairs associated with morphological diversification in a plant model organism (Arabidopsis thaliana). Classifying these paralogous gene pairs into high, low, and no morphological diversification groups, based on knock-out data, we found that the divergence rate of both gene expression and protein sequences were significantly higher in either high or low morphological diversification groups compared with those in the no morphological diversification group. These results strongly suggest that the divergence of both expression and protein sequence are important sources for morphological diversification of duplicate genes. Although both mechanisms are not mutually exclusive, our analysis suggested that changes of expression pattern play the minor role (33%–41%) and that changes of protein sequence play the major role (59%–67%) in morphological diversification. Finally, we examined to what extent duplicate genes are associated with expression or protein divergence exerting morphological diversification at the whole-genome level. Interestingly, duplicate genes randomly chosen from A. thaliana had not experienced expression or protein divergence that resulted in morphological diversification. These results indicate that most duplicate genes have experienced minor functionalization

Assessing the Dependence of an Urban System in Japan on Forest Ecosystem Services: A Case Study

Abstract With the progress of urbanization, the importance of biodiversity conservation and sustainable ecosystem service use in urban systems has been entirely acknowledged. We are recognizing the need to redesign city systems from the viewpoint of the relationship between urban activities and natural ecosystems. In this study, we evaluated the dependence of human activities within a large metropolitan region on ecosystem services. Our evaluation focused on the civilian sector (which consists of business and residential activities) of the municipalities of Osaka prefecture, Japan. This study applied a framework known as Ecosystem Services Use (ESU), an ecological footprint-based evaluation method, in order to identify the characteristics of Forest Ecosystem Service Use (FESU) by a municipality. FESU was estimated in hectares by integrating various statistics on human activities and using conversion functions that reflect the features of the urban systems of each municipality. The results showed that FESUCO2, the variable representing the forest area needed to compensate for carbon dioxide emissions, represented the largest portion of total FESU in all municipalities, indicating that energy consumption through urban activities plays a significant role in increasing dependence on forest ecosystems. Additionally, a cluster analysis was performed with variables related to municipality character, FESU, and external dependence. The 43 municipalities of Osaka were clustered into five groups. By applying the ESU framework, this case study demonstrates a viable method of quantitatively evaluating the dependence of urban activities on ecosystem services and helps us understand the sustainability of cities’ use of ecosystem services

逆転写酵素・DNAポリメラーゼを用いたRT-PCRによる増幅反応で確認されたペッパーマイルドモットルウイルス（PMMoV）感染ピーマンの果実種子におけるウイルスの効果的な不活性化方法

A method for efficient inactivation Papper mild mottle virus (PMMoV) in harvested seeds of green pepper was examined based on the infectivity on the leaves of Nicotina glutinosa L.(a local host) and a reverse transcription and polymerase chain reaction (RT-PCR)-based amplification of the viral RNA. The seed homogenates from PMMoV-infected plants produced a large number of necrotic local lesion in N.glutinosa, but soaking the seeds in 10% (w/v) tri-sodium phosphate (Na3PO4) for 20 min or dry sterilization (70C,3h) effectivity eliminated the abundance of PMMoV. However, no necrotic lesion on N.glutinosa or the RT-PCR-basaed amplification was observed with seeds that has been disinfected by Na3PO4 in combination with dry sterilization

ピーマン(Capsicum annuum L.)に導入されたＬ２抵抗性遺伝子を打破する日本産トバモウイルス系統ペッパーマイルドモットルウイルス(PMMoV)の疫学的調査

To understand the epidemiological aspects of tobamovirus infecting the L resistance genotypes of green pepper, fifteen isolates were collected from geographically different fields and were chracterized by their biological properties. All isolates infected L1 and L2 plants systemically, but were localized in L3 and L4 plants. The symptomatology on several test plants and the reactivity to an antiserum showed that they were identical to that of a Japanese strain of pepper mild mottle virus (PMMoV-J). The viral infection was also confirmed by a reverse transcription and polymerase chain reaction (RT-PCR) with oligonucleotide primers that amplity the coat protein gene of PMMoV-RNA. On the other hand, the RT-PCR allowed us to detect PMMoV in seeds of some commercial cultivars of green pepper. Viruses isolated from the seeds could infect L2 plants systemically. Further analysis of the nucleotide sequence of the predicted coat protein gene revealed that the isolates from the commercial seeds were identical to that of PMMoV-J. These results indicated that the L2 resistance-breaking tobamovirus has prevailed in fields of green pepper in Japan. and that infected seeds may be one of the initial sources of the viral infection

RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome

The RIKEN Arabidopsis Genome Encyclopedia (RARGE) database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments. RARGE provides tools for searching by resource code, sequence homology or keyword, and rapid access to detailed information on the resources. We have isolated 245 946 RAFL cDNA clones and collected 11 933 transposon-tagged lines, which are available from the RIKEN Bioresource Center and are stored in RARGE. The RARGE web interface can be accessed at http://rarge.gsc.riken.jp/. Additionally, we report 90 000 new RAFL cDNA clones here

ECOMICS: A Web-Based Toolkit for Investigating the Biomolecular Web in Ecosystems Using a Trans-omics Approach

Ecosystems can be conceptually thought of as interconnected environmental and metabolic systems, in which small molecules to macro-molecules interact through diverse networks. State-of-the-art technologies in post-genomic science offer ways to inspect and analyze this biomolecular web using omics-based approaches. Exploring useful genes and enzymes, as well as biomass resources responsible for anabolism and catabolism within ecosystems will contribute to a better understanding of environmental functions and their application to biotechnology. Here we present ECOMICS, a suite of web-based tools for ECosystem trans-OMICS investigation that target metagenomic, metatranscriptomic, and meta-metabolomic systems, including biomacromolecular mixtures derived from biomass. ECOMICS is made of four integrated webtools. E-class allows for the sequence-based taxonomic classification of eukaryotic and prokaryotic ribosomal data and the functional classification of selected enzymes. FT2B allows for the digital processing of NMR spectra for downstream metabolic or chemical phenotyping. Bm-Char allows for statistical assignment of specific compounds found in lignocellulose-based biomass, and HetMap is a data matrix generator and correlation calculator that can be applied to trans-omics datasets as analyzed by these and other web tools. This web suite is unique in that it allows for the monitoring of biomass metabolism in a particular environment, i.e., from macromolecular complexes (FT2DB and Bm-Char) to microbial composition and degradation (E-class), and makes possible the understanding of relationships between molecular and microbial elements (HetMap). This website is available to the public domain at: https://database.riken.jp/ecomics/

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org

A flexible representation of omic knowledge for thorough analysis of microarray data

BACKGROUND: In order to understand microarray data reasonably in the context of other existing biological knowledge, it is necessary to conduct a thorough examination of the data utilizing every aspect of available omic knowledge libraries. So far, a number of bioinformatics tools have been developed. However, each of them is restricted to deal with one type of omic knowledge, e.g., pathways, interactions or gene ontology. Now that the varieties of omic knowledge are expanding, analysis tools need a way to deal with any type of omic knowledge. Hence, we have designed the Omic Space Markup Language (OSML) that can represent a wide range of omic knowledge, and also, we have developed a tool named GSCope3, which can statistically analyze microarray data in comparison with the OSML-formatted omic knowledge data. RESULTS: In order to test the applicability of OSML to represent a variety of omic knowledge specifically useful for analysis of Arabidopsis thaliana microarray data, we have constructed a Biological Knowledge Library (BiKLi) by converting eight different types of omic knowledge into OSML-formatted datasets. We applied GSCope3 and BiKLi to previously reported A. thaliana microarray data, so as to extract any additional insights from the data. As a result, we have discovered a new insight that lignin formation resists drought stress and activates transcription of many water channel genes to oppose drought stress; and most of the 20S proteasome subunit genes show similar expression profiles under drought stress. In addition to this novel discovery, similar findings previously reported were also quickly confirmed using GSCope3 and BiKLi. CONCLUSION: GSCope3 can statistically analyze microarray data in the context of any OSML-represented omic knowledge. OSML is not restricted to a specific data type structure, but it can represent a wide range of omic knowledge. It allows us to convert new types of omic knowledge into datasets that can be used for microarray data analysis with GSCope3. In addition to BiKLi, by collecting various types of omic knowledge as OSML libraries, it becomes possible for us to conduct detailed thorough analysis from various biological viewpoints. GSCope3 and BiKLi are available for academic users at our web site