Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model

<p>Abstract</p> <p>Background</p> <p>Modelling of time series data should not be an approximation of input data profiles, but rather be able to detect and evaluate dynamical changes in the time series data. Objective criteria that can be used to evaluate dynamical changes in data are therefore important to filter experimental noise and to enable extraction of unexpected, biologically important information.</p> <p>Results</p> <p>Here we demonstrate the effectiveness of a Markov model, named the Linear Dynamical System, to simulate the dynamics of a transcript or metabolite time series, and propose a probabilistic index that enables detection of time-sensitive changes. This method was applied to time series datasets from <it>Bacillus subtilis </it>and <it>Arabidopsis thaliana </it>grown under stress conditions; in the former, only gene expression was studied, whereas in the latter, both gene expression and metabolite accumulation. Our method not only identified well-known changes in gene expression and metabolite accumulation, but also detected novel changes that are likely to be responsible for each stress response condition.</p> <p>Conclusion</p> <p>This general approach can be applied to any time-series data profile from which one wishes to identify elements responsible for state transitions, such as rapid environmental adaptation by an organism.</p

Effectiveness of outpatient-based group cognitive-behavioral therapy in Japanese patients with mood disorders and neurotic disorders

Background: Although the effectiveness of group cognitive-behavioral therapy (GCBT) has been studied, evidence is still not sufficient. Objective: The aim of the present study is to consider the effectiveness of GCBT with mood disorders and neurotic disorders. Methods: The present study assessed a total of 32 patients who were classified as F3 (mood disorders) or F4 (neurotic disorders) according to the ICD-10, and who attended GCBT sessions offered at The Tokai University Hospital. Depression and mood in these patients were assessed before and after GCBT by using the Center for Epidemiologic Studies Depression Scale (CES-D) and the Profile of Mood States (POMS). Results: A comparison of pre- and post-GCBT CES-D scores among all patients as well as within F3 and F4 groups showed a significant decrease in CES-D scores after GCBT. As for the POMS, a comparison of pre- and post-GCBT scores among all patients showed a significant improvement in “vigor” and “confusion” scores after GCBT. Discussion: The present study demonstrated that GCBT can relieve depression and improve some mood states. Furthermore, the GCBT sessions offered proved to be effective even when administered to a group of participants consisting of both mood disorders and neurotic disorder patients

保育所幼児の栄養摂取状況と腸内細菌叢との関連

【目的】我が国では、幼児期の栄養素等摂取量を定量的に示した研究が少なく、日本人の食事摂取基準(2015年版)では小児の十分な資料が存在しない場合は、成人の値から外挿して栄養素等の基準値が求められている。本研究では、保育所幼児の栄養素等の摂取状況を明らかにし、食生活、生活習慣と関わりのある腸内細菌叢を評価指標として検討した。【方法】調査期間は平成26年12月から平成27年3月である。調査対象者は福岡県上毛町の同意が得られた保育所幼児83名である。調査内容は1)食事の実態調査は秤量記録法で食品名を食事記録ノートに記入および同日の食前食後の料理写真撮影、2)排便調査、3)採便後の腸内細菌叢の分析である。分析は(株)テクノスルガ・ラボに依頼し、Nagashima法によりT-RFLPで解析した。解析はすべて統計解析ソフトSPSS Statistics ver.22を用いた。この研究は中村学園大学の倫理委員会から承諾を得ている。【結果】1日あたりの栄養摂取状況で、男女ともに推定エネルギー必要量、たんぱく質の推奨量、脂質と食塩相当量の目標量は基準値よりも高い数値を示した。食物繊維、炭水化物の目標量、カルシウムと鉄、ビタミンAの推奨量は基準値に対して低い数値を示した。栄養素と腸内細菌叢の関連をみるとカルシウムのBifidobacteriumの割合は低摂取群に比べ高摂取群が有意に高い数値を示した。特に、食物繊維の摂取量では基準値に対して不足している人が38.3%を占め、食物繊維摂取量と腸内細菌叢の関連をみると基準値である中摂取群が低摂取群に比べ、推定される群菌のLactobacillales目の割合が高い数値であった。【考察】幼児の健康増進や生活習慣病予防には腸内環境改善が重要であり、栄養的にバランスのよい食事の摂取が不可欠であると考えられる

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Development of a Japanese Version of the Index of Sexual Satisfaction for Use in Couples with Young Children

The occurrence of sexual dysfunction in couples after childbirth is well recognized, yet sexual satisfaction in couples with young children (CYC) has received little research attention. This study sought to enable this construct to be measured by developing and validating a Japanese version of the Index of Sexual Satisfaction (ISS) in CYC. Data were collected using a self-administered questionnaire. Scale construction and validation were conducted using two independent samples drawn from 316 mothers and 272 fathers in Japan who had at least one child aged 6 or younger. Two underlying factors were identified using exploratory factor analysis: sexual satisfaction, measured by eight items, and sexual dissatisfaction, measured by three. Polychoric ordinal alpha coefficients indicated the reliability of the resulting scale (overall: 0.89, factor 1: 0.89, factor 2: 0.78), and confirmatory factor analysis and testing supported its validity, showing good model fit (goodness of fit index: 0.984, root mean square residual: 0.062) and satisfactory composite reliability (scale: 0.93, factor 1: 0.90, factor 2: 0.81) and average variance extracted (all &ge;0.5). The Japanese version of the ISS for Couples with Young Children will be useful for investigating sexual satisfaction, which is essential to marital stability

Genetic Heterogeneity among Strains of Treponema phagedenis-Like Spirochetes Isolated from Dairy Cattle with Papillomatous Digital Dermatitis in Japan ▿

Papillomatous digital dermatitis (PDD) is an infectious foot disease of cattle that is prevalent throughout the world. Although it has been prevalent in Japan since the first case was reported in 1992, full epidemiological and bacteriological examinations have not been conducted. We collected 91 lesions of PDD from 80 dairy cattle on 12 farms in eight regions of Japan to isolate the spirochetes that are frequently detected in lesions. We isolated 40 strains of spirochetes from 24 cattle (30.0%) by a simple two-step culture technique, in which the biopsy samples were incubated at 4°C for 48 to 72 h in an enrichment broth supplemented with antibiotics, which improved the rate of isolation, and then inoculated on selective agar plates. All spirochetes examined were catalase positive and oxidase negative and showed weak beta-hemolytic activity. Enzyme activities were identical to those of Treponema phagedenis ATCC 27087. Sequencing of the 16S rRNA gene showed that all strains isolated had >99% identity to those of the T. phagedenis type strain and of T. phagedenis-like strains isolated from PDD lesions in the United States and Europe. Pulsed-field gel electrophoresis and PCR-based random amplified polymorphism DNA methods revealed considerable diversity among strains isolated not only from different cattle but also from the same individuals. These findings may provide further evidence for the role of these treponemes in the pathogenesis of persistent PDD

Development of a Novel Nutrition-Related Multivariate Biomarker for Mild Cognitive Impairment Based on the Plasma Free Amino Acid Profile

Nutritional epidemiology has shown the importance of protein intake for maintaining brain function in the elderly population. Mild cognitive impairment (MCI) may be associated with malnutrition, especially protein intake. We explored blood-based biomarkers linking protein nutritional status with MCI in a multicenter study. In total, 219 individuals with MCI (79.5 &plusmn; 5.7 year) from 10 institutions and 220 individuals who were cognitively normal (CN, 76.3 &plusmn; 6.6 year) in four different cities in Japan were recruited. They were divided into the training (120 MCI and 120 CN) and validation (99 MCI and 100 CN) groups. A model involving concentrations of PFAAs and albumin to discriminate MCI from CN individuals was constructed by multivariate logistic regression analysis in the training dataset, and the performance was evaluated in the validation dataset. The concentrations of some essential amino acids and albumin were significantly lower in MCI group than CN group. An index incorporating albumin and PFAA discriminated MCI from CN participants with the AUC of 0.705 (95% CI: 0.632&ndash;0.778), and the sensitivities at specificities of 90% and 60% were 25.3% and 76.8%, respectively. No significant association with BMI or APOE status was observed. This cross-sectional study suggests that the biomarker changes in MCI group may be associated with protein nutrition