Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators

BACKGROUND: Identification of protein-protein interactions (PPIs) is essential for a better understanding of biological processes, pathways and functions. However, experimental identification of the complete set of PPIs in a cell/organism (“an interactome”) is still a difficult task. To circumvent limitations of current high-throughput experimental techniques, it is necessary to develop high-performance computational methods for predicting PPIs. RESULTS: In this article, we propose a new computational method to predict interaction between a given pair of protein sequences using features derived from known homologous PPIs. The proposed method is capable of predicting interaction between two proteins (of unknown structure) using Averaged One-Dependence Estimators (AODE) and three features calculated for the protein pair: (a) sequence similarities to a known interacting protein pair (F(Seq)), (b) statistical propensities of domain pairs observed in interacting proteins (F(Dom)) and (c) a sum of edge weights along the shortest path between homologous proteins in a PPI network (F(Net)). Feature vectors were defined to lie in a half-space of the symmetrical high-dimensional feature space to make them independent of the protein order. The predictability of the method was assessed by a 10-fold cross validation on a recently created human PPI dataset with randomly sampled negative data, and the best model achieved an Area Under the Curve of 0.79 (pAUC(0.5%) = 0.16). In addition, the AODE trained on all three features (named PSOPIA) showed better prediction performance on a separate independent data set than a recently reported homology-based method. CONCLUSIONS: Our results suggest that F(Net), a feature representing proximity in a known PPI network between two proteins that are homologous to a target protein pair, contributes to the prediction of whether the target proteins interact or not. PSOPIA will help identify novel PPIs and estimate complete PPI networks. The method proposed in this article is freely available on the web at http://mizuguchilab.org/PSOPIA

Large-fruited Tomato Production as Affected by Root-zone Extension and Wick Addition During Cultivation in a Capillary Wick System

This study was conducted to investigate the possibility to use capillary wick system in large-fruited tomato production. The first experiment in the autumn-winter season of 2006 was carried out to investigate the effects of the amount of substrate on growth and yield of tomato. Treatments involved growing large-fruited tomato in one box (2.8ℓ/plant) continuously, or adding substrate at flowering of the 7th truss in a 2nd box (5.6ℓ/plant). Fruit yield was higher when the root-zone was extended with double the substrate volume. The second experiment in spring-summer season of 2007 was aimed at improving growth and yield of tomato by extension of root-zone and addition of wick. Tomato plants were either grown in one box with one wick continuously, or with addition of substrate in a 2nd box at flowering of the 4th truss. Additionally, one more wick was inserted into 50% of the 2nd boxes. Half of the plants were grown in two boxes with one wick, and the other half with two wicks. Higher yield was obtained from the plants grown in two boxes with two wicks, suggesting that fruit yield was increased by increasing water transport through wick addition coupled with root-zone extension. Plant growth and fruit yield of large-fruited tomato was stable without blossom-end rot when root-zone was extended and half strength of Ohtsuka-A nutrient solution supplied through the capillary wick system. There was, however, a slight sign of physiological disorder at the leaf margins similar to potassium deficiency.「防根給水ひも」を利用した底面給水法が大玉トマト生産に適用可能かどうかを検討した．2006年秋ﾝ冬季の実験では，培地量がトマトの生育と収量に及ぼす影響について調査した．大玉トマトを終始1stBox（＝2.8ℓ･plant－1）で栽培する処理区と７段花房開花時に2ndBox（＝2.8ℓ）に培地を追加し，最終的に１stBox + 2ndBox（＝5.6ℓ･plant－1）で栽培する処理区を比較した結果，培地量を２倍にし，根域を拡張した処理区の収量が高くなった．2007年春ﾝ夏季の実験では根域拡張および「ひも」適用本数の増加によりトマトの生育収量を改善出来るかを検討するため，終始 1stBox，「ひも」1本で栽培する区，4段花房開花時に培地を追加し最終的に1stBox + 2ndBoxで栽培するが，そこには「ひも」は配さない区，培地を加えると同時に「ひも」を配する区の3区でトマトを栽培した．その結果，1stBox + 2ndBox，「ひも」2本で栽培したトマトが最も収量が高かった．培地追加時に「ひも」を配することで水輸送量が増大した事が収量増加に繋がったものと考えられた．以上の結果より，生育途中で培地量を増やすと同時に，もう1本の「ひも」を配置して大塚A処方1/2濃度で終始管理すれば，生育中期にK欠乏と思しき葉縁の黄変が見られるものの，尻腐れ果実のほとんど発生しない安定したトマト生産が可能であるといえる

Pericarp Characteristics of the F(1) Hybrid Medium-Fruited Tomato between the Male Sterile Mutant (T-4) of the Large-Fruited 'First' and a Small-Fruited Pure Line with Soft Pericarp

Breeding for a soft pericarp in medium-sized tomato fruit was conducted by crossing the male sterile mutant (T-4) of the large-fruited 'First' and a small-fruited pure line with a soft pericarp (S). Pericarp characteristics of the F(1) hybrid (named MS-II) were compared with the parents and two similar medium-fruited tomato cultivars, 'Red ore' and 'Frutica'. Pericarp firmness in MS-II was lower as compared with that of both T-4 and S. Differences in pericarp firmness among MS-II, 'Red ore' and 'Frutica' were dependent on truss. In the first truss, MS-II developed fruits with a softer pericarp than 'Red ore', but with a firmer pericarp than 'Frutica'. In the second and third trusses, pericarp firmness of the fruit in MS-II tended to be lower than those of the other two cultivars. The thickness of the exocarp cuticle in MS-II was lower than that in 'Red ore', but was no different to that in 'Frutica'. Thus genotypic differences in pericarp firmness among MS-II, 'Red ore' and 'Frutica' seem to be derived from differences in the degree of cutin development in the epidermal perimeter. A thinner cuticle can explain pericarp softness in the fruits above the second truss in MS-II.薄皮果柔の中玉トマト品種育成を目的とし，‘ファースト’花粉非崩壊型雄性不稔系統 (T-4) を種子親，果皮の軟らかい小果固定系統 (S) を花粉親とするF(1)雑種 (MS-II) の特性について，両親系統および既存の中玉F(1)品種‘レッドオーレ’，‘フルティカ’のそれと比較した．両親系統と比較したところ，MS-IIの果実硬度は花粉親である軟果皮Sと同等となり，果皮硬度はSよりも低い値となった．3段摘心栽培において，MS-IIの果実硬度は第1段では2品種と差は無かったが，上位果房ほど両品種よりも低くなる傾向を示した．果皮硬度は，第1果房では‘レッドオーレ’よりも低く，‘フルティカ’よりも高かったが，上位果房ほど両品種よりも低い値となる傾向を示した．MS-IIの外果皮におけるクチクラ厚を測定したところ，‘フルティカ’と同等となり，‘レッドオーレ’よりも低かった．また，MS-IIのクチクラ層の発達程度が2品種よりも低いことが観察され，MS-IIの果皮硬度が2品種よりも低い傾向を示すのは，外果皮におけるクチクラ層の発達程度が低いためと推測された

Influences of Surface Morphology of Nanostructured Rutile TiO2 Nanorods/Nanoflowers as Photoelectrode on the Performance of Dye-sensitized Solar Cell

Aligned  Rutile  TiO2  nanorods  (r-TNRs)  and  TiO2  nanoflowers  (r-TNFs)  were  successfully  prepared  by  hydrothermal method. Using hydrochloric acid (HCl) as chelating agent and titanium butoxide (TBOT) as precursor, aligned r-TNRs with r-TNFs were successfully growth onto fluorine-doped tin oxide (FTO) with different morphologies. The influences of surface morphologies to the rutile based Dye-sensitized solar cell (DSC) efficiency are discussed. The highest light-to-electric  energy  conversion efficiency,  1.80%  is  achieved  using  different  concentration  under  simulated  solar  light illumination of 100 mWcm-2 (1.5 AM)

Microperforated leaf blotting on polyvinylidene difluoride and nylon membranes to analyze spatial distribution of endogenous and viral gene expression in plant leaves

Leaf blotting to detect proteins and investigate their spatial distribution in leaves has so far mainly been used to detect viral coat proteins that accumulate abundantly in infected leaves, but rarely to detect endogenous plant proteins. We improved the method for detecting endogenous proteins. We found that microperforating leaves with bundled pins before blotting, then pressing leaves with a rolling pin onto polyvinylidene difluoride (PVDF) membranes enabled even blotting of sap. This microperforated leaf blotting (mPLB) was also suitable for use with nylon membranes to detect leaf RNA. The mPLB revealed that accumulation of two endogenous proteins, calmodulin-like rgs-CaM and actin, was respectively positively and negatively associated with that of viral coat protein in tobacco leaves infected with cucumber mosaic virus (CMV). When a tobacco plant primed with benzothiadiazole was inoculated with CMV, mPLB showed that the infection was restricted to some areas of the leaf, and that in these areas the mRNA encoding tobacco pathogenesis-related protein 1, an indicator of salicylic acid-mediated immune responses, was induced. These results demonstrate the effectiveness of mPLB for investigating the spatial distribution of endogenous and viral gene expression in leaves

Effect of Supplied Amount and Strength of Nutrient Solution on Growth, Yield, and Fruit Quality of Strawberry ‘Saga-honoka’ Grown with Sufficiently Elevated CO2

The effects of supplied amount and strength of nutrient solution were investigated for strawberry (Fragaria×ananassa Duch. cv. Saga-honoka) grown with peat bags in elevated CO2 environment (800-2500 ppm in the day time, November 4 to April 7). Three strengths (L : low-80%, M : standard-100% and H : high-120%) of nutrient solution (N : 8.85, P : 0.85, K : 3.90, Ca : 2.05, Mg : 0.93 mM ; half strength of Ohtsuka A solution) were compared. Around 20% of discharged rate (discharged/supplied amount of nutrient solution) was kept for these 3 plots and 30 to 40% of the rate was kept for additional plot of 80%-solution (L2) by altering the supplied amount of 80%-solution. As almost no nitrate could be detected in drainage of L, nutrient supply was probably insufficient throughout the experiment. Total amount of nitrogen supply was lower than the other 3 plots and leaf area was the smallest after December. Although there was no significant difference in yield and fruit quality, the rate of tip burn affected flowers was lowest in L2 and highest in H. Thus, around 30-40% of drainage rate and 50-60 mS・m−1 of drainage EC may be desirable target values for ‘Saga-honoka’ strawberry grown with peat based substrate.イチゴ‘さがほのか’を用いて，高CO2濃度条件下(日中800～2500ppm)での栽培における培養液濃度と施用量の影響について検討した．培養液は排液率20%を目標に，大塚Ａ処方を30～50%濃度で適宜変更する慣行区を標準として，濃度をその1.2倍，0.8倍とする高濃度区と低濃度区，さらに低濃度区においては，給液量を1.2倍(排液率35%)とする低濃度多量区を設け，計４処理区とした．排液率20%を目標とした低濃度培養液管理では，12月以降の排液中NO3-Nは検出限界以下であり，栽培期間を通して養分が不足しがちであった．また，全Ｎ施用量も他の３処理区と比較すると少なくなり，１月以降の葉面積が小さくなった．収量・果実品質においては処理区間で有意な差は認められなかったが，チップバーン発生率は，高濃度区で高く，低濃度多量区の発生率が最も低かった．低濃度多量区では，葉面積も大きくなったことから，‘さがほのか’においては，排液率30～40%，排液EC50～60mS・m-1を目標とした低濃度での培養液管理が望ましいといえる

Application of continuous light in a plant factory system 4. Physiological changes and concept of injury induction in plant leaves under continuous light

Physiological changes and concept of injury induction occurring under continuous light are comprehensively reviewed. Continuous light usually reduces photosynthetic rate, which may relate to changes in transpiration and leaf necrosis caused by reactive oxygen species. Other factors apart from photosynthesis may also affect leaf injuries occurring under continuous light. Continuous light sometimes increases carbohydrate and some secondary metabolite contents

Morphological Character and Corm Quality of Somatic Hybrid of Taro (Colocasia esculenta Schott)

　Morphological character and quality of corm in somatic hybrid No.12 obtained by protoplast fusion between taro (Colocasia esulenta Schott) cvs. ‘Yatsugahira’and ‘Malaysisa No.4’were investigated. The number of shoot and leaf was smaller than those of ‘Yatsugashira’and was larger than ‘Malaysia No.4’. The length of leaf blade and petiole were shoeter than the two parents. The number of corm was smaller than the two parents. Generally, the shape of top was comoact as compared the two parents. The total weight of corms was about a half of that of ‘Yatsugashira’, and a thirs of that of ‘Malaysia No.4’. The weight of mother corm of somatic hybrid No.12 was 400-500g. The corm morphology of somatic hybrid No.12 was almost intermediate between the two parents. The upper surface of mother corm of somatic hybrid No.12 was smooth; it was much different from that of mother corm of ‘Yatsugashira’. Starch content of borm was similae to ‘Yatsugashira’and smaller than ‘Malaysia No.4’. Sugar and amino acid contents of somatic hybrid No.12 were higher than those of the two parents. Calcium oxalate content was to the parents