Advances and Applications in Bioinformatics and Chemistry最新文献_第8页

Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies. 基因毒性应激诱导的NF-κB信号转导的逻辑网络预测治疗干预策略的假定目标结构。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2009-01-01 Epub Date: 2009-12-03 DOI: 10.2147/aabc.s8211

Rainer Poltz, Raimo Franke, Katrin Schweitzer, Steffen Klamt, Ernst-Dieter Gilles, Michael Naumann

{"title":"Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies.","authors":"Rainer Poltz, Raimo Franke, Katrin Schweitzer, Steffen Klamt, Ernst-Dieter Gilles, Michael Naumann","doi":"10.2147/aabc.s8211","DOIUrl":"https://doi.org/10.2147/aabc.s8211","url":null,"abstract":"Genotoxic stress is induced by a broad range of DNA-damaging agents and could lead to a variety of human diseases including cancer. DNA damage is also therapeutically induced for cancer treatment with the aim to eliminate tumor cells. However, the effectiveness of radio- and chemotherapy is strongly hampered by tumor cell resistance. A major reason for radio- and chemotherapeutic resistances is the simultaneous activation of cell survival pathways resulting in the activation of the transcription factor nuclear factor-kappa B (NF-κB). Here, we present a Boolean network model of the NF-κB signal transduction induced by genotoxic stress in epithelial cells. For the representation and analysis of the model, we used the formalism of logical interaction hypergraphs. Model reconstruction was based on a careful meta-analysis of published data. By calculating minimal intervention sets, we identified p53-induced protein with a death domain (PIDD), receptor-interacting protein 1 (RIP1), and protein inhibitor of activated STAT y (PIASy) as putative therapeutic targets to abrogate NF-κB activation resulting in apoptosis. Targeting these structures therapeutically may potentiate the effectiveness of radio-and chemotherapy. Thus, the presented model allows a better understanding of the signal transduction in tumor cells and provides candidates as new therapeutic target structures.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"2 ","pages":"125-38"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s8211","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30142068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Identification of longevity genes with systems biology approaches. 用系统生物学方法鉴定长寿基因。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2009-01-01 Epub Date: 2009-02-27 DOI: 10.2147/aabc.s4070

Yuanyou Tan, John M Bush, Weijiu Liu, Fusheng Tang

{"title":"Identification of longevity genes with systems biology approaches.","authors":"Yuanyou Tan, John M Bush, Weijiu Liu, Fusheng Tang","doi":"10.2147/aabc.s4070","DOIUrl":"https://doi.org/10.2147/aabc.s4070","url":null,"abstract":"Identification of genes involved in the aging process is critical for understanding the mechanisms of age-dependent diseases such as cancer and diabetes. Measuring the mutant gene lifespan, each missing one gene, is traditionally employed to identify longevity genes. While such screening is impractical for the whole genome due to the time-consuming nature of lifespan assays, it can be achieved by in silico genetic manipulations with systems biology approaches. In this review, we will introduce pilot explorations applying two approaches of systems biology in aging studies. One approach is to predict the role of a specific gene in the aging process by comparing its expression profile and protein-protein interaction pattern with those of known longevity genes (top-down systems biology). The other approach is to construct mathematical models from previous kinetics data and predict how a specific protein contributes to aging and antiaging processes (bottom-up systems biology). These approaches allow researchers to simulate the effect of each gene's product in aging by in silico genetic manipulations such as deletion or over-expression. Since simulation-based approaches are not as widely used as the other approaches, we will focus our review on this effort in more detail. A combination of hypothesis from data-mining, in silico experimentation from simulations, and wet laboratory validation will make the systematic identification of all longevity genes possible.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"2 ","pages":"49-56"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s4070","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30142063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

The development of an affinity evaluation and prediction system by using protein-protein docking simulations and parameter tuning. 基于蛋白质-蛋白质对接模拟和参数调优的亲和性评估与预测系统的开发。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2009-01-01 Epub Date: 2009-01-12 DOI: 10.2147/aabc.s3646

Koki Tsukamoto, Tatsuya Yoshikawa, Kiyonobu Yokota, Yuichiro Hourai, Kazuhiko Fukui

{"title":"The development of an affinity evaluation and prediction system by using protein-protein docking simulations and parameter tuning.","authors":"Koki Tsukamoto, Tatsuya Yoshikawa, Kiyonobu Yokota, Yuichiro Hourai, Kazuhiko Fukui","doi":"10.2147/aabc.s3646","DOIUrl":"https://doi.org/10.2147/aabc.s3646","url":null,"abstract":"A system was developed to evaluate and predict the interaction between protein pairs by using the widely used shape complementarity search method as the algorithm for docking simulations between the proteins. We used this system, which we call the affinity evaluation and prediction (AEP) system, to evaluate the interaction between 20 protein pairs. The system first executes a “round robin” shape complementarity search of the target protein group, and evaluates the interaction between the complex structures obtained by the search. These complex structures are selected by using a statistical procedure that we developed called ‘grouping’. At a prevalence of 5.0%, our AEP system predicted protein–protein interactions with a 50.0% recall, 55.6% precision, 95.5% accuracy, and an F-measure of 0.526. By optimizing the grouping process, our AEP system successfully predicted 10 protein pairs (among 20 pairs) that were biologically relevant combinations. Our ultimate goal is to construct an affinity database that will provide cell biologists and drug designers with crucial information obtained using our AEP system.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"2 ","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s3646","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30142650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 19

Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST. 利用BLAST和PSI-BLAST对结构衍生的氨基酸取代基质检测蛋白同源物的效果进行评价。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2009-01-01 Epub Date: 2009-06-05 DOI: 10.2147/aabc.s5553

Nalin Cw Goonesekere

引用次数: 1

Computer applications for prediction of protein-protein interactions and rational drug design. 预测蛋白质-蛋白质相互作用和合理药物设计的计算机应用。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2009-01-01 Epub Date: 2009-11-10

Solène Grosdidier, Max Totrov, Juan Fernández-Recio

{"title":"Computer applications for prediction of protein-protein interactions and rational drug design.","authors":"Solène Grosdidier, Max Totrov, Juan Fernández-Recio","doi":"","DOIUrl":"","url":null,"abstract":"In recent years, protein-protein interactions are becoming the object of increasing attention in many different fields, such as structural biology, molecular biology, systems biology, and drug discovery. From a structural biology perspective, it would be desirable to integrate current efforts into the structural proteomics programs. Given that experimental determination of many protein-protein complex structures is highly challenging, and in the context of current high-performance computational capabilities, different computer tools are being developed to help in this task. Among them, computational docking aims to predict the structure of a protein-protein complex starting from the atomic coordinates of its individual components, and in recent years, a growing number of docking approaches are being reported with increased predictive capabilities. The improvement of speed and accuracy of these docking methods, together with the modeling of the interaction networks that regulate the most critical processes in a living organism, will be essential for computational proteomics. The ultimate goal is the rational design of drugs capable of specifically inhibiting or modifying protein-protein interactions of therapeutic significance. While rational design of protein-protein interaction inhibitors is at its very early stage, the first results are promising.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"2 ","pages":"101-23"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30143024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolution of a domain conserved in microtubule-associated proteins of eukaryotes. 真核生物微管相关蛋白中一个保守结构域的进化。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2008-01-01 Epub Date: 2008-09-23 DOI: 10.2147/aabc.s3211

Alex S Rajangam, Hongqian Yang, Tuula T Teeri, Lars Arvestad

{"title":"Evolution of a domain conserved in microtubule-associated proteins of eukaryotes.","authors":"Alex S Rajangam, Hongqian Yang, Tuula T Teeri, Lars Arvestad","doi":"10.2147/aabc.s3211","DOIUrl":"https://doi.org/10.2147/aabc.s3211","url":null,"abstract":"The microtubule network, the major organelle of the eukaryotic cytoskeleton, is involved in cell division and differentiation but also with many other cellular functions. In plants, microtubules seem to be involved in the ordered deposition of cellulose microfibrils by a so far unknown mechanism. Microtubule-associated proteins (MAP) typically contain various domains targeting or binding proteins with different functions to microtubules. Here we have investigated a proposed microtubule-targeting domain, TPX2, first identified in the Kinesin-like protein 2 in Xenopus. A TPX2 containing microtubule binding protein, PttMAP20, has been recently identified in poplar tissues undergoing xylogenesis. Furthermore, the herbicide 2,6-dichlorobenzonitrile (DCB), which is a known inhibitor of cellulose synthesis, was shown to bind specifically to PttMAP20. It is thus possible that PttMAP20 may have a role in coupling cellulose biosynthesis and the microtubular networks in poplar secondary cell walls. In order to get more insight into the occurrence, evolution and potential functions of TPX2-containing proteins we have carried out bioinformatic analysis for all genes so far found to encode TPX2 domains with special reference to poplar PttMAP20 and its putative orthologs in other plants.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"1 ","pages":"51-69"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s3211","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30142645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Identification of significant genes in genomics using Bayesian variable selection methods. 利用贝叶斯变量选择方法鉴定基因组学中的重要基因。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2008-01-01 Epub Date: 2008-07-01 DOI: 10.2147/aabc.s3624

Eugene Lin, Lung-Cheng Huang

引用次数: 11

Discrimination between biological interfaces and crystal-packing contacts. 区分生物界面和晶体填充接触。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2008-01-01 Epub Date: 2008-11-02 DOI: 10.2147/aabc.s4255

Yuko Tsuchiya, Haruki Nakamura, Kengo Kinoshita

{"title":"Discrimination between biological interfaces and crystal-packing contacts.","authors":"Yuko Tsuchiya, Haruki Nakamura, Kengo Kinoshita","doi":"10.2147/aabc.s4255","DOIUrl":"https://doi.org/10.2147/aabc.s4255","url":null,"abstract":"A discrimination method between biologically relevant interfaces and artificial crystal-packing contacts in crystal structures was constructed. The method evaluates protein-protein interfaces in terms of complementarities for hydrophobicity, electrostatic potential and shape on the protein surfaces, and chooses the most probable biological interfaces among all possible contacts in the crystal. The method uses a discriminator named as \"COMP\", which is a linear combination of the complementarities for the above three surface features and does not correlate with the contact area. The discrimination of homo-dimer interfaces from symmetry-related crystal-packing contacts based on the COMP value achieved the modest success rate. Subsequent detailed review of the discrimination results raised the success rate to about 88.8%. In addition, our discrimination method yielded some clues for understanding the interaction patterns in several examples in the PDB. Thus, the COMP discriminator can also be used as an indicator of the \"biological-ness\" of protein-protein interfaces.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"1 ","pages":"99-113"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s4255","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30142648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 25

Prion disease induced alterations in gene expression in spleen and brain prior to clinical symptoms. 朊病毒病在出现临床症状前可诱导脾和脑的基因表达改变。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2008-01-01 Epub Date: 2008-09-07 DOI: 10.2147/aabc.s3411

Hyeon O Kim, Greg P Snyder, Tyler M Blazey, Richard E Race, Bruce Chesebro, Pamela J Skinner

{"title":"Prion disease induced alterations in gene expression in spleen and brain prior to clinical symptoms.","authors":"Hyeon O Kim, Greg P Snyder, Tyler M Blazey, Richard E Race, Bruce Chesebro, Pamela J Skinner","doi":"10.2147/aabc.s3411","DOIUrl":"https://doi.org/10.2147/aabc.s3411","url":null,"abstract":"Prion diseases are fatal neurodegenerative disorders that affect animals and humans. There is a need to gain understanding of prion disease pathogenesis and to develop diagnostic assays to detect prion diseases prior to the onset of clinical symptoms. The goal of this study was to identify genes that show altered expression early in the disease process in the spleen and brain of prion disease-infected mice. Using Affymetrix microarrays, we identified 67 genes that showed increased expression in the brains of prion disease-infected mice prior to the onset of clinical symptoms. These genes function in many cellular processes including immunity, the endosome/lysosome system, hormone activity, and the cytoskeleton. We confirmed a subset of these gene expression alterations using other methods and determined the time course in which these changes occur. We also identified 14 genes showing altered expression prior to the onset of clinical symptoms in spleens of prion disease infected mice. Interestingly, four genes, Atp1b1, Gh, Anp32a, and Grn, were altered at the very early time of 46 days post-infection. These gene expression alterations provide insights into the molecular mechanisms underlying prion disease pathogenesis and may serve as surrogate markers for the early detection and diagnosis of prion disease.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"1 ","pages":"29-50"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s3411","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30141694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 25

Is gene activity in plant cells affected by UMTS-irradiation? A whole genome approach. 植物细胞中的基因活性是否受到umts辐射的影响?全基因组方法。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2008-01-01 Epub Date: 2008-10-08 DOI: 10.2147/aabc.s3570

Julia C Engelmann, Rosalia Deeken, Tobias Müller, Günter Nimtz, M Rob G Roelfsema, Rainer Hedrich

{"title":"Is gene activity in plant cells affected by UMTS-irradiation? A whole genome approach.","authors":"Julia C Engelmann, Rosalia Deeken, Tobias Müller, Günter Nimtz, M Rob G Roelfsema, Rainer Hedrich","doi":"10.2147/aabc.s3570","DOIUrl":"https://doi.org/10.2147/aabc.s3570","url":null,"abstract":"Mobile phone technology makes use of radio frequency (RF) electromagnetic fields transmitted through a dense network of base stations in Europe. Possible harmful effects of RF fields on humans and animals are discussed, but their effect on plants has received little attention. In search for physiological processes of plant cells sensitive to RF fields, cell suspension cultures of Arabidopsis thaliana were exposed for 24 h to a RF field protocol representing typical microwave exposition in an urban environment. mRNA of exposed cultures and controls was used to hybridize Affymetrix-ATH1 whole genome microarrays. Differential expression analysis revealed significant changes in transcription of 10 genes, but they did not exceed a fold change of 2.5. Besides that 3 of them are dark-inducible, their functions do not point to any known responses of plants to environmental stimuli. The changes in transcription of these genes were compared with published microarray datasets and revealed a weak similarity of the microwave to light treatment experiments. Considering the large changes described in published experiments, it is questionable if the small alterations caused by a 24 h continuous microwave exposure would have any impact on the growth and reproduction of whole plants.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"1 ","pages":"71-83"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s3570","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30142646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10