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Orthology finding tools are valuable for analyzing biological data from multiple species and predicting the functions of uncharacterized genes. Although several tools are available for this purpose, the characteristics of their results for plant genes are not well compared. In this hackathon, we examined three tools (OMA, OrthoDB, and Ensembl Plants) by extracting ortholog pairs between Arabidopsis and soybean and analyzing each result, focusing on five plant genes with varying degrees of conservation. We observed that changes in the taxonomic ranges of OMA and OrthoDB affected ortholog detection, and the range of ortholog detection across the three tools was inconsistent, suggesting the importance of comparing multiple tools to obtain more accurate information on orthologs.

The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.

We previously demonstrated that expression of a Krüppel-like zinc finger transcription factor, GLIS1, dramatically increases under hypoxic conditions via a transcriptional mechanism induced by HIF-2α cooperating with AP-1 members. In this study, we focused on the functional roles of GLIS1 in breast cancer. To uncover its biological function, the effects of altered levels of GLIS1 in breast cancer cell lines on cellular growth, wound-healing and invasion capacities were assessed. Knockdown of GLIS1 using siRNA in BT-474 cells resulted in significant growth stimulation under normoxia, while attenuation was found in the cell invasion assay under hypoxic conditions. In MDA-MB-231 cells expressing exogenous 3xFLAG-tagged GLIS1, GLIS1 attenuated cell proliferation and enhanced cell mobility and invasion capacities under normoxia. In addition, breast cancer cells expressing GLIS1 acquired resistance to irradiation. Whole transcriptome analysis clearly demonstrated that downstream signals of GLIS1 are related to various cellular functions. Among the genes with increased expression, we focused on WNT5A. Knockdown of WNT5A indicated that enhancement of acquired cell motility in the MDA-MB-231 cells expressing GLIS1 was mediated, at least in part, by WNT5A. In an analysis of publicly available data, patients with estrogen receptor-negative breast cancer showing high levels of GLIS1 expression showed much worse prognosis than those with low levels. In summary, hypoxia-induced GLIS1 plays significant roles in breast cancer cells via regulation of gene expression related to cell migration and invasion capacities, resulting in poorer prognosis in patients with advanced breast cancer.

Anticholinergic organophosphate (OP) agents act on the diverse serine hydrolases, thereby revealing unexpected biological effects. Epidemiological studies indicate a relationship between the OP exposure and development of attention-deficit/hyperactivity disorder (ADHD)-like symptoms, whereas no plausible mechanism for the OP-induced ADHD has been established. The present investigation employs ethyl octylphosphonofluoridate (EOPF) as an OP-probe, which is an extremely potent inhibitor of endocannabinoid (EC, anandamide and 2-arachidonoylglycerol)-hydrolyzing enzymes: that is, fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MAGL). An ex vivo experiment shows that EOPF treatment decreases FAAH and MAGL activities and conversely increases EC levels in the rat brain. Subsequently, EOPF (treated intraperitoneally once at 0, 1, 2, or 3 mg/kg) clearly induces ADHD-like behaviors (in elevated plus-maze test) in both Wistar and spontaneously hypertensive rats. The EOPF-induced behaviors are reduced by a concomitant administration of cannabinoid receptor inverse agonist SLV-319. Accordingly, the EC system is a feasible target for OP-caused ADHD-like behaviors in adolescent rats.

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/)

A binuclear tetra-acetate bridged GdIII complex [Gd2(μ2-O2CMe)4(H2L)2](ClO4)2·2H2O·2MeOH was synthesized, where H2L = bis(5-methylimidazol-4-yl-methylideneaminopropyl)methylamine. The linear polydentate ligand H2L functions as a binding group to two GdIII ions. Two GdIII ions are bridged by two acetate in η1:η1:μ2 fashion and other two in η2:η1:μ2 fashion. The GdIII⋯GdIII distance of 3.920(6) A is shorter than 4.183(1) A of the bis-acetate bridged GdIII complex [{GdIII(O2CMe)3(H2O)2}2]·4H2O. A weak anti-ferromagnetic GdIII–GdIII interaction was observed.

A SCO iron(III) complex [FeIII(Him)2(4MeOhapen)]CF3SO3 was synthesized, where Him = imidazole and 4-MeOhapen = N,N′-bis(2-oxy-4-methoxyacetophenylidene)ethylenediamine. FeIII ion has an octahedral coordination geometry with N2O2 donor atoms of the equatorial tetradentate ligand (4-MeOhapen) and two nitrogen atoms of two imidazoles (Him) at the axial positions. The adjacent cations are bridged by CF3SO3− ion through NH⋯O hydrogen bonds between Him and CF3SO3− to give a one-dimensional chain structure {[FeIII(Him)2(4MeO-hapen)]CF3SO3}1∞. The magnetic susceptibility measurements showed that complex exhibits an abrupt spin transition between a single HS phase and a symmetry-breaking [HS–HS–HS–LS] phase and another transition around 80 K. The single-crystal X-ray analyses at 296 and 150 K revealed the structures at a single HS and [HS–HS–HS–LS] states.

Solvent-free spin crossover (SCO) iron(III) complex, [FeIII(Him)2(hapen)]SbF6 (Him = imidazole, H2hapen = N,N′-bis(2-hydroxyacetophenylidene)ethylenediamine), is synthesized. The FeIII ion has an octahedral coordination geometry, with N2O2 donor atoms of hapen and N2 atoms of two imidazoles at the axial positions. The saturated five-membered chelate ring of hapen moiety assumes a gauche-type δ- or λ-conformation to give chiral species of δ-[FeIII(Him)2(hapen)]+ or λ-[FeIII(Him)2(hapen)]+. One imidazole is hydrogen-bonded to phenoxo oxygen atom of hapen of the adjacent unit to give a hydrogen-bonded chiral one-dimensional structure, {δ-[FeIII(Him)2(hapen)]+}1∞ or {λ-[FeIII(Him)2(hapen)]+}1∞. The adjacent chains with the opposite chiralities are arrayed alternately. The temperature dependences of the magnetic susceptibilities revealed an abrupt one-step spin transition between high-spin (S = 5/2) and low-spin (S = 1/2) states at the spin transition temperature of T1/2 = 105 K. The crystal structures were determined at 296 and 100 K, where the populations of HS:LS of high- and low-spin ratio are evaluated to be 1:0 and 0.3:0.7, respectively, based on magnetic measurements. During the spin transition from 296 K to 100 K, the average Fe–N distance and O–Fe–O angle decrease to a regular octahedron by 0.16 Å and 13.4°, respectively. The structural change in the coordination environment is transmitted to the adjacent spin crossover (SCO) sites along the chiral 1D chain through hydrogen-bonds. The abrupt SCO profile and the spin transition temperature for the isomorphous compounds [FeIII(Him)2(hapen)]Y (Y = PF6, AsF6, SbF6) are ascribed to the chiral hydrogen-bonded 1D structure and chain-anion interaction.

Spin crossover (SCO) iron(III) complexes exhibiting thermal hysteresis, [FeIII(Him)2(3-MeOsalen)]·H2O·EtOH·X (Him = imidazole, 3-MeOsalen = N,N′-bis(3-methoxysalicylidene)ethylenediaminato, and X = PF6, AsF6, SbF6), were synthesized in ethanol. The FeIII ion has an octahedral coordination geometry with N2O2 donor atoms of the planar tetradentate ligand (3-MeOsalen) and two nitrogen atoms of two imidazoles at the axial positions. Through H2O and EtOH the complex-cations are assembled into a hydrogen-bonded 2D network structure and the anion X is accommodated in the void of the 2D network. The temperature dependences of the magnetic susceptibilities revealed an abrupt and two-step spin transition with thermal hysteresis for the PF6 and AsF6 salts.

Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required. However, life scientists have difficulty utilizing the available data due to its sheer magnitude and complicated access. We have developed a web tool for browsing reference gene expression pattern of mammalian tissues and cell lines measured using different methods, which should facilitate the reuse of the precious data archived in several public databases. The web tool is called Reference Expression dataset (RefEx), and RefEx allows users to search by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro, gene expression patterns, or biological categories based on Gene Ontology. RefEx also provides information about genes with tissue-specific expression, and the relative gene expression values are shown as choropleth maps on 3D human body images from BodyParts3D. Combined with the newly incorporated Functional Annotation of Mammals (FANTOM) dataset, RefEx provides insight regarding the functional interpretation of unfamiliar genes. RefEx is publicly available at http://refex.dbcls.jp/.

Individual and small clusters of cancer cells may detach from the edges of a main tumor and invade vessels, which can act as the origin of metastasis; however, the mechanism for this phenomenon is not well understood. Using cancer tissue-originated spheroids, we studied whether disturbing the 3D architecture of cancer spheroids can provoke the reformation process and progression of malignancy. We developed a mechanical disruption method to achieve homogenous disruption of the spheroids while maintaining cell-cell contact. After the disruption, 9 spheroid lines from 9 patient samples reformed within a few hours, and 3 of the 9 lines exhibited accelerated spheroid growth. Marker expression, spheroid forming capacity, and tumorigenesis indicated that stemness increased after spheroid disruption. In addition, the spheroid forming capacity increased in 6 of 11 spheroid lines. The disruption signature determined by gene expression profiling supported the incidence of remodeling and predicted the prognosis of patients with colorectal cancer. Furthermore, WNT and HER3 signaling were increased in the reformed spheroids, and suppression of these signaling pathways attenuated the increased proliferation and stemness after the disruption. Overall, the disruption and subsequent reformation of cancer spheroids promoted malignancy-related phenotypes through the activation of the WNT and ERBB pathways.

Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively. This review consists of two major sections covering: 1) improvement and utilization of RDF data in various domains of the life sciences and 2) meta-data about these RDF data, the resources that store them, and the service quality of SPARQL Protocol and RDF Query Language (SPARQL) endpoints. The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining. The second section describes how we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery. By enhancing the harmonization of these two layers of machine-readable data and knowledge, we improve the way community wide resources are developed and published. Moreover, we outline best practices for the future, and prepare ourselves for an exciting and unanticipatable variety of real world applications in coming years.

In recent years, biological web resources such as databases and tools have become more complex because of the enormous amounts of data generated in the field of life sciences. Traditional methods of distributing tutorials include publishing textbooks and posting web documents, but these static contents cannot adequately describe recent dynamic web services. Due to improvements in computer technology, it is now possible to create dynamic content such as video with minimal effort and low cost on most modern computers. The ease of creating and distributing video tutorials instead of static content improves accessibility for researchers, annotators and curators. This article focuses on online video repositories for educational and tutorial videos provided by resource developers and users. It also describes a project in Japan named TogoTV (http://togotv.dbcls.jp/en/) and discusses the production and distribution of high-quality tutorial videos, which would be useful to viewer, with examples. This article intends to stimulate and encourage researchers who develop and use databases and tools to distribute how-to videos as a tool to enhance product usability.

Cellular dedifferentiation signifies the withdrawal of cells from a specific differentiated state to a stem cell-like undifferentiated state. However, the mechanism of dedifferentiation remains obscure. Here we performed comparative transcriptome analyses during dedifferentiation in mature adipocytes (MAs) to identify the transcriptional signatures of multipotent dedifferentiated fat (DFAT) cells derived from MAs. Using microarray systems, we explored similarly expressed as well as significantly differentially expressed genes in MAs during dedifferentiation. This analysis revealed significant changes in gene expression during this process, including a significant reduction in expression of genes for lipid metabolism concomitantly with a significant increase in expression of genes for cell movement, cell migration, tissue developmental processes, cell growth, cell proliferation, cell morphogenesis, altered cell shape, and cell differentiation. Our observations indicate that the transcriptional signatures of DFAT cells derived from MAs are summarized in terms of a significant decrease in functional phenotype-related genes and a parallel increase in cell proliferation, altered cell morphology, and regulation of the differentiation of related genes. A better understanding of the mechanisms involved in dedifferentiation may enable scientists to control and possibly alter the plasticity of the differentiated state, which may lead to benefits not only in stem cell research but also in regenerative medicine.

Hematopoiesis in teleost fish is maintained in the kidney. We previously reported that Hoechst dye efflux activity of hematopoietic stem cells (HSCs) is highly conserved in vertebrates, and that Hoechst can be used to purify HSCs from teleost kidneys. Regulatory molecules that are strongly associated with HSC activity may also be conserved in vertebrates. In this study, we identified evolutionarily conserved molecular components in HSCs by comparing the gene expression profiles of zebrafish, murine, and human HSCs. Microarray data of zebrafish kidney side population cells (zSPs) showed that genes involved in cell junction and signal transduction tended to be up-regulated in zSPs, whereas genes involved in DNA replication tended to be down-regulated. These properties of zSPs were similar to those of mammalian HSCs. Overlapping gene expression analysis showed that 40 genes were commonly up-regulated in these 3 HSCs. Some of these genes, such as egr1, gata2, and id1, have been previously implicated in the regulation of HSCs. In situ hybridization in zebrafish kidney revealed that expression domains of egr1, gata2, and id1 overlapped with that of abcg2a, a marker for zSPs. These results suggest that the overlapping genes identified in this study are regulated in HSCs and play important roles in their functions.

The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). This resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0560-6) contains supplementary material, which is available to authorized users.

One way that aerobic biological systems counteract the generation of reactive oxygen species (ROS) is with superoxide dismutase proteins SOD1 and SOD2 that metabolize superoxide radicals to molecular oxygen and hydrogen peroxide or scavenge oxygen radicals produced by the extensive oxidation-reduction and electron-transport reactions that occur in mitochondria. We characterized SOD1 and SOD2 of Bombyx mori isolated from the fat body of larvae. Immunological analysis demonstrated the presence of BmSOD1 and BmSOD2 in the silk gland, midgut, fat body, Malpighian tubules, testis and ovary from larvae to adults. We found that BmSOD2 had a unique expression pattern in the fat body through the fifth instar larval developmental stage. The anti-oxidative functions of BmSOD1 and BmSOD2 were assessed by exposing larvae to insecticide rotenone or vasodilator isosorbide dinitrate, which is an ROS generator in BmN4 cells; however, exposure to these compounds had no effect on the expression levels of either BmSOD protein. Next, we investigated the physiological role of BmSOD1 and BmSOD2 under environmental oxidative stress, applied through whole-body UV irradiation and assayed using quantitative RT-PCR, immunoblotting and microarray analysis. The mRNA expression level of both BmSOD1 and BmSOD2 was markedly increased but protein expression level was increased only slightly. To examine the differences in mRNA and protein level due to UV irradiation intensity, we performed microarray analysis. Gene set enrichment analysis revealed that genes in the insulin signaling pathway and PPAR signaling pathway were significantly up-regulated after 6 and 12 hours of UV irradiation. Taken together, the activities of BmSOD1 and BmSOD2 may be related to the response to UV irradiation stress in B. mori. These results suggest that BmSOD1 and BmSOD2 modulate environmental oxidative stress in the cell and have a specific role in fat body of B. mori during pupation.

Schizandrin (SZ) is one of the lignan components from Schisandra fruits. A highly sensitive and precise method for the determination of SZ in human plasma was developed involving selected-ion monitoring with gas chromatography-mass spectrometry using a fused-silica capillary column. A 0.1-ml plasma sample was used for solid-phase extraction. A good linear relationship was obtained in the concentration range studied (2.0–500 ng/ml) and the method was sufficiently accurate and precise to support clinical pharmacokinetic studies. After oral administration of SZ at a dose of 15 mg to healthy male subjects, the average value of the maximum plasma concentration of SZ was 96.1±14.1 ng/ml. The plasma concentration of this substance could be monitored for 8 h after administration.

After oral administration of schizandrin (1) to rat, the bile was collected and treated with beta-glucuronidase and arylsulfatase. Eleven metabolites, SZ-M0 (3), SZ-M1 (4), SZ-M2 (5), SZ-M3 (6), SZ-M4 (7), SZ-M5 (8), SZ-M6 (9), SZ-M7 (10), SZ-M8 (11), SZ-M9 (12) and SZ-M10 (13) were isolated from the bile treated with the enzymes. The bile after oral administration of 1 to dog was collected and treated with enzymes in the same way, and eight metabolites, 3-8, 10 and SZ-MD2 (14) were isolated from the bile treated with enzymes. The structures of these metabolites were determined on the basis of chemical and spectral studies. The major metabolite in the bile of rat was 7 and the major metabolites in the bile of dog were 7 and 14.

The absorption and excretion of gomisin A (TJN-101) in rats whose livers were injured by carbon tetrachloride (CCl4) were investigated. After intravenous administration of TJN-101 at a dose of 5 mg/kg, the terminal elimination half-life was 1.5 h in the CCl4-treated rats, which was two times that in normal rats. The mean area under the blood concentration-time curve (AUC) value of TJN-101 in the CCl4-treated rats was twice that in normal rats, and this difference was significant (p less than 0.05). Therefore, the total body clearance of TJN-101 in the CCl4-treated rats decreased less than half of that in normal rats. Similar results were observed when it was administered orally. In the CCl4-treated rats, the serum concentration of Met. B, which was identified as a demethylenated substance and one of major metabolites, tended to decrease more than that in normal rats. On the other hand, the cumulative biliary excretion ratio of TJN-101 in 24 h after dosing in the CCl4-treated rats was 2.5 times that in normal rats. The excretion rate of Met. B in the bile in the CCl4-treated rats tended to be delayed. However, the quantitative variance of biliary excretion of Met. B was not found in both groups. The urinary excretion of TJN-101 or Met. B in 72 h after dosing in the CCl4-treated rats was lower than that in normal rats. Similar results were also observed in excretion in the feces.(ABSTRACT TRUNCATED AT 250 WORDS)

PAROXYSMAL nocturnal hemoglobinuria is a rare acquired disease caused by an unusual susceptibility of erythrocytes to the lytic action of complement. The abnormal erythrocytes are thought to originate from the clonal proliferation of bone marrow progenitors altered by somatic mutation.1 Erythrocytes from patients with paroxysmal nocturnal hemoglobinuria have been shown to be deficient in membrane glycoproteins, such as decay-accelerating factor (DAF)2 , 3 and a factor called either homologous restriction factor4 (HRF) or C8-binding protein5 (C8bp). DAF can inhibit the formation and induce the dissociation of C3 convertases of the classical and alternative pathways of complement activation.6 7 8 HRF/C8bp appears to limit the . . .

Plasma uric acid (UA) levels decrease following clinical progression and stage development of Parkinson’s disease (PD). However, the molecular mechanisms underlying decreases in plasma UA levels remain unclear, and the potential to apply mutagenesis to a PD model has not previously been discovered. We identified a unique mutant of the silkworm Bombyx mori (B.mori) op. Initially, we investigated the causality of the phenotypic “op” by microarray analysis using our constructed KAIKO functional annotation pipeline. Consequently, we found a novel UA synthesis-modulating pathway, from DJ-1 to xanthine oxidase, and established methods for large-scale analysis of gene expression in B. mori. We found that the mRNA levels of genes in this pathway were significantly lower in B. mori op mutants, indicating that downstream events in the signal transduction cascade might be prevented. Additionally, levels of B.mori tyrosine hydroxylase (TH) and DJ-1 mRNA were significantly lower in the brain of B. mori op mutants. UA content was significantly lower in the B. mori op mutant tissues and hemolymph. The possibility that the B. mori op mutant might be due to loss of DJ-1 function was supported by the observed vulnerability to oxidative stress. These results suggest that UA synthesis, transport, elimination and accumulation are decreased by environmental oxidative stress in the B. mori op mutant. In the case of B. mori op mutants, the relatively low availability of UA appears to be due both to the oxidation of DJ-1 and to its expenditure to mitigate the effects of environmental oxidative stress. Our findings are expected to provide information needed to elucidate the molecular mechanism of decreased plasma UA levels in the clinical stage progression of PD.

Two children with juvenile rheumatoid arthritis (JRA) were given photosensitive dye Platonin in combination with prednisolone. Analysis of clinical and laboratory data showed that Platonin was efficacious in the improvement of the clinical symptoms and the severity of inflammation, or in the maintenance of the remission state. There were no adverse side effects during long-term administration of medication.