Eu2+賦活蛍光体のための新規Si系酸窒化物の合成

要約のみTohoku University垣花眞人課

GARNET – gene set analysis with exploration of annotation relations

<p>Abstract</p> <p>Background</p> <p>Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways or gene ontology (GO) terms. Major difficulties towards biological interpretation are integrating diverse types of annotation categories and exploring the relationships between annotation terms of similar information.</p> <p>Results</p> <p>GARNET (Gene Annotation Relationship NEtwork Tools) is an integrative platform for gene set analysis with many novel features. It includes tools for retrieval of genes from annotation database, statistical analysis & visualization of annotation relationships, and managing gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, we have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules - <it>gene set manager</it>, <it>gene set analysis</it> and <it>gene set retrieval</it>, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations.</p> <p>Conclusions</p> <p>GARNET (gene annotation relationship network tools) is an integrative platform for diverse types of gene set analysis, where complex relationships among gene annotations can be easily explored with an intuitive network visualization tool (<url>http://garnet.isysbio.org/</url> or <url>http://ercsb.ewha.ac.kr/garnet/</url>).</p

Phaeoviral infections are present in macrocystis, ecklonia and undaria (laminariales) and are influenced by wave exposure in ectocarpales

Two sister orders of the brown macroalgae (class Phaeophyceae), the morphologically complex Laminariales (commonly referred to as kelp) and the morphologically simple Ectocarpales are natural hosts for the dsDNA phaeoviruses (family ) that persist as proviruses in the genomes of their hosts. We have previously shown that the major capsid protein (MCP) and DNA polymerase concatenated gene phylogeny splits phaeoviruses into two subgroups, A and B (both infecting Ectocarpales), while MCP-based phylogeny suggests that the kelp phaeoviruses form a distinct third subgroup C. Here we used MCP to better understand the host range of phaeoviruses by screening a further 96 and 909 samples representing 11 and 3 species of kelp and Ectocarpales, respectively. Sporophyte kelp samples were collected from their various natural coastal habitats spanning five continents: Africa, Asia, Australia, Europe, and South America. Our phylogenetic analyses showed that while most of the kelp phaeoviruses, including one from , belonged to the previously designated subgroup C, new lineages of in 3 kelp species, , , , grouped instead with subgroup A. In addition, we observed a prevalence of 26% and 63% in kelp and Ectocarpales, respectively. Although not common, multiple phaeoviral infections per individual were observed, with the Ectocarpales having both intra- and inter-subgroup phaeoviral infections. Only intra-subgroup phaeoviral infections were observed in kelp. Furthermore, prevalence of phaeoviral infections within the Ectocarpales is also linked to their exposure to waves. We conclude that phaeoviral infection is a widely occurring phenomenon in both lineages, and that phaeoviruses have diversified with their hosts at least since the divergence of the Laminariales and Ectocarpales

Factor Structure of the Neurocognitive Tests: An Application of the Confirmative Factor Analysis in Stabilized Schizophrenia Patients

The purpose of the present study was to identify the factor structure of neurocognitive tests used on schizophrenia patients by using the confirmative factor analysis, and to assess the factor score differences of schizophrenia patients and healthy controls. Comprehensive neurocognitive tests were administered to stabilized schizophrenia patients (N=114) and healthy controls (N=120). In the results of factor analyses on patients, the multifactorial-6-factor model, which included the speed of processing, working memory, verbal learning and memory, visual learning and memory, attention/vigilance, and reasoning/problem solving as suggested by the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS), showed the better goodness of fit than any of the other models tested. And assessing the group differences of factor scores, we found the patients performed worse than the controls in all factors, but the result showed meaningful variations of impairments across the cognitive factors. Our study identifies the six major domains with multifactorial structure of cognitive abilities in schizophrenia patients and confirms the distinctive impairment patterns of each cognitive domain. These results may have utility in better understanding the pathology of schizophrenia as well as in genetic studies

Reappraisal of the toxicity test method using the green alga Ulva pertusa Kjellman (Chlorophyta),

This study was aimed to develop an objective way of quantifying the reproductive status of the green macroalga, Ulva pertusa using a vital stain and programmed automated analysis (by Image J program). The EC50 values (with 95% CI), the concentrations of toxicants inducing a reduction of 50% in sporulation after 96 h exposure, from the newly developed method were similar to those obtained by the conventional method: 0.651 (0.598-0.705) mg l(-1) for Cd, 0.144 (0.110-0.162) mg l(-1) for Cu, 0.180 (0.165-0.195) mg l(-1) for atrazine, 0.076 (0.049-0.094) mg l(-1) for diuron and 30.6 (26.5-34.4) ml l(-1) for DMSO, respectively. When the EC50 values from this study were compared to that those from literatures, the sensitivity for some toxicants was similar or higher than that of U. fasciata (1.930 mg l(-1) for germination for Cd), U. armoricana (0.250 mg l(-1) for Fv/Fm for Cu), U. reticulata (0.126-1.585 mg l(-1) for growth for Cu), and U. intestinalis (0.650 mg l(-1) for Fv/Fm for atrazine). The subjective views of the experimental performers can be eliminated using the newly developed method. The Ulva method gave consistent responses to Cu and Cd of internationally allowable ranges for effluents, implying that the method is a useful tool for monitoring industrial wastewaters containing these metals

Multiple and Consecutive Genome Editing Using i-GONAD and Breeding Enrichment Facilitates the Production of Genetically Modified Mice

Genetically modified (GM) mice are essential tools in biomedical research. Traditional methods for generating GM mice are expensive and require specialized personnel and equipment. The use of clustered regularly interspaced short palindromic repeats (CRISPR) coupled with improved-Genome editing via Oviductal Nucleic Acids Delivery (i-GONAD) has highly increased the feasibility of producing GM mice in research laboratories. However, genetic modification in inbred mouse strains of interest such as C57BL/6 (B6) is still challenging because of their low fertility and embryo fragility. We have successfully generated multiple novel GM mouse strains in the B6 background while attempting to optimize i-GONAD. We found that i-GONAD reduced the litter size in superovulated pregnant females but did not impact pregnancy rates. Natural mating or low-hormone dose did not increase the low fertility rate observed in superovulated B6 females. However, diet enrichment had a positive effect on pregnancy success. We also optimized breeding conditions to increase the survival of small litters by co-housing i-GONAD-treated pregnant B6 females with synchronized pregnant FVB/NJ companion mothers. Thus, GM mice generation was increased by an enriched diet and shared pup rearing with highly fertile females such as FVB/NJ. In the present study, we generated 16 GM mice using a CRISPR/Cas system to target individual and multiple loci simultaneously or consecutively. We also compared homology-directed repair efficiency using different methods for LoxP insertion for conditional knockout mouse production. We found that a two-step serial LoxP insertion, in which each LoxP sequence was inserted individually in different i-GONAD procedures, was a low-risk high-efficiency method for generating floxed mice

Designing for Collective Action: Utilizing Ostrom's Core-Relationship Model in the Co-design Process

The relationship between commons research and co-design has gained increasing attention as design challenges become more complex. This study explores their connection, focusing on the early phase of co-design research known as the "pre-design" phase. It proposes utilizing Elinor Ostrom's Core-Relationship Model in co-design research to identify and address key factors in collective action problems. The re-search question guiding this study is: How does Ostrom's Core-Relationship Model inform the identification and addressing of key factors in collective action problems in co-design research? To demonstrate the benefits of Ostrom's model, this study applies it to a specific use case involving the collective action problem of maintaining a clean shared space in a student-shared apartment in Finland. Data was collected through interviews with ten residents, two building representatives, and a housing advisor. The study follows a six-step process, including in vivo and pattern coding, identifying themes and sub-themes referencing the Core-Relationship model, exploring, and mapping structural variables, and linking them to core relationships to identify key variables. The results reveal the complex linkages among variables and their impact on cooperation and collective action outcomes. Two key variables were identified: face-to-face communication and the absence of voluntary resident selections. However, the Core-Relationship Model has limitations in comprehensively examining collective action problems in co-design, as it overlooks external factors such as neglected infrastructure facilities and the involvement of housing services. To overcome the limitations, this thesis delved into exploring the integration and supplementation of other frameworks proposed by Ostrom, such as the Institutional Analysis and Development (IAD) framework and the Eight design principles, with the core-relationship model. The objective was to explore the potential complementary effects of these frameworks on the core-relationship model and enhance its application in co-design re-search. This study contributes to the connection between commons literature and co-design by exploring the application of Ostrom's Core-Relationship Model and addressing its limitations. The findings evaluated the potential to introduce Ostrom's core-relationship model to co-design. This can potentially help co-design practitioners to incorporate external factors into their research and design processes. The findings of this thesis contribute to the ongoing movement of connecting commons literature and co-design, highlighting the importance of exploring different frameworks and developing innovative tools to expand the co-design knowledge repository