SAHG, a comprehensive database of predicted structures of all human proteins

Most proteins from higher organisms are known to be multi-domain proteins and contain substantial numbers of intrinsically disordered (ID) regions. To analyse such protein sequences, those from human for instance, we developed a special protein-structure-prediction pipeline and accumulated the products in the Structure Atlas of Human Genome (SAHG) database at http://bird.cbrc.jp/sahg. With the pipeline, human proteins were examined by local alignment methods (BLAST, PSI-BLAST and Smith–Waterman profile–profile alignment), global–local alignment methods (FORTE) and prediction tools for ID regions (POODLE-S) and homology modeling (MODELLER). Conformational changes of protein models upon ligand-binding were predicted by simultaneous modeling using templates of apo and holo forms. When there were no suitable templates for holo forms and the apo models were accurate, we prepared holo models using prediction methods for ligand-binding (eF-seek) and conformational change (the elastic network model and the linear response theory). Models are displayed as animated images. As of July 2010, SAHG contains 42 581 protein-domain models in approximately 24 900 unique human protein sequences from the RefSeq database. Annotation of models with functional information and links to other databases such as EzCatDB, InterPro or HPRD are also provided to facilitate understanding the protein structure-function relationships

SORL1 Is Genetically Associated with Late-Onset Alzheimer’s Disease in Japanese, Koreans and Caucasians

To discover susceptibility genes of late-onset Alzheimer’s disease (LOAD), we conducted a 3-stage genome-wide association study (GWAS) using three populations: Japanese from the Japanese Genetic Consortium for Alzheimer Disease (JGSCAD), Koreans, and Caucasians from the Alzheimer Disease Genetic Consortium (ADGC). In Stage 1, we evaluated data for 5,877,918 genotyped and imputed SNPs in Japanese cases (n = 1,008) and controls (n = 1,016). Genome-wide significance was observed with 12 SNPs in the APOE region. Seven SNPs from other distinct regions with p-values ,261025 were genotyped in a second Japanese sample (885 cases, 985 controls), and evidence of association was confirmed for one SORL1 SNP (rs3781834, P=7.3361027 in the combined sample). Subsequent analysis combining results for several SORL1 SNPs in the Japanese, Korean (339 cases, 1,129 controls) and Caucasians (11,840 AD cases, 10,931 controls) revealed genome wide significance with rs11218343 (P=1.7761029) and rs3781834 (P=1.0461028). SNPs in previously established AD loci in Caucasians showed strong evidence of association in Japanese including rs3851179 near PICALM (P=1.7161025) and rs744373 near BIN1 (P = 1.3961024). The associated allele for each of these SNPs was the same as in Caucasians. These data demonstrate for the first time genome-wide significance of LOAD with SORL1 and confirm the role of other known loci for LOAD in Japanese. Our study highlights the importance of examining associations in multiple ethnic populations

Reliability and validity of the Japanese version of 20-item Positive and Negative Affect Schedule

本研究は,日本語版The Positive and Negative Affect Schedule (PANAS)の20項目の信頼性と妥当性を検討することが目的であった。大学生442名を対象に質問紙調査を実施した。因子分析により,ポジティブ感情(10項目)とネガティブ感情(10項目)の2因子構造が示された。妥当性は,人生に対する満足尺度,主観的幸福感尺度,自己記入式抑うつ性尺度,状態不安検査との相関を用いて検討した。その結果,ポジティブ感情は,人生に対する満足尺度および主観的幸福感尺度との問に正の相関関係を示した。他方,ネガティブ感情は,自己記入式抑うつ性尺度および状態不安検査との間に正の相関関係を示した。信頼性は,内的整合性とI-T相関の結果から,信頼性の高さが示された。以上から,日本語版PANAS20項目の信頼性と妥当性が確認された

Is Self-Rated Health Associated with Blood Immune Markers in Healthy Individuals?

Background: Although self-rated health (SRH) has been established as a robust predictor of morbidity and mortality, the immunological mechanisms underpinning this relationship are poorly understood. Purpose: This study examined the association of SRH with humoral and cellular immune markers in healthy individuals who reported no physical illnesses. Method: A total of 116 healthy Japanese white-collar employees (79 women and 37 men) at a pharmaceutical company, aged 23-62 (mean 32) years, underwent a blood draw for the measurement of circulating immune (T, B, and natural killer (NK)) cells, inflammatory cytokines (interleukin-6 (IL-6) and tumor necrosis factor-α (TNF- α)), and plasma immunoglobulin G (IgG) and completed a health survey including SRH. The question regarding SRH ranged from 'very good (coded 1)' to 'very poor (coded 5).' Hierarchical multiple regression analysis was carried out to calculate the relationship between SRH and immune markers. Results: In this sample, poor SRH was positively correlated with B (CD19+) cell numbers (β=.260, p<.05) and IgG levels (β=.335, p<.01), even after adjusting for depressive symptoms, age, education, marital status, smoking, alcohol consumption, physical activity, body mass index, sex, and sex × SRH interaction. The interaction between SRH and sex on the immune markers was not significant. Conclusion: Although the connection between SRH and immune markers was not strong in this context, the results suggest that poor SRH may be associated with reduced humoral immune system capacity to respond to new/latent challenges. The results provide some support for the immunological basis of SRH in healthier individuals

Observation of equatorial plasma bubbles by the airglow imager on ISS-IMAP

Using 630 nm airglow data observed by an airglow imager on the International Space Station (ISS), the occurrence of equatorial plasma bubbles (EPBs) is studied. In order to examine the physical mechanisms in the boundary region between the Earth and the outer space, an ionosphere, mesosphere, upper atmosphere, and plasmasphere mapping (IMAP) mission had been conducted onboard the ISS since October 2012. The visible light and infrared spectrum imager (VISI) is utilized in the ISS-IMAP mission for nadir-looking observation of the earth’s atmospheric airglow. In this study, we automatically select EPBs according to the criterion for extracting the tilted dark lines from VISI data. Using the selected events, the dependence of the occurrence rate of EPBs is examined. There is no other report of the occurrence rate of EPBs using downward-looking visible airglow data (630 nm). In this result, the occurrence rate is high at all longitudes in the equinoctial seasons. In the solstice seasons, in contrast, the occurrence rate is very small especially in the Pacific and American sectors. This result is basically consistent with previous studies, e.g., those determined by plasma density data on DMSP satellites.During the June solstice in 2013, EPBs were observed in association with geomagnetic storms that occurred due to a southward turning of the IMF Bz. Using these events, we examined the storm-time features of the occurrence of EPBs in the Pacific-American sectors during the June solstice. In these sectors, where the occurrence rate of EPBs is very small during solstice seasons, some EPBs were observed in the peak and recovery phases of the storms. This result shows that the prompt penetration of electric fields causes the development of EPBs, in the data we analyzed, the geomagnetic storms did not inhibit the generation of EPB in the Pacific–American sectors