叉头转录因子FoxO1的生物遗传信息学分析

叉头转录因子FoxO1是一种重要的调控因子,其广泛参与机体的各项生命活动,对其生物信息学的分析,可以更清楚和直观的了解FoxO1基因的结构和功能,为后期发育、分化、代谢和进化等作用机制的深入研究提供重要的理论基础。本试验运用生物信息学手段对牛FoxO1基因的结构和功能进行预测分析,结果表明FoxO1蛋白为不稳定的亲水性酸性蛋白质,主要定位在细胞核,含有七个半胱氨酸残基,其中六个半胱氨酸形成三个二硫键,3个氨基酸具有59个潜在磷酸化位点,作为非分泌型蛋白,无信号肽和跨膜区域,其二级结构中,无规则卷曲所占比例高达75.42%,且在第165-259位氨基酸之间,其叉头域有95个保守的氨基酸残基。

基于化学生物信息学探究大泻肺汤“体-用-化”功能配伍治疗慢性阻塞性肺疾病的活性成分

目的基于敦煌《辅行诀五脏用药法要》(简称《辅行诀》)“体-用-化”辨证理论,运用化学生物信息学方法探究大泻肺汤“体-用-化”功能配伍治疗慢性阻塞性肺疾病(COPD)的活性成分。方法基于“体-用-化”辨证理论,对大泻肺汤各药味进行分组。通过网络药理学方法探究各组治疗COPD的关键靶点及关键成分,采用基于分子对接的虚拟筛选方法对大泻肺汤全方中能够与成药性靶点磷酸二酯酶4有效结合来发挥治疗COPD的成分进行筛选。结果肺脏各组具有通过靶向RAC-α-丝氨酸/苏氨酸蛋白激酶、丝裂原活化蛋白激酶等靶点,调控磷脂酰肌醇-3-激酶等信号通路发挥改善机体呼吸困难的潜在功能;肺的子脏-肾脏各组可通过靶向基质金属蛋白酶2、表皮生长因子受体2等靶点,调控核因子κB等信号通路,从而发挥辅助减轻COPD患者肺部炎症、调节机体呼吸的作用。分子对接结果发现代表性化合物甘草利酮、Phaseol、甘草吡喃香豆素和Glyzaglabrin可能是大泻肺汤防治COPD的潜在活性成分。结论本研究利用化学生物信息学方法对敦煌大泻肺汤进行“体-用-化”功能配伍分组治疗COPD潜在起效的成分及作用机制进行挖掘,为敦煌大泻肺汤的临床推广应用奠定了基础。

化学生物信息学方法在医药研究中的应用

在医药探究中每一个步骤和环节都会涉及到化学生物学方面的知识,所以对化学生物信息学方法在医药研究中的应用进行分析,对提高医药研究水平具有一定的现实意义。该文分析了化学生物信息学以及主要研究内容,药物信息提取的几种形式并展望了化学生物信息学科方法在医药研究中的应用。

化学生物信息学方法在医药研究中的应用

化学生物信息学属于综合性较强学科,囊括信息技术、生命科学、数学算法、化学知识、生物科学等内容,通过建立模型,针对化学生物信息进行分析,挖掘相关数据潜在应用价值,分析数据资源中的隐含意义,为此,化学、生物信息学方法可以针对各类信息进行搜集、分析、处理、应用,为探索全新药物疗效及作用奠定了基础。 文章通过分析化学、生物信息学方法在医药研究中的应用方略,以期推动生物制药产业稳健发展。

纳米尺度和单分子水平上的化学生物学研究

化学生物学是化学与生命科学交叉融合的新兴学科。在纳米尺度和单分子水平上原位、活体、实时研究化学生物信息是化学生物学的重要研究方向。分析化学工作者利用纳米技术和分子生物学的最新研究成果 ,在这一研究方向取得了重要进展 ,为化学生物学的发展做出了积极贡献。本文重点介绍实验室利用生物亲和性核壳纳米颗粒和分子信标核酸探针所发展的一系列原位、活体、实时检测、分离生命体内痕量活性物质的新原理、新技术及其在化学生物学研究中的应用。

基于中医药化学生物信息学探讨归芪白术方抑制葡萄膜黑色素瘤细胞增殖的物质基础

目的利用药效团模型-分子对接-结合自由能计算的虚拟筛选策略结合细胞生物学实验的中医药化学生物信息学方法,挖掘归芪白术方中靶向磷脂酰肌醇3-激酶(phosphatidylinositide 3-kinases,PI3K)抑制葡萄膜黑色素瘤(uveal melanoma,UM)细胞增殖的成分。方法构建PI3K抑制剂药效团模型,并对归芪白术方化合物进行虚拟筛选,对符合药效团模型的成分进行分子对接和结合自由能计算,选择潜在抑制成分进行生物学实验评价。利用CCK-8和克隆形成试验检测潜在抑制成分对UM细胞增殖的影响;流式细胞术检测UM细胞周期和凋亡情况;JC-10染色法检测UM细胞线粒体膜电位;Western blotting检测PI3K及下游通路蛋白表达。结果药效团模型包括2个氢键受体、2个芳环中心以及排除体积。CCK-8结果显示10、20、40、80μmol·L^(-1)槲皮素、川陈皮素、桔皮素,20、40、80μmol·L^(-1)桑辛素可抑制UM细胞的增殖。克隆形成试验显示不同浓度的槲皮素、川陈皮素、桔皮素、桑辛素均可明显抑制细胞的克隆增殖。流式细胞术结果显示桔皮素、槲皮素将细胞阻滞在G0/G1期,川陈皮素、桑辛素将UM细胞阻滞在G2/M期。JC-10染色法结果显示槲皮素、川陈皮素、桔皮素、桑辛素均可使UM细胞的线粒体膜电位降低,Western blotting结果显示4种化合物均可靶向PI3K发挥作用,但其影响的下游通路不同。结论本研究基于中医药化学生物信息学的方法挖掘了归芪白术方抑制UM细胞增殖的物质基础,为中药复方的现代化开发提供参考。

敦煌医方大泻肺汤对肺炎的体外活性及其作用机制的化学生物信息学分析

目的利用化学生物信息学探讨敦煌医方大泻肺汤防治肺炎的有效性、作用机制及功效组配伍特点。方法通过细胞实验研究大泻肺汤冻干粉溶液对肺上皮细胞增殖活性的影响。根据药味功效将方子分为清热、化痰、养阴3个功效组。利用TCMSP数据库和文献检索获取大泻肺汤化学成分,并在Swiss Target Prediction数据库预测其作用靶点。借助DrugBank、TTD、Genecards及DisGeNET数据库检索肺炎疾病靶点。采用STRING数据库和Cytoscape构建交集靶点互作网络和“药味-成分-靶点-通路”网络,DAVID数据库进行KEGG通路富集分析,分析功效分组配伍规律的科学内涵。利用Schr?dinger软件进行分子对接评估靶点-化合物亲和力,分子动力学模拟探究动态分子机制。结果细胞实验显示大泻肺汤能够维持肺上皮细胞增殖、逆转LPS诱导的肺上皮细胞线粒体活性降低和减少细胞凋亡。复杂网络分析结果显示大泻肺汤3个功效组富集的通路主要分布于炎症调节和降低气道黏液高分泌2个模块,各模块间通过共有靶标基因联结又各有侧重。分子对接结果显示化合物槲皮素、黄芩素、异鼠李素等可能是大泻肺汤起效的多靶点成分,SRC、EGFR、PPARA等靶点与各个潜在活性化合物之间的亲和力较好,可能是大泻肺汤防治肺炎的潜在作用靶点。分子动力学模拟结果显示潜在活性化合物槲皮素与其靶蛋白SRC形成了稳定的分子间作用。结论本研究初步揭示了大泻肺汤防治肺炎的物质基础和分子机制,并探讨了大泻肺汤不同功效组协同防治肺炎的科学内涵,为其现代化开发和临床推广提供化学生物信息学参考。

基于化学生物信息学方法探讨黄芪通过调节能量代谢发挥“补气”功效的物质基础和分子机制

目的 阐释黄芪发挥“补气”功效调节能量代谢的物质基础和生物学机制。方法 TCMSP数据库及文献检索收集黄芪潜在活性成分,SEA数据库进行基于结构相似性的靶点预测,GeneCards、OMIM、TTD数据库获取能量代谢靶点。Cytoscape软件构建黄芪调节能量代谢靶点蛋白-蛋白相互作用网络图,并进行GO和KEGG富集分析。黄芪全成分与关键靶点进行分子对接和层次聚类分析评估靶点-成分亲和力,采用CCK-8法、流式细胞术、ATP试剂盒检测黄芪代表性化合物对H9C2心肌细胞、GES-1胃上皮细胞能量代谢的影响,并进行结合模式分析。结果 网络药理学结果显示,黄芪调节能量代谢潜在作用靶点有126个;GO和KEGG富集分析表明,黄芪调节能量代谢可能与氧化还原过程、蛋白及酶合成的基因表达有关。其中,SIRT1及PPARγ是参与能量代谢调节的关键靶点。分子对接及层次聚类显示黄芪成分对SIRT1及PPARγ具有较好的靶向性,结合分子对接打分值筛选出3个代表性化合物进行体外实验验证;槲皮素、山奈酚能够促进H9C2心肌细胞、GES-1胃上皮细胞能量代谢。结合模式分析表明,槲皮素、山奈酚与SIRT1、PPARγ之间具有较好的结合能力。结论 本研究通过中医药化学生物信息学方法初步阐释了黄芪调节能量代谢的物质基础和生物机制,为黄芪通过“补气”发挥行滞通痹功效的中医内涵提供了科学依据。

Bioinformatics Analysis of IPIs in Five Northern Medicinal Plants

This study analyzed and predicted following aspects of isopentenyl py- rophosphate isomerases （IPIs） of five north medicinal plants using bioinformatics methods and tools： physical and chemical properties, hydrophobicity/hydrophilicity, trans-membrane domain, secondary structure, subcellular localization and so on. The results showed that： there was no notable difference among the physical and chem- ical properties of IPIs of the five north medicinal plants; the IPIs were mainly hy- drophilic; the IPIs were mainly located in chloroplasts by subcellular localization; serine phosphorylation sites were the most; the secondary structures mainly consist- ed of c^-helixes and random coils; no signal peptide existed, indicating that the pro- tein IPI was non-secreted protein; no trans-membrane domain existed; and one functional domain was shown, Le., Nudix Hydrolase Superfamily. This study is of great significance to research on IPI gene functions, deep research on north medic- inal plants, improvement of efficacy of north medicinal plants and rational develop- ment and utilization of medicinal plant resources.

Isolation and analysis of pepper ACC oxidase gene partial sequence

Ethylene plays an extensive role in plant growth and development.. 1-aminocyclopropane-1-carboxylate （ACC） oxidase （ACO） is the key enzyme in ethylene biosynthesis. In this study, a 354 g DNA and a 213 bp cDNA base pair （bp） candidate fragment was amplified from pepper with primers derived from the ACO sequence （AJ011109） reported by Ernesto. The putative new gene was analyzed by bioinformatics tools.

Cloning, Analysis and Prokaryotic Expression of DsSP Gene from Dunaliella salina

[Objective] The purpose of this study was to clone a starch phosphorylase gene from Dunaliella salina and to preliminarily analyze its basic properties and protein expression. [Method] RT-PCR and RACE （rapid amplification of cDNA ends） method was used for gene cloning; basic properties of the gene were analyzed using bioinformatics method; prokaryotic expression vector PGS21a-DsSP was constructed and transformed into E. coil BL21; the fusion protein was purified and detected by GST-SefinoseTM Kit and Western Blot, respectively. [Result] A starch phos-phorylase gene （GenBank accession No. KF061044） named DsSP was successfully isolated from D. salina. Basic properties, subcellular localization, secondary structure and tertiary structure of the protein were analyzed and predicted. The fusion protein was found in the supernatant and inclusion bodies. The supernatant protein was successfully purified. Western Blot analysis showed that the fusion protein was successfully expressed in E. coil BL21. [Conclusion] This study laid experimental foun- dation for further clarifying the function and mechanism of DsSP.

Bioinformatics Analysis on Histone H3-lys-4 Methyltransferase MLL3

[Objective] This study aimed to conduct bioinformatics analysis of histone H3-1ys-4 （H3K4） methyltransferase MLL3 in animals, thus exploring its relatively conservative evolution to reveal the role of histon H3K4 trimethyltransferase MLL3 in human cancers. [Method] By using bioinformatics method, gene structure, amino acid sequences, phylogenetic tree, chromosomal localization and synteny of mouse MLL3 were analyzed. [Result] Primary structure of the encoded mouse MLL3 protein con- tained seven zinc finger domains, an HMG-box （High mobility group-box protein）, a FYRN （F/Y-rich N-terminus） domain, a FYRC （F/Yrich C-terminus） domain, a SET domain and a postSET domain. Results of sequence comparison and homology showed that 19 animal species in this study all had these structures basically, which indicated that these structures were relatively conserved in the evolution; specifically, the SET domain was highly conserved and was necessary to maintain the activity of histone methyltransferases. Results of phylogenetic analysis showed that the loca- tions of the 19 animal species in evolutionary tree were consistent with the taxo- nomic status. Results of synteny analysis showed that there were the same gene in the upstream and downstream of the mouse and human MLL3 gene which were located on different chromosomes, indicating that the mouse and human MLL3 gene had collinearity. [Conclusion] This study had revealed the primary structure of MLL3 nucleotide sequence and amino acid sequence, which had not only laid the foundation for the future research of high-level structure and function of MLL3 protein but also provided the basis for the follow-up study of primer design, promoter analysis, gene cloning and regulation patterns of localization and expression of mouse MLL3 gene.

Isolation and bioinformatics analysis of differentially methylated genomic fragments in human gastric cancer

AIM:To isolate and analyze the DNA sequences which are methylated differentially between gastric cancer and normal gastric mucosa. METHODS: The differentially methylated DNA sequences between gastric cancer and normal gastric mucosa were isolated by methylation-sensitive representational difference analysis (MS-RDA). Similarities between the separated fragments and the human genomic DNA were analyzed with Basic Local Alignment Search Tool (BLAST). RESULTS: Three differentially methylated DNA sequences were obtained, two of which have been accepted by GenBank. The accession numbers are AY887106 and AY887107. AY887107 was highly similar to the 11th exon of LOC440683 (98%), 3' end of LOC440887 (99%), and promoter and exon regions of DRD5 (94%). AY887106 was consistent (98%) with a CpG island in ribosomal RNA isolated from colorectal cancer by Minoru Toyota in 1999. CONCLUSION: The methylation degree is different between gastric cancer and normal gastric mucosa. The differentially methylated DNA sequences can be isolated effectively by MS-RDA.

SPARCL1, Shp2, MSH2, E-cadherin, p53, ADCY-2 and MAPK are prognosis-related in colorectal cancer

AIM: To investigate the expression of markers that are correlated with the prognosis of colorectal cancer (CRC) patients. METHODS: One hundred and fifty-six CRC patientswere followed up for more than 3 years after radical surgery. Immunohistochemical (IHC) analysis was performed to detect the expression of 14 pathway-related markers (p53, APC, p21ras, E-cadherin, endothelin-B receptor, Shp2, ADCY-2, SPARCL1, neuroligin1, hsp27, mmp-9, MAPK, MSH2 and rho) in specimens from these patients. Bioinformatics analysis involving a Support Vector Machine (SVM) was used to determine the best prognostic model from combinations of these markers. RESULTS: Seven markers (SPARCL1, Shp2, MSH2, E-cadherin, p53, ADCY-2 and MAPK) were significantly related to the prognosis and clinical pathological features of the CRC patients (P < 0.05). Prognostic models were established through SVM from combinations of these 7 markers and proved able to differentiate patients with dissimilar survival, especially in stage Ⅱ/Ⅲ patients. According to the best prognostic model, the p53/SPARCL1 model, patients having high p53 and low SPARCL1 expression had about 50% lower 3-year survival than others (P < 0.001). CONCLUSION: SPARCL1, Shp2, MSH2, E-cadherin, p53, ADCY-2 and MAPK are potential prognostic markers in CRC. A p53/SPARCL1 bioinformatics model may be used as a supplement to tumor-nodes-metastasis staging.

Methylation Characteristics of Perivisceral Fat Gene in Obese Rats with Phlegm-dampness Syndrome and the Effect of Wen Dan Decoction

Objective To observe the characteristics of gene methylation in obese rats with phlegm-dampness syndrome induced by the high-fat diet, and to study the effect of Wen Dan Decoction on gene methylation after the intervention. Methods Methylation sites of genes were detected by the MeDIP-seq method. Bioinformatics method was used to analyze the gene methylation characteristics of obesity with phlegmdampness syndrome and the effect of Wen Dan Decoction. Results (1) There were 3 242 methylation differential loci in dietinduced obesity with phlegm-dampness syndrome, of which 1 243 were down-regulated and 1 999 were up-regulated, involving 1 579 differential genes. GO analysis showed that "offactory receptor activity" and others were enriched. The possible signal pathways involved were "Olfactory transduction""Tuberculosis""Systemic lupus erythematosus" and "Ribosome".(2) After the intervention of Wen Dan Decoction in obesity with phlegmdampness syndrome, 4 046 different methylation loci were obtained, including 1 067 down-regulated loci and 2 979 up-regulated loci, involving 2 068 genes. GO analysis showed that "offactory receptor activity" and others were enriched. These genes involved seven signaling pathways, such as "Metabolic pathways".(3) Between diet-induced obesity with phlegm-dampness syndrome and Wen Dan Decoction intervening obesity with the phlegm-dampness syndrome, 582 common genes of methylation differential genes were obtained. After the intervention of Wen Dan Decoction, the number of GO enrichment items was more than that of obesity with phlegm-dampness syndrome, and even the same GO enrichment items involved more genes. Conclusions The phlegm-dampness syndrome of obesityinduced by diet had the characteristics of gene methylation changes, and the intervention of Wen Dan Decoction could also affect the status of gene methylation. The genes affected by Wen Dan Decoction were closely related to the methylation gene of phlegm-dampness syndrome of obesity-induced by diet but covered a wider range.

Bioinformotics Analysis for Coding SNPs of the HLA-DQA1 Gene Involved in Susceptibility to Cervical Cancer

OBJECTIVE To analyze coding SNPs of the HLA-DQA1 gene involved in susceptibility for cervical cancer by a bioinformatics approach, and to choose some SNPs that may have an association with cervical cancer. METHODS By a SNPper tool we extracted SNPs from a public database (dbSNP), exporting them in FASTA formats suitable for subsequent use. Then we used PARSESNP as a tool for the analysis of the cSNPs. RESULTS In the cSNPs of the HLA-DQA1 gene, we find that rs9272693 and rs9272703, are made up of missense mutations which convert a codon for one amino acid into a codon for a different amino acid. We chose a PSSM Difference >10 as a lower level for the scores of changes predicted to be deldterious. CONCLUSION We used a bioinformatics approach for cSNPs analysis of the HLA-DQA1 gene. This method can select the variants in a conserved region, and give a PSSM Difference score. But the results need to be verified in cervical cancer patients and a control population.

Molecular cloning and transcriptional analysis of a NPY receptor-like in common Chinese cuttlefish Sepiella japonica

Neuropeptide Y(NPY) has a pivotal role in the regulation of many physiological processes. In this study, the gene encoding a NPY receptor-like from the common Chinese cuttlefish Sepiella japonica( SjNPYR-like) was identified and characterized. The full-length SjNPYR-like cDNA was cloned containing a 492-bp of 5′ untranslated region(UTR), 1 182 bp open reading frame(ORF) encoding a protein of 393 amino acid residues, and 228 bp of 3′ UTR. The putative protein was predicted to have a molecular weight of 45.54 kDa and an isoelectric point(pI) of 8.13. By informatic analyses, SjNPYR-like was identified as belonging to the class A G protein coupled receptor(GPCR) family(the rhodopsin-type). The amino acid sequence contained 12 potential phosphorylation sites and five predicted N-linked glycosylation sites. Multiple sequence alignment and 3D structure modeling were conducted to clarify SjNPYR bioinformatics characteristics. Phylogenetic analysis identifies it as an NPYR with identity of 33% to Lymnaea stagnalis NPFR. Transmembrane properties of SjNPYR-like were demonstrated in vitro using HEK293 cells and the p EGFP-N1 plasmid. Relative quantifi cation of SjNPYR-like mRNA level confi rmed a high level expression and broad distribution of SjNPYR-like in various tissues of female S. japonica. In addition, the transcriptional profile of SjNPYR-like in the brain, liver, and ovary during gonadal development was analyzed. The results provide basic understanding on the molecular characteristics of SjNPYR-like and its potentially physical functions.

Mitosis-specific acetylation tunes Ran effector binding for chromosome segregation

Stable transmission of genetic information during cell division requires faithful mitotic spindle assembly and chromosome segregation. The Ran GTPase plays a key role in mitotic spindle assembly. However, how the generation of a chemical gradient of Ran-GTP at the spindle is coupled to mitotic post-translational modifications has never been characterized. Here, we solved the complex structure of Ran with the nucleotide release factor Mogl and delineated a novel mitosis-specific acetylation-regulated Ran-Mogl interaction dur- ing chromosome segregation. Our structure-guided functional analyses revealed that Mogl compotes with RCCl for Ran binding in a GTP/GDP-dependent manner. Biochemical characterization demonstrated that Mogl-bound Ran prevents RCCl binding and subse- quent GTP loading. Surprisingly, Ran is a bono fide substrate of TIP60, and the acetylation of Lys134 by TIP60 liberates Mogl from Ran binding during mitosis. Importantly, this acetylation-elicited switch of Ran binding to RCC1 promotes high level of Ran-GTP, which is essential for chromosome alignment. These results establish a previously uncharacterized regulatory mechanism in which TIP60 pro- vides a homeostatic control of Ran-GTP level by tuning Ran effector binding for chromosome segregation in mitosis.

Chemomics and drug innovation

Chemomics is an interdisciplinary study using approaches from chemoinformatics,bioinformatics,synthetic chemistry,and other related disciplines.Biological systems make natural products from endogenous small molecules (natural product building blocks) through a sequence of enzyme catalytic reactions.For each reaction,the natural product building blocks may contribute a group of atoms to the target natural product.We describe this group of atoms as a chemoyl.A chemome is the complete set of chemoyls in an organism.Chemomics studies chemomes and the principles of natural product syntheses and evolutions.Driven by survival and reproductive demands,biological systems have developed effective protocols to synthesize natural products in order to respond to environmental changes;this results in biological and chemical diversity.In recent years,it has been realized that one of the bottlenecks in drug discovery is the lack of chemical resources for drug screening.Chemomics may solve this problem by revealing the rules governing the creation of chemical diversity in biological systems,and by developing biomimetic synthesis approaches to make quasi natural product libraries for drug screening.This treatise introduces chemomics and outlines its contents and potential applications in the fields of drug innovation.

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

Realizing personalized medicine requires integrating diverse data types with bioinformatics.The most vital data are genomic information for individuals that are from advanced next-generation sequencing(NGS) technologies at present.The technologies continue to advance in terms of both decreasing cost and sequencing speed with concomitant increase in the amount and complexity of the data.The prodigious data together with the requisite computational pipelines for data analysis and interpretation are stressors to IT infrastructure and the scientists conducting the work alike.Bioinformatics is increasingly becoming the rate-limiting step with numerous challenges to be overcome for translating NGS data for personalized medicine.We review some key bioinformatics tasks,issues,and challenges in contexts of IT requirements,data quality,analysis tools and pipelines,and validation of biomarkers.