Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress.

Plant-specific NAC transcription factors (TFs) play important roles in regulating diverse biological processes, including development, senescence, growth, cell division and responses to environmental stress stimuli. Within the soybean genome, we identified 152 full-length GmNAC TFs, including 11 membrane-bound members. In silico analysis of the GmNACs, together with their Arabidopsis and rice counterparts, revealed similar NAC architecture.

Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops.

Accumulated transcriptome data can be used to investigate regulatory networks of genes involved in various biological systems. Co-expression analysis data sets generated from comprehensively collected transcriptome data sets now represent efficient resources that are capable of facilitating the discovery of genes with closely correlated expression patterns. In order to construct a co-expression network for barley, we analyzed 45 publicly available experimental series, which are composed of 1,347 sets of GeneChip data for barley.

Genome-wide expression profiling of soybean two-component system genes in soybean root and shoot tissues under dehydration stress.

Two-component systems (TCSs) play vital functions in the adaptation of plants to environmental stresses. To identify soybean TCS genes involved in the regulation of drought stress response, we performed tissue-specific expression profiling of all 83 putative TCS genes in plants subjected to dehydration. Under well-watered conditions, the majority of soybean TCS genes were expressed higher in the root tissues.

Toxicity and metabolism of copper pyrithione and its degradation product, 2,2'-dipyridyldisulfide in a marine polychaete.

We conducted acute toxicity tests and sediment toxicity tests for copper pyrithione (CuPT) and a metal pyrithione degradation product, 2,2'-dipyridyldisulfide [(PS)2], using a marine polychaete Perinereis nuntia. The acute toxicity tests yielded 14-d LC50 concentrations for CuPT and (PS)2 of 0.06 mg L(-1) and 7.

Impeding Xist expression from the active X chromosome improves mouse somatic cell nuclear transfer.

Cloning mammals by means of somatic cell nuclear transfer (SCNT) is highly inefficient because of erroneous reprogramming of the donor genome. Reprogramming errors appear to arise randomly, but the nature of nonrandom, SCNT-specific errors remains elusive. We found that Xist, a noncoding RNA that inactivates one of the two X chromosomes in females, was ectopically expressed from the active X (Xa) chromosome in cloned mouse embryos of both sexes.

Genome-wide analysis of two-component systems and prediction of stress-responsive two-component system members in soybean.

In plants, the two-component systems (TCSs) play important roles in regulating diverse biological processes, including responses to environmental stress stimuli. Within the soybean genome, the TCSs consist of at least 21 histidine kinases, 13 authentic and pseudo-phosphotransfers and 18 type-A, 15 type-B, 3 type-C and 11 pseudo-response regulator proteins. Structural and phylogenetic analyses of soybean TCS members with their Arabidopsis and rice counterparts revealed similar architecture of their TCSs.

Peripheral B cells may serve as a reservoir for persistent hepatitis C virus infection.

A recent study by our group indicated that peripheral B cells in chronic hepatitis C (CHC) patients are infected with hepatitis C virus (HCV). This raised the logical question of how HCV circumvents the antiviral immune responses of B cells. Because type I interferon (IFN) plays a critical role in the innate antiviral immune response, IFNβ expression levels in peripheral B cells from CHC patients were analyzed, and these levels were found to be comparable to those in normal B cells, which suggested that HCV infection failed to trigger antiviral immune responses in B cells.

Temperature-dependent aposematic behavior in the newt Cynops pyrrhogaster.

Aposematic animals advertise their unprofitability to potential predators via morphological and behavioral signals. Strong signals are detectable and memorable for the predators, and such signals would therefore be expected to be most effective. However, many apparently well-defended animals do not have very conspicuous signals.

Functional genomics of soybean for improvement of productivity in adverse conditions.

Global soybean production is frequently impacted by various stresses, including both abiotic and biotic stresses. To develop soybean plants with enhanced tolerance to different stressors, functional genomics of soybean and a comprehensive understanding of available biotechnological resources and approaches are essential. In this review, we will discuss recent advances in soybean functional genomics which provide unprecedented opportunities to understand global patterns of gene expression, gene regulatory networks, various physiological, biochemical, and metabolic pathways as well as their association with the development of specific phenotypes.

The effect on intracytoplasmic sperm injection outcome of genotype, male germ cell stage and freeze-thawing in mice.

Background: Intracytoplasmic sperm injection (ICSI) has been widely used to study the mechanisms of mammalian fertilization and to rescue male-factor infertility in humans and animals. However, very few systematic analyses have been conducted to define factors affecting the efficiency of ICSI. In this study, we undertook a large-scale series of ICSI experiments in mice to define the factors that might affect outcomes.

Syntheses of mono- and dinuclear silylplatinum complexes bearing a diphosphino ligand via stepwise bond activation of unsymmetric disilanes.

Zero-valence platinum complex [Pt(dppe)(eta(2)-C(2)H(4))] (1, dppe = 1,2-bis(diphenylphosphino)ethane) treated with disilanes HR(1)R(2)SiSiMe(3) (a, R(1) = R(2) = Me; b, R(1) = R(2) = Ph; c, R(1) = H, R(2) = Ph) afforded the corresponding disilanylplatinum hydrides [Pt(dppe)(H)(SiR(1)R(2)SiMe(3))] (2a-c) by oxidative addition of the Si-H bond to the platinum center. The 1,2-silyl migration in 2a,b led to the formation of bis(silyl)platinum complexes [Pt(dppe)(SiHR(1)R(2))(SiMe(3))] (3a,b) with a first-order rate constant of 7.2(2) x 10(-4) s(-1) at 25 degrees C for 2a and 3.

Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants.

Knowledge of phosphorylation events and their regulation is crucial to understand the functional biology of plants. Here, we report a large-scale phosphoproteome analysis in the model monocot rice (Oryza sativa japonica 'Nipponbare'), an economically important crop. Using unfractionated whole-cell lysates of rice cells, we identified 6,919 phosphopeptides from 3,393 proteins.

A platform for functional prediction and comparative analyses of transcription factors of legumes and beyond.

Sequence-specific DNA-binding transcription factors (TFs) are key molecular switches that control many of the biological processes in a cell or organism. Recent completion of the genomic sequences of soybean (Glycine max), Locus japonicus and Medicago truncatula has enabled us to carry out large-scale data mining to identify and annotate regulatory TFs for functional and comparative genomics of the TF repertoires of these three major legumes in themselves or with those of other species. The identified TFs of each legume were grouped in 61 TF families, and these TFs all together were integrated into a so-called LegumeTFDB (http://legumetfdb.

Genomics and bioinformatics resources for crop improvement.

Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species. A combinatorial approach using multiple omics platforms and integration of their outcomes is now an effective strategy for clarifying molecular systems integral to improving plant productivity. Furthermore, promotion of comparative genomics among model and applied plants allows us to grasp the biological properties of each species and to accelerate gene discovery and functional analyses of genes.

Enhanced expression of lymphomagenesis-related genes in peripheral blood B cells of chronic hepatitis C patients.

Epidemiological data indicate a close relationship between chronic hepatitis C virus (HCV) infection and B-cell non-Hodgkin's lymphoma (B-NHL), suggesting that chronic HCV infection is, at least in part, associated with B-lymphomagenesis. However, experimental data concerning these conditions remains elusive. In this study, we confirmed that peripheral blood B cells of chronic hepatitis C (CHC) patients were infected with HCV.

Genetic verification of Bordetella pertussis seed strains used for production of Japanese acellular pertussis vaccines.

In Japan, the Bordetella pertussis strain Tohama provided by the National Institute of Health, Japan has been used for the production of acellular pertussis (aP) vaccines since 1981. In the present study, in order to verify the genetic consistency of B. pertussis vaccine seed strains, we analyzed the genetic properties of the working seeds obtained from five Japanese vaccine manufacturers, and compared them with those of B.

Coprophagy-related interspecific nocturnal interactions between Japanese macaques (Macaca fuscata yakui) and sika deer (Cervus nippon yakushimae).

The influence of sympatric large animals on the sleeping behavior of primates in the wild is still largely unknown. In this study, we observed behaviors of wild Japanese macaques (Macaca fuscata yakui) at their sleeping sites, using a highly sensitive video camera. We found evidence of nocturnal interspecific interactions, such as agonistic interactions, between Japanese macaques and sika deer (Cervus nippon yakushimae).

Enhanced RIG-I expression is mediated by interferon regulatory factor-2 in peripheral blood B cells from hepatitis C virus-infected patients.

Chronic hepatitis C patients carry the risk of developing into B-cell non-Hodgkin's lymphoma (B-NHL). To clarify the mechanisms underlying this association, we first investigated the molecular markers of B cells from hepatitis C virus (HCV)-infected patients. CD19-positive cells were isolated as B cells from the peripheral blood mononuclear cells of patients infected with the hepatitis C virus and IFN-related gene expression was analyzed.

Identification and prediction of abiotic stress responsive transcription factors involved in abiotic stress signaling in soybean.

Abiotic stresses such as extreme temperature, drought, high salinity, cold and waterlogging often result in significant losses to the yields of economically important crops such as soybean (Glycine max L.). Transcription factors (TFs) which bind to DNA through specific cis-regulatory sequences either activate or repress gene transcription have been reported to act as control switches in stress signaling.

Toxicity of metal pyrithione photodegradation products to marine organisms with indirect evidence for their presence in seawater.

We evaluated the acute toxicities of the metal pyrithiones (MePTs)--copper pyrithione (CuPT) and zinc pyrithione (ZnPT)--to four species of marine algae and a marine crustacean (Tigriopus japonicus). We also performed acute toxicity tests using six of the main MePT photodegradation products: pyridine-N-oxide (PO); 2-mercaptopyridine (HPS); pyridine-2-sulfonic-acid (PSA); 2-mercaptopyridine-N-oxide (HPT); 2,2'-dithio-bis-pyridine ([PS](2)); and 2,2'-dithio-bis-pyridine-N-oxide ([PT](2))-and three marine organisms representing three trophic levels: an alga (Skeletonema costatum), a crustacean (T. japonicus), and a fish (Pagrus major).

Correlation exploration of metabolic and genomic diversity in rice.

Background: It is essential to elucidate the relationship between metabolic and genomic diversity to understand the genetic regulatory networks associated with the changing metabolo-phenotype among natural variation and/or populations. Recent innovations in metabolomics technologies allow us to grasp the comprehensive features of the metabolome. Metabolite quantitative trait analysis is a key approach for the identification of genetic loci involved in metabolite variation using segregated populations.

LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors.

Unlabelled: We have established a database named LegumeTFDB to provide access to transcription factor (TF) repertoires of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula. LegumeTFDB integrates unique information for each TF gene and family, including sequence features, gene promoters, domain alignments, gene ontology (GO) assignment and sequence comparison data derived from comparative analysis with TFs found within legumes, in Arabidopsis, rice and poplar as well as with proteins in NCBI nr and UniProt. We also analyzed the promoter regions for all of the TFs to identify all types of cis-motifs provided by the PLACE database.

Inflammatory reaction in the herniated degenerative disc materials in miniature dachshunds.

Histological and immunohistochemical studies were conducted using herniated intervertebral disc materials obtained surgically from 39 miniature dachshunds. Infiltration of inflammatory cells, such as macrophages, neutrophils, T or B lymphocytes, and multinucleated giant cells, were identified in intervertebral disc materials in 23 cases. Furthermore, proliferations of connective tissue, including neovascularization, were also observed in 17 cases.

In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean.

Sequence-specific DNA-binding transcription factors (TFs) are often termed as 'master regulators' which bind to DNA and either activate or repress gene transcription. We have computationally analysed the soybean genome sequence data and constructed a proper set of TFs based on the Hidden Markov Model profiles of DNA-binding domain families. Within the soybean genome, we identified 4342 loci encoding 5035 TF models which grouped into 61 families.

Equilibrium vitrification of mouse embryos.

For the cryopreservation of embryos, vitrification has various advantages, but it also has disadvantages because embryos are vitrified with a considerable supercooling (i.e., in nonequilibrium).