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Although fruit development primarily depends on photoassimilation by leaves, immature green fruits can also directly assimilate atmospheric CO2. To elucidate the process of C accumulation due to direct assimilation by fruit, we conducted a 13CO2 exposure experiment in an orchard in late June with immature ‘Fuji’ apples (Malus domestica). Four fruits from three trees were enclosed in transparent plastic bags and exposed to 13CO2 using an in-situ exposure system. Fruits were collected prior to and immediately following exposure in early July, late September and mid-November, and 13C concentrations in the peduncle, skin, flesh and core (including seeds) were measured. The higher assimilated 13C concentrations measured following exposure indicated that the fruits directly assimilated atmospheric 13C. The 13C concentration in fruit skin was higher immediately after exposure and in early July compared with that prior to exposure. In late September and mid-November, 13C concentrations were close to natural levels.

Motivation Understanding life cannot be accomplished without making full use of biological data, which are scattered across databases of diverse categories in life sciences. To connect such data seamlessly, identifier (ID) conversion plays a key role. However, existing ID conversion services have disadvantages, such as covering only a limited range of biological categories of databases, not keeping up with the updates of the original databases and outputs being hard to interpret in the context of biological relations, especially when converting IDs in multiple steps. Results TogoID is an ID conversion service implementing unique features with an intuitive web interface and an application programming interface (API) for programmatic access. TogoID currently supports 65 datasets covering various biological categories. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. Availability and implementation The TogoID service is freely available on the TogoID website (https://togoid.dbcls.jp/) and the API is also provided to allow programmatic access. To encourage developers to add new dataset pairs, the system stores the configurations of pairs at the GitHub repository (https://github.com/togoid/togoid-config) and accepts the request of additional pairs. Supplementary information Supplementary data are available at Bioinformatics online.

14C is the most important radionuclide for assessing exposure dose around the Rokkasho nuclear fuel reprocessing plant, Aomori Prefecture, Japan. A simplified model with ample margins has been used so far for the assessment of the dose derived from 14C. Realistic dose estimate of 14C using more realistic model is necessary for safety. Apple production is an important core industry in Aomori Prefecture. To construct the dynamic model for apple, using 13C as a tracer to substitute for 14C, we collected data on 13C abundance in organs including fruit after 13CO2 exposure at various fruit growth stages. We developed 13CO2 exposure systems for three intact fruit-bearing shoots (1), whole mature tree (2) and young potted trees (3). Systems (1) and (2) also can determine net amounts of carbon and 13C photoassimilated. System (3) is capable of precise feedback control of 13CO2 and 12CO2 concentrations based on on-time determination.

In this study, we aimed to investigate the photoassimilation process of 14CO2 into agricultural plants through determining the photoassimilated carbohydrate-13C in each part (leaves, current branch and fruit) of the fruit-bearing apple shoots exposed to 13CO2 in different growth stages (early and late fruit development stages). The carbohydrate content was assessed as soluble (ethanol-extracted fraction) and other (HCl-extracted and residual fractions) components. The total (i.e. sum of the three fractions) bulk carbohydrate concentrations in all parts of the shoots were statistically similar between different growth stages. The changes in the concentration of 13C-labeled soluble carbohydrate (i.e. ethanol-extracted fraction) to the total content between different growth stages were statistically unclear among all parts of the shoot. These results suggest that the distribution ratio of photoassimilated 13C in soluble and other components in the apple shoot was thereabout constantly independent of the growth stages.

Purpose To investigate surgical outcomes of macular hole retinal detachment (MHRD) in highly myopic eyes. Design Multicenter, retrospective case study. Participants One hundred ten eyes with retinal detachment resulting from macular hole (MH) were evaluated. Methods The medical records of consecutive patients who underwent vitrectomy between January 2010 and December 2015, inclusive, to treat MHRD in 10 hospitals of the Japan Clinical Retinal Study Team were reviewed. Main Outcome Measures Retinal reattachment rate and MH closure rate after the initial surgery. Results One hundred ten eyes of 110 patients were studied. The retina was reattached in 85% of eyes and MH was closed in 52% of eyes after the initial surgery. Eyes with gas tamponade achieved higher reattachment rate than those with silicone oil tamponade. Conclusions The gas tamponade group achieved better retinal reattachment rate than silicone oil tamponade group. Gas tamponade could be the first choice for MHRD.

Evaluating the transfer and metabolism of carbon (C) in apple fruit is key to estimating the potential accumulation of atmospheric

The aim of this prospective study was to evaluate the changes in stereopsis in patients who underwent vitrectomy for macular hole (MH) and assess the relationship between stereopsis and retinal microstructures. Fifty-two patients who underwent successful vitrectomy for unilateral MH and 20 control participants were recruited. We examined stereopsis using the Titmus Stereo Test (TST) and TNO stereotest (TNO), optical coherence tomography, and best-corrected visual acuity measurements, preoperatively, and at 3, 6, and 12 months postoperatively. As a result, preoperative and postoperative 3, 6, and 12-month values of stereopsis assessed by TST (log) were 2.7, 2.2, 2.2, and 2.2, respectively. TNO (log) were 2.8, 2.5, 2.4, and 2.4, respectively. Stereopsis in MH after surgery was significantly worse than that in normal participants (p

Rapid progress is being made in mass spectrometry (MS)-based proteomics, yielding an increasing number of larger datasets with higher quality and higher throughput. To integrate proteomics datasets generated from various projects and institutions, we launched a project named jPOST (Japan ProteOme STandard Repository/Database, https://jpostdb.org/) in 2015. Its proteomics data repository, jPOSTrepo, began operations in 2016 and has accepted more than 10 TB of MS-based proteomics datasets in the past two years. In addition, we have developed a new proteomics database named jPOSTdb in which the published raw datasets in jPOSTrepo are reanalyzed using standardized protocol. jPOSTdb provides viewers showing the frequency of detected post-translational modifications, the co-occurrence of phosphorylation sites on a peptide and peptide sharing among proteoforms. jPOSTdb also provides basic statistical analysis tools to compare proteomics datasets.

Apple MdMADS13 has a transcription factor with MADS domain. Moreover, it is expressed specifically at petals and carpels. The product forms a dimer with MdPISTILLATA (MdPI) protein as a class B gene for floral organ formation. Reportedly, in parthenocarpic cultivars of apple (Spencer Seedless, Wellington Bloomless, Wickson and Noblow) the MdPI function is lost by genome insertion of retrotransposon, which cultivars show a homeotic mutation of floral organs, petals to sepals and stamens to carpels. Apple fruit is pome from receptacle tissue, and MdSEPALLATA (MdMADS8/9) and AGAMOUS homologues MdMADS15/22 involved in the fruit development, the transgenic apple suppressed these gene showed poor fruit development and abnormal flower formation. This article describes that the MdMADS13 retained expression after blossom and small fruits of parthenocarpic cultivars. Yeast two-hybrid experiment showed specific binding between MdPI and MdMADS13 proteins. Furthermore, transgenic Arabidopsis with 35S::MdMADS13 have malformed stamens and carpels. These results suggest strongly that MdMADS13 is related to flower organ formation as a class B gene with MdPI.

The columnar apple ‘McIntosh Wijcik’, which is a mutation of ‘McIntosh’ shoots, has short internodes, thick stems, upright growth, poor lateral branches, and increased spur density. These columnar traits are controlled by a single dominant gene known as Co. We previously identified a putative dioxygenase gene (designated as 91071) as a promising Co candidate (expressed in the shoot apices of ‘McIntosh Wijcik’). However, tissue expression and function of the 91071 gene in noncolumnar apples is still not clear. In this study, we used reverse transcription polymerase chain reaction to demonstrate that the 91071 gene is mainly expressed in the roots of noncolumnar apples, whereas it is also expressed in shoot apices and leaves of columnar apples. In situ hybridization revealed that the 91071 gene is expressed at the primordium of lateral roots and root tips of both noncolumnar and columnar apple trees and in the shoot meristem and leaf primordium in the columnar apple ‘McIntosh Wijcik’. Grafting experiments of noncolumnar scion onto columnar rootstocks revealed that the columnar growth phenotype is not transmissible from rootstock to scion. These results indicated that ectopic expression of the 91071 gene in aerial parts causes columnar growth, whereas the expression of the 91071 gene in roots does not produce columnar growth. Furthermore, transgenic apples overexpressing the 91071 gene showed larger median adventitious root length and higher median number of lateral roots than control apples. Our result suggests that the 91071 gene may be related to root development.

This study investigated the influence of the rotary axis of a 5-axis machine tool on the tool-workpiece compliance. The evaluation focused on the influence of the rotation angle and clamping condition of the B axis on the compliance variation. A method was determined to calculate the tool-workpiece compliance in an arbitrary direction from compliances measured using orthogonal triaxial excitations. Then, the tool-workpiece compliance of a 5-axis machine tool was evaluated and displayed using a color map. The compliance map showed that the magnitude of the compliance varied by up to 40% with changes in the B axis rotation angle and its clamping condition. A drastic change in the negative real part of the compliance was also detected in the compliance map. The results of an experimental modal analysis are used to discuss the cause of the compliance variation. The bending mode of the B axis is an important mode because the change in the bending direction due to B axis rotation has a great influence on the direction dependency of the compliance magnitude and the stability limit. A cutting experiment was conducted to verify the correspondence between the evaluated compliance and the vibrational amplitude in a real cutting process. The compliance variation in the compliance map corresponded to the amplitude variation of the vibration in an end milling process. The compliance map revealed that the vibration synchronized with the passing cycle of cutters was decreased by 80% by unclamping the B axis.

Evaluating the transfer and metabolism of carbon (C) in apple fruit is key to estimating the potential accumulation of atmospheric 14C in fruit near and around nuclear facilities. We developed a dynamic compartment model for apple fruit-bearing shoots, assuming that the shoots are a simple unit of source and sink for photoassimilates. Fruit-bearing shoots of Malus domestica “Fuji” at different fruit growth stages were exposed to 13CO2 in situ, followed by sampling at 72 h after exposure or at harvest. The 13C/(13C+12C) mole ratio in fruits, leaves, and current branch were measured to construct a five-compartment model of 13C (fruit, each fast and slow component of leaves, and current branch). The C inventories in the compartments were presented in accordance with the measured growth curves of C in the organs. The model simulated the 13C dynamics in plant tissues well. Simulation results of photoassimilate distribution using the model indicated that the retention of photoassimilated C at the harvest depended on the growth rate of C in the organs at the exposure.

Juiciness and freshness play a critical role in consumers’ choice of apples, and objective measurements of the traits are essential for adding a premium to fruits with high consumer demand. Juiciness and freshness were sensory evaluated by four apple-breeding experts. The score of sensory juiciness decreased with decreased instrumental measurements of water content (WC), firmness, and apoplastic solution (AS). The influence of firmness on sensory juiciness was not linear, and perception of juiciness rapidly decreased when firmness decreased below 60 N. The sensory freshness score was related to titratable acidity (TA), firmness, and the AS. A nonlinear regression model for freshness indicated that freshness was less likely to be perceived as the AS in flesh tissue decreased, and the perception of freshness rapidly decreased when firmness decreased below 60 N or TA decreased below 0.25 g 100 ml−1. The firmness of fruit treated with 1-MCP hardly decreased during storage. The titratable acidity of fruit treated with 1-MCP decreased; however, the degree of the decrease was significantly lower than that of non-treated fruit. The AS immediately decreased just after harvest and was not significantly different in most cases between 1-MCP-treated and non-treated fruit during storage. Therefore, measurements of firmness and TA were useful for distinguishing 1-MCP-treated fruit from non-treated fruit and the AS is necessary to distinguish between stored fruit and that just after harvest. The performance of calibration models developed by NIR spectroscopy for TA, firmness, and AS was lower than that for soluble solids content (SSC), which is used to grade apples by NIR spectroscopy in Japanese packing houses. Therefore, it is impractical to grade fruit by freshness using calibration models. However, high correlation coefficients were obtained in the calibration model for WC. The correlation coefficient of WC was about as high as that of SSC. Therefore, apples could be graded by juiciness using the calibration model for WC with the auxiliary use of calibration models for firmness and AS.

TogoGenome is a genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches. All the information is stored as Resource Description Framework (RDF) data, and the reporting web pages are generated on the fly using SPARQL Protocol and RDF Query Language (SPARQL) queries. TogoGenome provides a semantic-faceted search system by gene functional annotation, taxonomy, phenotypes and environment based on the relevant ontologies. TogoGenome also serves as an interface to conduct semantic comparative genomics by which a user can observe pan-organism or organism-specific genes based on the functional aspect of gene annotations and the combinations of organisms from different taxa. The TogoGenome database exhibits a modularized structure, and each module in the report pages is separately served as TogoStanza, which is a generic framework for rendering an information block as IFRAME/Web Components, which can, unlike several other monolithic databases, also be reused to construct other databases. TogoGenome and TogoStanza have been under development since 2012 and are freely available along with their source codes on the GitHub repositories at https://github.com/togogenome/ and https://github.com/togostanza/, respectively, under the MIT license.

To investigate surgical outcomes of macular hole retinal detachment (MHRD) in highly myopic eyes.Multicenter, retrospective case study.One hundred ten eyes with retinal detachment resulting from macular hole (MH) were evaluated.The medical records of consecutive patients who underwent vitrectomy between January 2010 and December 2015, inclusive, to treat MHRD in 10 hospitals of the Japan Clinical Retinal Study Team were reviewed.Retinal reattachment rate and MH closure rate after the initial surgery.One hundred ten eyes of 110 patients were studied. The retina was reattached in 85% of eyes and MH was closed in 52% of eyes after the initial surgery. Eyes with gas tamponade achieved higher reattachment rate than those with silicone oil tamponade.The gas tamponade group achieved better retinal reattachment rate than silicone oil tamponade group. Gas tamponade could be the first choice for MHRD.

MAPLE is an automated system for inferring the potential comprehensive functions harbored by genomes and metagenomes. To reduce runtime in MAPLE analyzing the massive amino acid datasets of over 1 million sequences, we improved it by adapting the KEGG automatic annotation server to use GHOSTX and verified no substantial difference in the MAPLE results between the original and new implementations.

Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes.

The objective of this study was to investigate the effects of temperature treatments on anthocyanin accumulation and ethylene production in the fruit of early- and medium-maturing cultivars that were harvested early during fruit ripening. We first investigated the effects of various temperature treatments on anthocyanin accumulation in detached apples of ‘Tsugaru’, ‘Tsugaru Hime’, ‘Akane’ and ‘Akibae’ using an incubator. Three years of experiments demonstrated that at harvest, the lower-temperature treatments induced anthocyanin accumulation in ‘Tsugaru’, ‘Tsugaru Hime’, and ‘Akibae’ fruits, whereas the increases in anthocyanin accumulation under the 25 °C treatment were similar to those under the 15 and 20 °C treatments in ‘Akane’ fruit. The rate of ethylene production did not increase substantially during the temperature treatments in any of the four cultivars, except after the treatments of ‘Tsugaru’ fruit at harvest. The inhibition of ethylene action by the application of 1-methylcyclopropene (1-MCP) to detached fruits at harvest suppressed anthocyanin development under 15 and 20 °C temperature treatments in ‘Tsugaru’, ‘Tsugaru Hime’, and ‘Akibae’, but not in ‘Akane’. In the second experiment, we investigated changes in the anthocyanin concentration in attached fruit of ‘Misuzu Tsugaru’ under different temperature conditions in a greenhouse. At harvest, the anthocyanin concentration in fruit under the hotter climatic condition (29 °C 12 hours/19 °C 12 hours) was lower than that under the control condition (25 °C 12 hours/15 °C 12 hours). During the last week before harvest, anthocyanin development proceeded rapidly in fruit skin not only under the control condition, but also under the hotter climatic condition. The rapid accumulation of anthocyanin in the fruit skin of ‘Misuzu Tsugaru’ at harvest under a relatively high temperature (25 °C) condition was confirmed by the experiment using an incubator. At harvest, the maximum level of ethylene production in fruits sampled from trees grown under the hotter climatic condition was 9-fold higher than that in fruits from trees grown under the control condition. These results indicate that the comparison of pigmentation potential after the 15 or 25 °C treatments using detached fruit was effective for estimating anthocyanin accumulation in fruit skins under hotter climatic conditions in early- and medium-maturing cultivars that were harvested early and that a hotter climatic condition during ripening increased ethylene production in apple fruit after harvest.

Motivation: Metabolic pathway analysis is crucial not only in metabolic engineering but also in rational drug design. However, the biosynthetic/biodegradation pathways are known only for a small portion of metabolites, and a vast amount of pathways remain uncharacterized. Therefore, an important challenge in metabolomics is the de novo reconstruction of potential reaction networks on a metabolome-scale. Results: In this article, we develop a novel method to predict the multistep reaction sequences for de novo reconstruction of metabolic pathways in the reaction-filling framework. We propose a supervised approach to learn what we refer to as ‘multistep reaction sequence likeness’, i.e. whether a compound–compound pair is possibly converted to each other by a sequence of enzymatic reactions. In the algorithm, we propose a recursive procedure of using step-specific classifiers to predict the intermediate compounds in the multistep reaction sequences, based on chemical substructure fingerprints/descriptors of compounds. We further demonstrate the usefulness of our proposed method on the prediction of enzymatic reaction networks from a metabolome-scale compound set and discuss characteristic features of the extracted chemical substructure transformation patterns in multistep reaction sequences. Our comprehensively predicted reaction networks help to fill the metabolic gap and to infer new reaction sequences in metabolic pathways. Availability and implementation: Materials are available for free at http://web.kuicr.kyoto-u.ac.jp/supp/kot/ismb2014/ Contact: goto@kuicr.kyoto-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.

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.

We report for the first time the a-Si:H/μc-Si:H/μc-Si:H triple-junction solar cells fabricated on W-textured ZnO having a very high haze value which can improve light scattering effect. For further enhancement of light confinement effects, p-type a-SiOx:H and μc-SiOx:H as wide-gap window-layers, n-type μc-SiOx:H as intermediate layers and a back reflector were employed in these solar cells too. From theoretical analysis, we have found an advantage of a-Si:H/μc-Si:H/μc-Si:H structure for an application to low-concentration photovoltaics. For the fabricated solar cells, a conversion efficiency of 8.86% at 1 sun and and 9.86% under 7.2 suns, and a total photocurrent from each subcell of 24.1 mA/cm2 were achieved although there was still a current mismatch among component subcells.

Major advancements have recently been made in mass spectrometry-based proteomics, yielding an increasing number of datasets from various proteomics projects worldwide. In order to facilitate the sharing and reuse of promising datasets, it is important to construct appropriate, high-quality public data repositories. jPOSTrepo (https://repository.jpostdb.org/) has successfully implemented several unique features, including high-speed file uploading, flexible file management and easy-to-use interfaces. This repository has been launched as a public repository containing various proteomic datasets and is available for researchers worldwide. In addition, our repository has joined the ProteomeXchange consortium, which includes the most popular public repositories such as PRIDE in Europe for MS/MS datasets and PASSEL for SRM datasets in the USA. Later MassIVE was introduced in the USA and accepted into the ProteomeXchange, as was our repository in July 2016, providing important datasets from Asia/Oceania. Accordingly, this repository thus contributes to a global alliance to share and store all datasets from a wide variety of proteomics experiments. Thus, the repository is expected to become a major repository, particularly for data collected in the Asia/Oceania region.

The identification of orthologous genes in an increasing number of fully sequenced genomes is a challenging issue in recent genome science. Here we present KEGG OC (http://www.genome.jp/ tools/oc/), a novel database of ortholog clusters (OCs). The current version of KEGG OC contains 1 176 030 OCs, obtained by clustering 8 357 175 genes in 2112 complete genomes (153 eukaryotes, 1830 bacteria and 129 archaea). The OCs were constructed by applying the quasi-clique-based clustering method to all possible protein coding genes in all complete genomes, based on their amino acid sequence similarities. It is computationally efficient to calculate OCs, which enables to regularly update the contents. KEGG OC has the following two features: (i) It consists of all complete genomes of a wide variety of organisms from three domains of life, and the number of organisms is the largest among the existing databases; and (ii) It is compatible with the KEGG database by sharing the same sets of genes and identifiers, which leads to seamless integration of OCs with useful components in KEGG such as biological pathways, pathway modules, functional hierarchy, diseases and drugs. The KEGG OC resources are accessible via OC Viewer that provides an interactive visualization of OCs at different taxonomic levels.

Fruit thinning is an essential part of the commercial production of quality apples. A portion of the excessive fruitlets is abscised, or shed, physiologically as a self-regulatory mechanism; however, the degree of abscission varies depending on the environmental conditions and cultivars. The number of abscised fruitlets within a cluster is influenced by the number of leaves in the cluster. In some cultivars, the fewer leaves there are in a cluster, the larger the number of fruitlets undergo abscission is. Conversely, the growth rate of a fruit cluster is marginally influenced by the number of leaves in the cluster and appears constant for each cultivar. The constant growth rates of fruit clusters indicate the source strength, which supports the growth of individual fruitlets (sink organ) on the tree. The cultivar differences in the percentage of fruitlet abscission were highly correlated with the source strength of the cultivars, indicating that the rate of abscised fruitlets was determined by the source strength of the cultivars. The number of days between full bloom and diminishing growth of abscising fruitlets was also correlated with the source strength. Therefore, a cultivar with low source strength is prone to abscising many fruitlets at an early date compared with one with high source strength. The source strength of a cultivar, therefore, can be a useful index for selecting cultivars characterized by easy and early abscission.

Rosaceae is a large family, however, our understanding of its phylogeny is based largely on morphological observations. To understand the relationship between subfamilies Rosoideae, Amygdaloideae, Maloideae and Spiraeoideae at a molecular level, we isolated and compared the plant phosphatidyl ethanolamine-binding protein-like genes TERMINAL FLOWER1 (TFL1)-like and CENTRORADIALIS (CEN)-like, which are involved in the control of shoot meristem identity and flowering time. A comparison of gene structures and phylogenetic tree analyses by the Neighbor-Joining method showed that each of the two TFL1-like (MdTFL1-1 and MdTFL1-2) and CEN-like genes (MdCENa and MdCENb) in Maloideae were classified into two distinct clades. The TFL1-like and CEN-like genes of Gillenia in Spiraeoideae belonged to monophyletic Maloideae groups, suggesting that Gillenia and Maloideae have a common near ancestor. However, the Gillenia TFL1-like gene does not contain the insertion sequence of the third intron that is found in MdTFL1-2-like genes of the members of Maloideae such as apple, Korean whitebeam, quince, and Siberian mountain ash. Therefore, after the Maloideae ancestor genome became polyploid through hybridization between Gillenia-like species or genome doubling, an insertion sequence of the third intron of MdTFL1-2-like genes was generated.

Gene network inference engine based on supervised analysis (GENIES) is a web server to predict unknown part of gene network from various types of genome-wide data in the framework of supervised network inference. The originality of GENIES lies in the construction of a predictive model using partially known network information and in the integration of heterogeneous data with kernel methods. The GENIES server accepts any 'profiles' of genes or proteins (e.g. gene expression profiles, protein subcellular localization profiles and phylogenetic profiles) or pre-calculated gene-gene similarity matrices (or 'kernels') in the tab-delimited file format. As a training data set to learn a predictive model, the users can choose either known molecular network information in the KEGG PATHWAY database or their own gene network data. The user can also select an algorithm of supervised network inference, choose various parameters in the method, and control the weights of heterogeneous data integration. The server provides the list of newly predicted gene pairs, maps the predicted gene pairs onto the associated pathway diagrams in KEGG PATHWAY and indicates candidate genes for missing enzymes in organism-specific metabolic pathways. GENIES (http://www.genome.jp/tools/genies/) is publicly available as one of the genome analysis tools in GenomeNet.

The apple (Malus × domestica Borkh.) is one of the commercially important fruit crops in the worldwide. The apple has a relatively long juvenile period (up to 4 years) and a long reproductive period between the flower initiation and the mature fruit (14-16 months), which prevent the fruit breeding. Therefore, the understanding of the flowering system is important to improve breeding efficiency in the apple. In this study, to examine the temporal and spatial expression patterns of the floral genes, MdTFL1, MdAP1 (MdMASD5), AFL2, and MdFT, we conducted in situ hybridization analysis in the apple shoot apex. In vegetative phase, MdTFL1 was expressed on the rib meristem zone. When vegetative meristem began converting into inflorescence meristem, the expression level of MdTFL1 was drastically decreased. At the early stage of inflorescence meristem, the expression levels of AFL2, MdFT, and MdAP1 were up-regulated in the leaf primordia and the upper region of cell layers on the shoot apex. In late stage, the expression levels of AFL2 and MdAP1 were up-regulated in the young floral primordia. At a more advanced stage, high expression of MdAP1 was observed in the inflorescence primordium through the inner layer of sepal primordia and the outer layer of receptacle primordia and floral axis. Our results suggest that AFL2, MdFT, and MdAP1 affect to convert from the vegetative meristem into the inflorescence meristem after the decline of MdTFL1 expression. After that, AFL2 and MdAP1 promote the formation of the floral primordia and floral organs.

Apple has a relatively long juvenile growth period, taking approximately 8 years to reach the flowering stage. This period has impeded breeding programs. Since MdTFL1 (an ortholog of TERMINAL FLOWER1) is strongly related to juvenility/vegetative and flower initiation in apple, its studies will provide insight into relationship between phytohormones and juvenile/vegetative growth and flower bud formation. In this study, we monitored expression of the MdTFL1 promoter-β-glucuronidase (GUS) fusion construct in apple tissues in vitro, to determine which plant growth regulators affect its expression. Expression of MdTFL1 was induced strongly throughout newly generated young shoots of cytokinin-treated plants and in apices of shoots on medium containing cytokinin+auxin. These results suggest that cytokinin may induce MdTFL1 expression to maintain the juvenile form at the base of plant, and that cytokinin and auxin determine whether the shoot apical meristem will transit from the vegetative to the reproductive state.

リンゴわい性台木利用樹における晩材変色を調査するとともに，低温処理による変色の再現を試み，さらに，細胞障害率から耐凍性の台木品種間差異を検討した．‘ふじ’および‘ジョナゴールド’の成木における晩材変色はJM7台樹よりもJM1台樹に有意に多くみられた．JM7，M.9，M.26台利用の‘みしまふじ’1年生苗を凍結処理して変色程度と細胞障害率を調査した．形成層とその周辺部に褐変が認められ，低温による変色を再現できた．細胞障害率は穂木部でM.9が高く，台木部でM.9，JM7，M.26の順に高かった．本試験の結果と凍害の発生状況から，低温による細胞障害率の台木品種間における差異が圃場条件下での凍害症状の発症程度に影響する可能性が示された．

SummaryMost cultivars of European pear (Pyrus communis L.) exhibit S-RNase-based gametophytic self-incompatibility (SI), but the cultivar, ‘Grand Champion’, is partially self-compatible (SC). We used pollination and molecular genetic approaches to study the cause of the partial SC, and its effects on fruit set and quality. ‘Grand Champion’ was genotyped to SbSe by an S-RNase-based cleaved amplified polymorphic sequence marker system. Crossing ‘Grand Champion’ with pollen from an SI cultivar, ‘California’ (SbSe), showed that partial SC was caused by the disruption of pistil function. Of the Sb- and Se-RNase alleles cloned from ‘Grand Champion’, the Sb-RNase allele had two nonsynonymous nucleotide substitutions compared with the Sb-RNase allele previously cloned from ‘Doyenne du Comice’, but it retained the typical primary structure of S-RNases of the Maloideae. The sequence of the Sb-RNase allele from ‘Grand Champion’ was also obtained from two SI cultivars: ‘Josephine de Malines’ and ‘Urbaniste’. Similar ...

To quantify the severity of aniseikonia in patients undergoing vitrectomy for idiopathic macular hole (MH) and to examine any relationship between aniseikonia and the foveal microstructure.Prospective, consecutive, interventional case series.We included 56 eyes of 56 patients who underwent vitrectomy to treat idiopathic MH.We examined visual acuity, aniseikonia using the New Aniseikonia Test, and foveal structure using optical coherence tomography (OCT) before and 3, 6, and 12 months after surgery. Based on OCT images, minimum and base diameters of MH, height of MH, and defect lengths of the external limiting membrane (ELM), ellipsoid zone, and interdigitation zone were assessed.Degree of aniseikonia before and after surgery.The mean aniseikonia was -3.2±4.6%, ranging from -15.5% to +5.0%. Of the patients, 55% had micropsia, 7% had macropsia, and 38% had no aniseikonia. The mean absolute value of aniseikonia improved significantly from 3.8±4.1% before surgery to 1.0±1.5% at 12 months after surgery (P0.0001). The preoperative mean absolute value of aniseikonia showed a significant correlation with minimum diameters of MH (P0.01), base diameters of MH (P0.01), and the defect length of ELM (P0.05). In multivariate analysis, preoperative aniseikonia showed a significant correlation with the defect length of ELM (P0.05). In contrast, postoperative aniseikonia was not associated with any of the parameters.Approximately half of MH patients had micropsia. Vitrectomy for MH improved aniseikonia. Preoperative aniseikonia was associated with MH size and the defect length of ELM.

EGENES is a knowledge-based database for efficient analysis of plant expressed sequence tags (ESTs) that was recently added to the KEGG suite of databases. It links plant genomic information with higher order functional information in a single database. It also provides gene indices for each genome. The genomic information in EGENES is a collection of EST contigs constructed from assembly of ESTs. Due to the extremely large genomes of plant species, the bulk collection of data such as ESTs is a quick way to capture a complete repertoire of genes expressed in an organism. Using ESTs for reconstructing metabolic pathways is a new expansion in KEGG and provides researchers with a new resource for species in which only EST sequences are available. Functional annotation in EGENES is a process of linking a set of genes/transcripts in each genome with a network of interacting molecules in the cell. EGENES is a multispecies, integrated resource consisting of genomic, chemical, and network information containing a complete set of building blocks (genes and molecules) and wiring diagrams (biological pathways) to represent cellular functions. Using EGENES, genome-based pathway annotation and EST-based annotation can now be compared and mutually validated. The ultimate goals of EGENES will be to: bring new plant species into KEGG by clustering and annotating ESTs; abstract knowledge and principles from large-scale plant EST data; and improve computational prediction of systems of higher complexity. EGENES will be updated at least once a year. EGENES is publicly available and is accessible by the following link or by KEGG's navigation system (http://www.genome.jp/kegg-bin/create_kegg_menu?category=plants_egenes).

Expressed sequence tag (EST) sequencing has proven to be an economically feasible alternative for gene discovery in species lacking a draft genome sequence. Ongoing large-scale EST sequencing projects feel the need for bioinformatics tools to facilitate uniform EST handling. This brings about a renewed importance for a universal tool for processing and functional annotation of large sets of ESTs. EGassembler (http://egassembler.hgc.jp/) is a web server, which provides an automated as well as a user-customized analysis tool for cleaning, repeat masking, vector trimming, organelle masking, clustering and assembling of ESTs and genomic fragments. The web server is publicly available and provides the community a unique all-in-one online application web service for large-scale ESTs and genomic DNA clustering and assembling. Running on a Sun Fire 15K supercomputer, a significantly large volume of data can be processed in a short period of time. The results can be used to functionally annotate genes, to facilitate splice alignment analysis, to link the transcripts to genetic and physical maps, design microarray chips, to perform transcriptome analysis and to map to KEGG metabolic pathways. The service provides an excellent bioinformatics tool to research groups in wet-lab as well as an all-in-one-tool for sequence handling to bioinformatics researchers.

The SNARE proteins are required for membrane fusion during intracellular vesicular transport and for its specificity. Only the unique combination of SNARE proteins (cognates) can be bound and can lead to membrane fusion, although the characteristics of the possible specificity of the binding combinations encoded in the SNARE sequences have not yet been determined. We discovered by whole genome sequence analysis that sequence motifs (conserved sequences) in the SNARE motif domains for each protein group correspond to localization sites or transport pathways. We claim that these motifs reflect the specificity of the binding combinations of SNARE motif domains. Using these motifs, we could classify SNARE proteins from 48 organisms into their localization sites or transport pathways. The classification result shows that more than 10 SNARE subgroups are kingdom specific and that the SNARE paralogs involved in the plasma membrane-related transport pathways have developed greater variations in higher animals and higher plants than those involved in the endoplasmic reticulum-related transport pathways throughout eukaryotic evolution.