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检索条件"任意字段=第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学"

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Modes of parasite profilin recognition by Toll-like receptors in mice and humans

Modes of parasite profilin recognition by Toll-like receptor...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Shoudao Yuan Tianren Li Tiandi Wei Jing Gong Cancer Research Center School of MedicineShandong University State Key Laboratory of Microbial Technology School of Life ScienceShandong University

Background:Profilin is involved in motility and invasion of apicomplexan（protozoan） parasites and is used for invading host *** 2005,mouse Toll-like receptor（TLR） 11 was found to initiate an innate immune response inducing interleukin-12（IL-12） upon sensing Toxoplasma gondii ***,the molecular mechanism of TLR11 binding profilins remains *** the other hand,the TLR11 expression is suppressed in ***, whether other TLRs can recognize parasite profilins in human instead of TLR11 becomes a mystery. Methods:We first analyzed the structural features of the crystal structure of *** profilin（PDB code:3NEC） and a homology model of mouse ***,protein-protein docking and molecular dynamics simulation（MDS） methods were used to generate a TLR11- profilin complex ***,a similarity search of the potential profilin-binding site based on structure features was performed across all human TLR models（TLR1-10）. Results:Electrostatic analysis reveals that the entire surface of the *** profilin is predominantly negatively charged,whereas TLR11 exhibits several positively charged *** and MDS studies provided a model of TLR 11-profilin complex structure. The model shows that the potential profilin-binding site is a positively charged patch located at LRR1 to LRR7 on TLR11,which is rich in Ser,Thr,Cys and lactam amino *** interestingly,a similar structure pattern just appeared on human TLR（exact TLR family number hidden due to unpublished data）.Accordingly,we proposed a potential model of human TLR interacting with profilin. Conclusions:The profilin-binding site of mouse TLR11 processes a specified structural *** suggest that human TLR that also has this pattern might recognize parasite *** it is true,it will enlighten new therapeutic measures for human infectious diseases.

关键词： parasite profilin TLR protein-protein docking

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PCR primer design in the Postgenomic Era

PCR primer design in the Postgenomic Era

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Wubin Qu Yang Zhou Yanchun Zhang Yiming Lu Yi Yang Chenggang Zhang Beijing Institute of Radiation Medicine State Key Laboratory of ProteomicsCognitive and Mental Health Research Center College of Life Science Sichuan UniversityKey Laboratory of Bio-Resources and Eco-Environment of MOEChengdu 610064China

Background:PCR is a key technology in molecular biological studies such as gene expression microarray experiments,construction of cDNA libraries and genome-wide genotyping of *** a result,the success of PCR is crucial and many efforts have been made to improve the PCR reaction,especially in primer *** being available of tremendous genome databases in postgenomic era,PCR primer design is benefited but also *** example,one of the benefit is the specificity of primers can be checked against the background genome DNA database,while the challenge is how to check primers against the huge genome DNA database *** addressed part of these problems and developed a suite of programs to help users to design high quality PCR primers. Methods and Results: l)We proposed and developed a program named MFEprimer to evaluate the quality of PCR primers against background DNA with multiple factors,including melting temperature, Gibbs free energy etc.[Wubin Qu,***.,2009,Bioinformatics]. 2)We use a k-mer index algorithm to accelerate the search process for primer binding sites and use thermodynamics to evaluate binding stability between each primer and its DNA template.[Wubin Qu,***.,2012,NAR Web Server Issue accepted] 3)With our core primer specificity checking program MFEprimer,we developed a multiplex PCR primer design software named ***,specificity,and other important factors all are optimized by MPprimer.[Zhiyong Shen#,Wubin Qu#,***.,2010, BMC Bioinformatics] 4)By utilizing the newly IT technology HTML5,we provided a visualized web server for primer design named *** utilizes HTML5 to display gene structure and JavaScript to interact with *** VizPrimer,users can focus their attention on gene structure and primer design strategy,without wasting time on calculating the exon position of splice variants or manually configuring the complicated parameters.[Yang Zhou#,Wubin Qu#,***.,2011, Bioinformatics] Conclusions:Our softwar

关键词： PCR primer design MFEprimer MPprimer VizPrimer

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Biomarkers screening for cardiac conduction diseases

Biomarkers screening for cardiac conduction diseases

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Brenda B.Su Marco Capecchi Cedric Manlhiot Yuqing Yan Edgar T Jaeggi Earl D.Silverman Robert M.Hamilton. 生命科学与生物技术学院哈尔滨师范大学哈尔滨医科大学生物信息科学与技术学院多伦多大学病童医院

Rational:Cardiac conduction disease is multifactorial complex *** factors play critical roles in formation of cardiac conductive tissue during fetal heart *** has been recognized that environmental factors also alter during fetal development increase the risk of cardiac conduction *** are few genes shown can be altered and effect on heart structure formation during the ***,the gene expression in conductive tissue in human fetal heart and the underlying molecular mechanisms remain poorly *** this study,we identify genes expressed preferentially within the atrial ventricular conductive junctional tissue(AVJ) in human fetal hearts as compared to the apical myocardium(Apx). Methods:Total RNA from six fetal hearts was extracted using Qiagen RNA kit and applied onto Affymetrix human Genome U133 plus 2(micro)*** results were analyzed by Affymetrix console and Partek? Genomics SuiteTM. Results:We found that 1532 genes significantly(p<0.01) expressed in atrial ventricular conductive junctional tissue than that in apex at 20-23 weeks of gestation,including 496 genes greater than 2-fold differential expression between fetal cardiac atrial ventricular junction and ***1D,CACNA1G and HTR4 expressed preferentially in human atrial ventricular conductive tissue.A subset of the data was confirmed by Real-Time PCR and immunostaining.245 genes highly expressed in human atrial ventricular conductive junctional tissue were matched to the gene expression in mouse atrial ventricular nodal cells and 103 genes were matched to E10.5 mouse the atrial ventricular node(p< 0.01). Conclusion:In conclusion,high-throughput approaches can provide specific markers for the human fetal atrial ventricular conduction system,which might be important targets in the pathophysiology of cardiac conduction diseases in heart development.

关键词： cardiac conduction diseases gene expression microarray atrial ventricular tissue

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Modeling regulatory networks in head and neck cancer

Modeling regulatory networks in head and neck cancer

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Yan Bin Li Huai Zhong Chen Jiaofang Shao Ming Zhan Department of Biology Hong Kong Baptist University Research Resource Branch NIANational Institutes of Health Head and Neck Surgery Branch NIDCDNational Institutes of Health Department of Systems Medicine and Bioengineering Methodist Hospital Research Institute

Background:Genes are coordinately regulated by multiple transcription factors (TFs) or other regulators to form regulatory networks to carry out complex and condition-specific biological functions in human cancer.p53 is the most mutated tumor suppressor gene in cancers,which are usually inflammatory with aberrant NF-B ***,how NF-B family members and p53 interact to globally regulate genes expression is not yet fully understood. Methods:Using head and neck squamous cell carcinoma(HNSCC) lines as the model system,we developed a novel integrative model based on Regulatory Component Analysis,which combined mRNA expression profile with regulator(TF and microRNA) binding for integrated analyses through matrix *** method particularly addresses the sparseness property in the matrix,which is an essential statistical parameter in modeling the regulatory components of regulators and their targets. Results:We identified regulatory programs of seven key TFs,NF-B,p53,AP1, CEBPB,EGR1,SP1 and STAT3,including 37 and 39 common target genes in the cell lines with wild type(wt) and mutant(mt) p53 status,*** observed that the majority of p53 targets are also co-regulated by NF-κB in p53 wt or mt subset of HNSCC cells,suggesting that both TFs play a tight concerted regulation on gene programs in the tumor ***,we further constructed regulatory networks of NF-κB,p53 and microRNAs 21 and *** results unraveled the cross-regulations among NF-κB, p53,and microRNAs,provided an insight into understanding of underlying regulatory mechanisms. Conclusions:Application of the newly developed method not only showed an efficient approach to inferring the regulatory networks in HNSCC datasets,as the inferred networks are biologically more meaningful than those by other methods,but also provides a model-based pipeline to study on regulatory networks in other biological complex systems.

关键词： regulatory components integrative modeling NF-κB p53 head and neck cancer

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TCDD inhibition of the activity of CK2 through binding to the ATP-competitive binding site of the catalytic subunit:Insight from computational studies

TCDD inhibition of the activity of CK2 through binding to th...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：许先进 Salvatore Cannistraro Anna Rita Bizzarri 苏计国陈慰祖王存新北京工业大学生命科学与生物工程学院 Biophysics and Nanoscience Centre CNISMDipartimento di Biologia ed Ecologia(DEB) Universita della TusciaViterbo 01100Italy 燕山大学理学院

Background:2,3,7,8-Tetrachlorodibenzo-p-dioxin(TCDD),a member of dioxin-type chemicals,is considered one of the most toxic environmental pollutants and has been proved to be one of the most potent tumor *** the aryl hydrocarbon receptor(AhR) which is considered a high-affinity receptor of TCDD,it has been shown that TCDD reduces rapidly the activity of CK2(casein kinaseⅡ) both in vivo and in vitro. Methods:The molecular similarity of TCDD with some known inhibitors of CK2αhas been ***,TCDD was docked to the receptor,considering two structures of CK2αfrom maize and human,*** chosen predicted CK2α-TCDD complexes were further refined by molecular dynamics(MD) simulations and by binding free energy calculations using MM/PBSA method. Results:The similarity analysis shows that TCDD shares high 3D shape and electrostatic potential similarities with the selected CK2α*** studies between the two crystal structures of CK2αand TCDD show that TCDD binds to the ATP-competitive binding site of CK2α.By applying flexible docking and MD simulation and binding free energy analysis,we found low values of binding free energy for all predicted binding modes, suggesting a high affinity of TCDD to CK2α. Conclusions:The results clearly show that TCDD binds to the ATP-competitive binding site of CK2αthus inducing an inhibition of its *** the crucial role of CK2 in various cellar progresses,such a result suggests that CK2 might play an important role in the toxic effects of TCDD;such an effects being not related to that acting through AhR *** further clarify the mechanisms of TCDD-induced toxic effects,further experimental studies on the interaction between CK2 and TCDD are recommended to be done.

关键词： TCDD CK2 inhibitor docking MM/PBSA

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Polymorphisms in seizure 6-like gene are associated with bipolar disorderⅠ:evidence of gene×gender interaction

Polymorphisms in seizure 6-like gene are associated with bip...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Chun Xu Jerald E.Mullersman Liang Wang Brenda Bin Su ChunXiang Mao Yolanda Posada Cynthia Camarillo Yu Mao Michael A Escamilla Kesheng Wang Texas Tech University Health Sciences Center Paul L.Foster School of MedicineDepartments of Psychiatry and Neurology and The Center of Excellence in NeuroscienceEI PasoTexas Office of Biostatistics and Epidemiology Center for Biologies Evaluation and ResearchFood and Drug AdministrationRockvilleMD 20852USA Univeristy of Toronto College of Bioinformatics Science and Technology Harbin Medical University Walden University

Background:Previous reports have suggested that there may be gene×gender interaction for bipolar disorder(BD)-associated genes/loci at 22q *** study aimed to investigate the associations of SEZ6L genetic variants with bipolar disorderⅠ(BD-Ⅰ) and to examine gender-specific genetic associations. Methods:605 BD-ⅠCaucasian cases and 1034 controls were selected from the publicly available data of the Whole Genome Association Study of *** increase power, an additional 362 Caucasian controls were added to this study from the Genome-Wide Association Study of *** total,605 BD-Ⅰcases and 1396 controls(934 males and 1067 females) were available for genetic association analysis of 118 SNPs within the SEZ6L gene using PLINK software. Results:16 SNPs showed significant gene x gender interactions influencing BD-Ⅰ(P<0.01).In addition,significant differences in the distribution of the alleles for these 16 SNPs were observed between the female BD-Ⅰpatients and healthy controls(P<0.015) but no significant associations were found for the male sample(P>0.05).The SNP rs4822691 showed the strongest association with BD-Ⅰin the female sample(P=2.18×10-4) and the strongest gene x gender interaction in influencing BD-Ⅰ(P = 9.16×10-5). Limitations:The findings of this study need to be replicated in independent samples. Conclusions:This is the first demonstration that genetic variants in the SEZ6L gene are associated with BD-Ⅰin female patients and provides additional compelling evidence for genetic variation at 22q11-13 that influences BD-Ⅰ*** present findings highlight the gene x gender interactions modifying BD-Ⅰsusceptibility.

关键词： SEZ6L bipolar disorder gender differences,susceptibility

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CistromeMap:A knowledgebase and web server for ChlP-Seq and DNase-Seq studies in mouse and human

CistromeMap:A knowledgebase and web server for ChlP-Seq and ...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Bo Qin Meng Zhou Ying Ge Len Taing Tao Liu Qian Wang Su Wang Junsheng Chen Lingling Shen Xikun Duan Shengen Hu Wei Li Henry Long Yong Zhang X.Shirley Liu Department of Bioinformatics School of Life Science and TechnologyTongji University Center for Functional Cancer Epigenetics Dana-Farber Cancer InstituteBostonMA02115USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard School of Public Health450 Brookline AveBostonMA02115USA Department of Information Technology China Novartis Institutes for BioMedical Research Co.Ltd. Division of Biostatistics Dan L Duncan Cancer Center and Department of Molecular and Cellular BiologyBaylor College of MedicineOne Baylor PlazaHoustonTX 77030USA

Transcription and chromatin regulators,and histone modifications play essential roles in gene expression *** have created CistromeMap as a web server to provide a comprehensive knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human. In total,CistromeMap contains 2711 ChlP-Seq datasets for transcription and chromatin regulators,2355 for histone modifications and variants,412 DNase-Seq,and 996 control *** systematically annotated the following metadata for each sample:cell line/ population,cell type,tissue origin,strain(for mouse),disease state,factor name,PubMed ID (for published data),data source,reference,and last *** on the original literature and online information about official gene symbol,cell line and tissue origin,we created our own ontology for better annotation and *** transcription and chromatin regulators,POLR2A,CTCF,ESR1,RELA,and EP300 are the most often profiled ChlP-Seq *** histone marks,H3K4me3,H3K27me3,H3K4mel,H3K36me3 and H3K9me3 ChlP-Seq are the most common,which together accounts for over 70%of all of the histone ChlP-Seq *** details of the above statistics are available at http://***. ***/pc/dcstats/,and will be automatically updated as more ChIP-Seq and DNase-Seq data become available.

关键词： knowledgebase ChlP-Seq DNase-Seq systematic annotation

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Evolution of the DHRS4 gene cluster and antisense AS1DHRS4

Evolution of the DHRS4 gene cluster and antisense AS1DHRS4

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Lei Feng Dongyang Huang Department of Cell Biology 22 Xinling RoadShantou University Medical College

Background:The DHRS4 gene encodes an NADP(H)-dependent retinol dehydrogenase /***4 and two genes(DHRS4L2 and DHRS4L1) that recently arose from gene duplication in human,an antisense transcript AS1DHRS4,devoted of the DHRS4 gene negatively regulates expression of all three *** order to analysis the evolution of the DHRS4 gene cluster and antisense AS1DHRS4,bioinformatics methods were performed to analysis it. Methods:Infernal-1.0.2 was run to searching DNA sequence databases for RNA structure and sequence similarities homologous sequences of AS1DHRS4 in fifteen species. Multiple sequence alignments and evolution analysis were completed by ClustalX2.0. Mega5.0 was used to estimate rates of molecular evolution.3'-RACE and 5'-RACE were conducted to obtain the full length of *** also transfected rhesus monkey siRNA to knockdown CO048964,and detected the knockdown effect by real-time PCR. Results:Sequence alignment of Infernal-1.0.2 shows that DHRS4 sequences are conserved in *** the sequence alignments,we realized that most primates have a single ***,human and rhesus monkeys contain two duplications,while marmosets and other vertebrates contain only one *** alignment showed that the AS1DHRS4 does not exist in mouse and rat even though both genomes have high similarity with the human ***1DHRS4 is conserved in all primates except in marmosets, but exists in the *** found an EST sequence CO048964 in rhesus monkey that transcribed at the opposite chain of the DHRS4 gene ***'s exon structure is extremely different from *** rhesus monkeys full length CO048964 was obtained through 3'-RACE and 5'-RACE in Frhk-4 cell line RNA,and devoted it *** ID: JQ686618,JQ686619,*** of rheASlDHRS4 in Frhk-4 cell led significant down regulation of DHRS4,which is opposite to AS1DHRS4 in human cells. Conclusions:The sequence of DHRS4 gene is conserved among the fifteen spec

关键词： long noncoding RNA evolution nature antisense transcripts DHRS4

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Combining docking and MM/GBSA to explore benzamide derivatives binding site on influenza NSl protein

Combining docking and MM/GBSA to explore benzamide derivativ...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Li Zhang Yanni Tan Fangliang Zheng Hongsheng Liu School of Life Science Liaoning University Research Center for Computer Simulating and Information Processing of Bio-macromolecules of Liaoning Liaoning University

Background:Non-structural protein 1,a highly conserved influenza virus protein, has been demonstrated previously to be a potential target for antiviral *** benzamide derivatives have been identified that inhibit NS1 function specifically and suppress virus *** the inhibition mechanism of these inhibitors in NSl is *** this paper,the binding site of these inhibitors to NS1 was explored. Methods:Potential ligand binding sites were predicted by Q-SiteFider and blind docking of JJ3297(a representative small molecule of benzamide derivatives) to *** order to find the inhibitor binding site,JJ3297 was submitted to docking simulations,in which JJ3297 were docked into each predicted binding sites of each NSl 3-D structures that retrieved from ***,a series of benzamide derivatives were docked into five predicted binding sites used 2Z0A as NSl 3-D *** order to identify the key features in the interaction between NSl and ligands,molecular dynamics simulation and MM-GBSA calculation were performed on JJ3297-NS1 complex. Results:Based on results of serveral docking studies on different NSl 3-D structures and different inhibitors,we found that these inhibitors bound with high affinity at a site located at RNA-binding *** predicted binding site is a conserved hydrophobic pocket that allow inhibitors to take part in van der Waals interactions with F14,W16,Q40, L43,154,T58 and K62 via its hydrophobic group,while the phenol hydroxyl and linking region acylamino group has formed several hydrogen bonding interactions with H17 and E55. From the MM-GBSA calculations,we find that the van der Waals interaction term provide the main driving force for the binding process,indicating that the hydrophobic groups are crucial for the inhibitory activity. Conclusions:The molecular docking and MM/PBSA method were combinational used to confirm the reasonable binding site of some small molecule inhibitors to *** uncovering of the bin

关键词： Influenza A virus Non-structural protein 1 inhibitor Molecular docking

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The effects of TNF-α and IL-13 on the generation of collagen in Human Hepatic Stellate Cell

The effects of TNF-α and IL-13 on the generation of collage...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Huiling Xiong Xiaoyu Shi Ying Zhou Wenlin Li Jiangxi Key Laboratory of Medical Biology Jiangxi Institute of Medical Science Department of Medical Experiment Nanchang University Department of Basic Medicine Nanchang University

Background:IL-13 which is produced by a variety of cells,mainly by activated type II T helper cells,is a multi-effectiveness of *** has confirmed that IL-13 is the primary cytokine that induces fibrosis,with IL-13 receptor alpha 1(IL-13Ral) combining to produce a fibrogenic *** addition,IL-13 receptor alpha 2(IL-13Ra2) is another receptor of IL-13 and its competitive inhibition of the combination of IL-13Ral and IL-13 can result in the interruption of the JAK/STAT signal transduction pathway which would mediates the fibrogenic *** necrosis factor-alpha(TNF-α) is a mononuclear factor which is produced mainly by monocytes/phagocytic cells with broad biological ***-αcan inhibit the expression of TGF-pi which promotes *** studies have found that TNF-αcan up-regulate the expression of IL-13Ra2 in the fibroblasts of lung and skin,which would inhibit the signal transduction pathway of IL-13-mediated *** this study,we will investigate whether IL-13Ra2 expresses in human hepatic stellate cell line LX-2,and whether TNF-αcan up-regulate the expression of IL-13Ra2,which would inhibit the synthesis of collagen in LX-2 cells. Methods:①Modality of LX-2 cells were observed by HE staining;②LX-2 cells were stimulated with TNF-αand IL-13 in different doses and with different time points;③The expression of IL-13Ral and IL-13Ra2 mRNA were evaluated by RT-PCR;④The expression of PCOLⅠmRNA was evaluated after LX-2 cells were stimulated with TNF-αand IL-13. First,LX-2 cells were stimulated with TNF-αand IL-13 in different doses and with different time *** expression of PCOL I mRNA were evaluated by ***,LX-2 cells were cultured and divided into four groups:control group,TNF-αgroup,IL-13 group and TNF-α+ IL-13 *** expression of PCOL I mRNA was evaluated by RT-PCR;⑤The expression of PCOL I protein was evaluated by immunohistochemisty;⑥The collagen content was evaluated by hydroxyproline assay. Results:①The activity of L

关键词： IL-13 TNF-α LX-2 PCOLI

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