Interdisciplinary Bio Central最新文献

Finding key factors of metabolic syndrome in lifestyle with National Health and Nutrition Examination Survey (NHANES) 利用全国健康与营养调查(NHANES)发现生活方式中代谢综合征的关键因素

Interdisciplinary Bio Central Pub Date : 2015-05-29 DOI: 10.4051/IBC.2015.7.2.0001

S. Jung, Suhyun Ha, Doheon Lee

引用次数: 0

An Approach for a Substitution Matrix Based on Protein Blocks and Physicochemical Properties of Amino Acids through PCA 一种基于蛋白质块和氨基酸理化性质的主成分分析取代矩阵方法

Interdisciplinary Bio Central Pub Date : 2014-11-05 DOI: 10.4051/IBC.2014.6.4.0003

Yo-Han Yoo, Youngki You, Insoo Jang, K. Lee, Heon Joo Kim, Kwan Hee Lee

{"title":"An Approach for a Substitution Matrix Based on Protein Blocks and Physicochemical Properties of Amino Acids through PCA","authors":"Yo-Han Yoo, Youngki You, Insoo Jang, K. Lee, Heon Joo Kim, Kwan Hee Lee","doi":"10.4051/IBC.2014.6.4.0003","DOIUrl":"https://doi.org/10.4051/IBC.2014.6.4.0003","url":null,"abstract":"Amino acid substitution matrices are essential tools for protein sequence analysis, homology sequence search in protein databases and multiple sequence alignment. The PAM matrix was the first widely used amino acid substitution matrix. The BLOSUM series then succeeded the PAM matrix. Most substitution matrixes were developed by using the statistical frequency of substitution between each amino acid at blocks representing groups of protein families or related proteins. However, substitution of amino acids is based on the similarity of physiochemical properties of each amino acid. In this study, a new approach was used to obtain major physiochemical properties in multiple sequence alignment. Frequency of amino acid substitution in multiple sequence alignment database and selected attributes of amino acids in physiochemical properties database were merged. This merged data showed the major physiochemical properties through principle components analysis. Using factor analysis, these four principle components were interpreted as flexibility of electronic movement, polarity, negative charge and structural flexibility. Applying these four components, BAPS was constructed and validated for accuracy. When comparing receiver operated characteristic (ROC50) values, BAPS scored slightly lower than BLOSUM and PAM. However, when evaluating for accuracy by comparing results from multiple sequence alignment with the structural alignment results of two test data sets with known three-dimensional structure in the homologous structure alignment database, the result of the test for BAPS was comparatively equivalent or better than results for prior matrices including PAM, Gonnet, Identity and Genetic code matrix.","PeriodicalId":207872,"journal":{"name":"Interdisciplinary Bio Central","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116230983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Sex and Population Differences in Intelligence Are Partly Caused by Sexual Selection: Hn Evolutionary Hypothesis 智力的性别和种群差异部分是由性选择引起的:一个进化假说

Interdisciplinary Bio Central Pub Date : 2014-11-03 DOI: 10.4051/IBC.2014.6.3.0002

Davide Piffer

{"title":"Sex and Population Differences in Intelligence Are Partly Caused by Sexual Selection: Hn Evolutionary Hypothesis","authors":"Davide Piffer","doi":"10.4051/IBC.2014.6.3.0002","DOIUrl":"https://doi.org/10.4051/IBC.2014.6.3.0002","url":null,"abstract":"Sexual dimorphism in intelligence suggests that this phenotype is a sexually selected trait. This view is supported by an overrepresentation (compared to the autosomal genome) of genes affecting cognition on the X chromosome. The aim of this study is to test the hypothesis that sexual selection can explain sex and country-level differences in performance on tests of fluid intelligence. Nationally representative samples from N = 44 countries were obtained from the Programme for International Student Assessment (PISA) Creative Problem Solving (CPS), which evaluates the core of intelligence, that is novel problem solving ability. Sexual selection has the double effect of increasing the prevalence of a favored phenotype and reducing genetic variation in sexually selected traits. Matching these predictions from evolutionary theory, the average country fluid intelligence is positively correlated to sexual dimorphism after partialling out per capita GDP and the latter in turn is inversely correlated to variance in intelligence scores within populations. Males have a higher variance than females but there is a negative correlation between male-female difference in variance and sexual dimorphism in intelligence, suggesting that selection reduces variance more in the selected sex. Average country male height is negatively correlated to sexual dimorphism in intelligence, a fact that supports the notion of a trade-off between physical and intellectual competition in the context of access to females. The results of this study, if replicated, imply that genome-wide association studies of cognition may benefit from a focus on sex chromosomes, which so far have been neglected. Another implication of this study is that intelligence has continued to evolve after different human populations migrated out of Africa and possibly up to the 19th century, as suggested by the substantial variability in sex differences even between neighbouring countries.","PeriodicalId":207872,"journal":{"name":"Interdisciplinary Bio Central","volume":"84 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131717358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Simple Statistical Tools to Detect Signals of Recent Polygenic Selection. 检测近期多基因选择信号的简单统计工具。

Interdisciplinary Bio Central Pub Date : 2014-02-25 DOI: 10.4051/IBC.2014.6.1.0001

Davide Piffer

{"title":"Simple Statistical Tools to Detect Signals of Recent Polygenic Selection.","authors":"Davide Piffer","doi":"10.4051/IBC.2014.6.1.0001","DOIUrl":"https://doi.org/10.4051/IBC.2014.6.1.0001","url":null,"abstract":"A growing body of evidence shows that most psychological traits are polygenic, that is they involve the action of many genes with small effects. However, the study of selection has disproportionately been on one or a few genes and their associated sweep signals (rapid and large changes in frequency). If our goal is to study the evolution of psychological variables, such as intelligence, we need a model that explains the evolution of phenotypes governed by many common genetic variants. This study illustrates simple statistical tools to detect signals of recent polygenic selection: a) ANOVA can be used to reveal significant deviation from random distribution of allele frequencies across racial groups. b) Principal component analysis can be used as a tool for finding a factor that represents the strength of recent selection on a phenotype and the underlying genetic variation. c) Method of correlated vectors: the correlation between genetic frequencies and the average phenotypes of different populations is computed; then, the resulting correlation coefficients are correlated with the corresponding alleles’ genome-wide significance. A significant difference between the allele frequencies for the three races was found. Post-hoc test revealed that East Asians had significantly higher frequencies of IQ increasing alleles than Africans. In contrast, the distribution of height increasing alleles did not differ among races. The second prediction, that alleles with large frequency differences between populations had a higher genome-wide significance value than alleles with small frequency differences, was confirmed by the analysis of the Pygmy vs non Pygmy data set.","PeriodicalId":207872,"journal":{"name":"Interdisciplinary Bio Central","volume":"739 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116999447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

The Establishment of Tumor Necrosis Factor Receptor-associated Protein1 (TRAP1) Transgenic Mice and Severe Fat Accumulation in the Liver of TRAP1 Mice during Liver Regeneration 肿瘤坏死因子受体相关蛋白1 (TRAP1)转基因小鼠的建立及TRAP1小鼠肝脏再生过程中肝脏严重脂肪堆积

Interdisciplinary Bio Central Pub Date : 2013-12-24 DOI: 10.4051/IBC.2013.5.4.0009

Chang-Nim Im, Ying Zheng, Sun Hye Kim, Taiqin Huang, D. Cho, Jeong-Sun Seo

引用次数: 2

Gregor Mendel and the Seven Genes (2) 孟德尔和七个基因(下)

Interdisciplinary Bio Central Pub Date : 2013-11-30 DOI: 10.4051/IBC.2013.5.4.0008

Y. Tateno

引用次数: 0

Gregor Mendel and the Seven Genes (1) 孟德尔和七个基因(上)

Interdisciplinary Bio Central Pub Date : 2013-10-31 DOI: 10.4051/IBC.2013.5.4.0007

Y. Tateno

引用次数: 0

Insect GPCRs and TRP Channels: Putative Targets for Insect Repellents 昆虫gpcr和TRP通道:驱蚊剂的推定靶点

Interdisciplinary Bio Central Pub Date : 2013-07-31 DOI: 10.4051/IBC.2013.5.3.0006

Sang Hoon Kim

引用次数: 8

Systematic Approach for Analyzing Drug Combination by Using Target-Enzyme Distance 用靶酶距离分析药物联合的系统方法

Interdisciplinary Bio Central Pub Date : 2013-04-25 DOI: 10.4051/IBC.2013.5.2.0003

Jaesub Park, Sunjae Lee, Kiseong Kim, Doheon Lee

{"title":"Systematic Approach for Analyzing Drug Combination by Using Target-Enzyme Distance","authors":"Jaesub Park, Sunjae Lee, Kiseong Kim, Doheon Lee","doi":"10.4051/IBC.2013.5.2.0003","DOIUrl":"https://doi.org/10.4051/IBC.2013.5.2.0003","url":null,"abstract":"Recently, the productivity of drug discovery has gradually decreased as the limitations of single-target-based drugs for various and complex diseases become exposed. To overcome these limitations, drug combinations have been proposed, and great efforts have been made to predict efficacious drug combinations by statistical methods using drug databases. However, previous methods which did not take into account biological networks are insufficient for elaborate predictions. Also, increased evidences to support the fact that drug effects are closely related to metabolic enzymes suggested the possibility for a new approach to the study drug combinations. Therefore, in this paper we suggest a novel approach for analyzing drug combinations using a metabolic network in a systematic manner. The influence of a drug on the metabolic network is described using the distance between the drug target and an enzyme. Target-enzyme distances are converted into influence scores, and from these scores we calculated the correla tions between drugs. The result shows that the influence score derived from the targetenzyme distance reflects the mechanism of drug action onto the metabolic network properly. In an analysis of the correlation score distribution, efficacious drug combina tions tended to have low correlation scores, and this tendency corresponded to the known properties of the drug combinations. These facts suggest that our approach is useful for prediction drug combinations with an advanced understanding of drug mechanisms.","PeriodicalId":207872,"journal":{"name":"Interdisciplinary Bio Central","volume":"384 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123092118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Creating Subnetworks from Transcriptomic Data on Central Nervous System Diseases Informed by a Massive Transcriptomic Network 从大量转录组学网络提供的中枢神经系统疾病转录组学数据创建子网络

Interdisciplinary Bio Central Pub Date : 2013-01-21 DOI: 10.4051/IBC.2013.5.1.0001

E. Wurtele, Yaping Feng, J. Syrkin-Nikolau

引用次数: 0