检索结果-内蒙古大学图书馆

Decreased HIV diversity after allogeneic stem cell transplantation of an HIV-1 infected patient: a case report

VIROLOGY JOURNAL 2010年第1期7卷 55-55页

作者： Kamp, Christel Wolf, Timo Bravo, Ignacio G. Kraus, Benjamin Krause, Birgit Neumann, Britta Winskowsky, Gudrun Thielen, Alexander Werner, Albrecht Schnierle, Barbara S. Paul Ehrlich Inst D-63225 Langen Germany Goethe Univ Frankfurt Sch Med Frankfurt Germany Commiss European Communities Directorate Hlth & Consumer Protect Hlth Threat Unit C3 L-2920 Luxembourg Luxembourg CSISP Valencia Spain Max Planck Inst Informat D-66123 Saarbrucken Germany

The human immunodeficiency virus type 1 (HIV-1) coreceptor use and viral evolution were analyzed in blood samples from an HIV-1 infected patient undergoing allogeneic stem cell transplantation (SCT). Coreceptor use was predicted in silico from sequence data obtained from the third variable loop region of the viral envelope gene with two software tools. Viral diversity and evolution was evaluated on the same samples by Bayesian inference and maximum likelihood methods. In addition, phenotypic analysis was done by comparison of viral growth in peripheral blood mononuclear cells and in a CCR5 (R5)-deficient T-cell line which was controlled by a reporter assay confirming viral tropism. In silico coreceptor predictions did not match experimental determinations that showed a consistent R5 tropism. Anti-HIV directed antibodies could be detected before and after the SCT. These preexisting antibodies did not prevent viral rebound after the interruption of antiretroviral therapy during the SCT. Eventually, transplantation and readministration of anti-retroviral drugs lead to sustained increase in CD4 counts and decreased viral load to undetectable levels. Unexpectedly, viral diversity decreased after successful SCT. Our data evidence that only R5-tropic virus was found in the patient before and after transplantation. Therefore, blocking CCR5 receptor during stem cell transplantation might have had beneficial effects and this might apply to more patients undergoing allogeneic stem cell transplantation. Furthermore, we revealed a scenario of HIV-1 dynamic different from the commonly described ones. Analysis of viral evolution shows the decrease of viral diversity even during episodes with bursts in viral load.

关键词： Human Immunodeficiency Virus position specific score matrix Viral Rebound Structure Treatment Interruption Undergo Stem Cell Transplantation

来源：评论

学校读者我要写书评

暂无评论

Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria

引用

BMC GENOMICS 2003年第1期4卷 34-34页

作者： Anantharaman, V Aravind, L NIH Natl Ctr Biotechnol Informat Natl Lib Med Bethesda MD 20894 USA

Background: A great diversity of multi-pass membrane receptors, typically with 7 transmembrane (TM) helices, is observed in the eukaryote crown group. So far, they are relatively rare in the prokaryotes, and are restricted to the well-characterized sensory rhodopsins of various phototropic prokaryotes. Results: Utilizing the currently available wealth of prokaryotic genomic sequences, we set up a computational screen to identify putative 7 (TM) and other multi-pass membrane receptors in prokaryotes. As a result of this procedure we were able to recover two widespread families of 7 TM receptors in bacteria that are distantly related to the eukaryotic 7 TM receptors and prokaryotic rhodopsins. Using sequence profile analysis, we were able to establish that the first members of these receptor families contain one of two distinct N-terminal extracellular globular domains, which are predicted to bind ligands such as carbohydrates. In their intracellular portions they contain fusions to a variety of signaling domains, which suggest that they are likely to transduce signals via cyclic AMP, cyclic diguanylate, histidine phosphorylation, dephosphorylation, and through direct interactions with DNA. The second family of bacterial 7 TM receptors possesses an alpha-helical extracellular domain, and is predicted to transduce a signal via an intracellular HD hydrolase domain. Based on comparative analysis of gene neighborhoods, this receptor is predicted to function as a regulator of the diacylglycerol-kinase-dependent glycerolipid pathway. Additionally, our procedure also recovered other types of putative prokaryotic multi-pass membrane associated receptor domains. Of these, we characterized two widespread, evolutionarily mobile multi-TM domains that are fused to a variety of C-terminal intracellular signaling domains. One of these typified by the Gram-positive LytS protein is predicted to be a potential sensor of murein derivatives, whereas the other one typified by the Escheric

关键词： Histidine Kinase position specific score matrix Bacterial Lineage Lineage specific Expansion Phyletic Pattern

来源：评论

学校读者我要写书评

暂无评论

Accelerated microevolution in an outer membrane protein (OMP) of the intracellular bacteria Wolbachia

引用

BMC EVOLUTIONARY BIOLOGY 2010年第1期10卷 48-48页

作者： Baldo, Laura Desjardins, Christopher A. Russell, Jacob A. Stahlhut, Julie K. Werren, John H. Univ Guelph Biodivers Inst Ontario Guelph ON N1G 2W1 Canada Univ Rochester Dept Biol Rochester NY 14627 USA Harvard Univ Dept Organism & Evolut Biol Cambridge MA 02138 USA Univ Calif Riverside Dept Biol Riverside CA 92521 USA

Background: Outer membrane proteins (OMPs) of Gram-negative bacteria are key players in the biology of bacterial-host interactions. However, while considerable attention has been given to OMPs of vertebrate pathogens, relatively little is known about the role of these proteins in bacteria that primarily infect invertebrates. One such OMP is found in the intracellular bacteria Wolbachia, which are widespread symbionts of arthropods and filarial nematodes. Recent experimental studies have shown that the Wolbachia surface protein (WSP) can trigger host immune responses and control cell death programming in humans, suggesting a key role of WSP for establishment and persistence of the symbiosis in arthropods. Results: Here we performed an analysis of 515 unique alleles found in 831 Wolbachia isolates, to investigate WSP structure, microevolution and population genetics. WSP shows an eight-strand transmembrane beta-barrel structure with four extracellular loops containing hypervariable regions (HVRs). A clustering approach based upon patterns of HVR haplotype diversity was used to group similar WSP sequences and to estimate the relative contribution of mutation and recombination during early stages of protein divergence. Results indicate that although point mutations generate most of the new protein haplotypes, recombination is a predominant force triggering diversity since the very first steps of protein evolution, causing at least 50% of the total amino acid variation observed in recently diverged proteins. Analysis of synonymous variants indicates that individual WSP protein types are subject to a very rapid turnover and that HVRs can accommodate a virtually unlimited repertoire of peptides. Overall distribution of WSP across hosts supports a non-random association of WSP with the host genus, although extensive horizontal transfer has occurred also in recent times. Conclusions: In OMPs of vertebrate pathogens, large recombination impact, positive selection, reduced str

关键词： Outer Membrane Protein Wolbachia Strain position specific score matrix Ancestral Allele Synonymous Variant

来源：评论

学校读者我要写书评

暂无评论

Predicting N-terminal myristoylation sites in plant proteins

引用

BMC GENOMICS 2004年第1期5卷 37-37页

作者： Podell, S Gribskov, M Univ Calif San Diego San Diego Supercomp Ctr La Jolla CA 92093 USA Univ Calif San Diego Dept Biol La Jolla CA 92093 USA

Background: N-terminal myristoylation plays a vital role in membrane targeting and signal transduction in plant responses to environmental stress. Although N-myristoyltransferase enzymatic function is conserved across plant, animal, and fungal kingdoms, exact substrate specificities vary, making it difficult to predict protein myristoylation accurately within specific taxonomic groups. Results: A new method for predicting N-terminal myristoylation sites specifically in plants has been developed and statistically tested for sensitivity, specificity, and robustness. Compared to previously available methods, the new model is both more sensitive in detecting known positives, and more selective in avoiding false positives. scores of myristoylated and non-myristoylated proteins are more widely separated than with other methods, greatly reducing ambiguity and the number of sequences giving intermediate, uninformative results. The prediction model is available at http://***/***. Conclusion: Superior performance of the new model is due to the selection of a plant-specific training set, covering 266 unique sequence examples from 40 different species, the use of a probability-based hidden Markov model to obtain predictive scores, and a threshold cutoff value chosen to provide maximum positive-negative discrimination. The new model has been used to predict 589 plant proteins likely to contain N-terminal myristoylation signals, and to analyze the functional families in which these proteins occur.

关键词： Hide Markov Model Training Sequence Amino Acid Frequency position specific score matrix Negative Sequence

来源：评论

学校读者我要写书评

暂无评论

In silico regulatory analysis for exploring human disease progression

引用

BIOLOGY DIRECT 2008年第1期3卷 24-24页

作者： Holloway, Dustin T. Kon, Mark DeLisi, Charles Boston Univ Dept Biochem Mol Biol & Cell Biol Boston MA 02215 USA Boston Univ Dept Math & Stat Boston MA 02215 USA

Background: An important goal in bioinformatics is to unravel the network of transcription factors (TFs) and their targets. This is important in the human genome, where many TFs are involved in disease progression. Here, classification methods are applied to identify new targets for 152 transcriptional regulators using publicly-available targets as training examples. Three types of sequence information are used: composition, conservation, and overrepresentation. Results: Starting with 8817 TF-target interactions we predict an additional 9333 targets for 152 TFs. Randomized classifiers make few predictions (similar to 2/18660) indicating that our predictions for many TFs are significantly enriched for true targets. An enrichment score is calculated and used to filter new predictions. Two case-studies for the TFs OCT4 and WT1 illustrate the usefulness of our predictions: Many predicted OCT4 targets fall into the Wnt-pathway. This is consistent with known biology as OCT4 is developmentally related and Wnt pathway plays a role in early development. Beginning with 15 known targets, 354 predictions are made for WT1. WT1 has a role in formation of Wilms' tumor. Chromosomal regions previously implicated in Wilms' tumor by cytological evidence are statistically enriched in predicted WT1 targets. These findings may shed light on Wilms' tumor progression, suggesting that the tumor progresses either by loss of WT1 or by loss of regions harbouring its targets. Targets of WT1 are statistically enriched for cancer related functions including metastasis and apoptosis. Among new targets are BAX and PDE4B, which may help mediate the established anti-apoptotic effects of WT1. Of the thirteen TFs found which co-regulategenes with WT1 (p = 0.02), 8 have been previously implicated in cancer. The regulatory-network for WT1 targets in genomic regions relevant to Wilms' tumor is provided. Conclusion: We have assembled a set of features for the targets of human TFs and used them to develop c

关键词： Support Vector Machine Positive Predictive Value Support Vector Machine Classifier Enrichment score position specific score matrix

来源：评论

学校读者我要写书评

暂无评论

Improving protein secondary structure prediction based on short subsequences with local structure similarity

引用

BMC GENOMICS 2010年第Sup4期11卷 S4-S4页

作者： Lin, Hsin-Nan Sung, Ting-Yi Ho, Shinn-Ying Hsu, Wen-Lian Acad Sinica Inst Informat Sci Bioinformat Lab Taipei Taiwan Acad Sinica Taiwan Int Grad Program Bioinformat Program Taipei 115 Taiwan Natl Chiao Tung Univ Inst Bioinformat Hsinchu Taiwan

Background: When characterizing the structural topology of proteins, protein secondary structure (PSS) plays an important role in analyzing and modeling protein structures because it represents the local conformation of amino acids into regular structures. Although PSS prediction has been studied for decades, the prediction accuracy reaches a bottleneck at around 80%, and further improvement is very difficult. Results: In this paper, we present an improved dictionary-based PSS prediction method called SymPred, and a meta-predictor called SymPsiPred. We adopt the concept behind natural language processing techniques and propose synonymous words to capture local sequence similarities in a group of similar proteins. A synonymous word is an n-gram pattern of amino acids that reflects the sequence variation in a protein's evolution. We generate a protein-dependent synonymous dictionary from a set of protein sequences for PSS prediction. On a large non-redundant dataset of 8,297 protein chains (DsspNr-25), the average Q(3) of SymPred and SymPsiPred are 81.0% and 83.9% respectively. On the two latest independent test sets (EVA Set_1 and EVA_Set2), the average Q(3) of SymPred is 78.8% and 79.2% respectively. SymPred outperforms other existing methods by 1.4% to 5.4%. We study two factors that may affect the performance of SymPred and find that it is very sensitive to the number of proteins of both known and unknown structures. This finding implies that SymPred and SymPsiPred have the potential to achieve higher accuracy as the number of protein sequences in the NCBInr and PDB databases increases. Conclusions: Our experiment results show that local similarities in protein sequences typically exhibit conserved structures, which can be used to improve the accuracy of secondary structure prediction. For the application of synonymous words, we demonstrate an example of a sequence alignment which is generated by the distribution of shared synonymous words of a pair of protein seq

关键词： Protein Secondary Structure Query Protein Residue Pair position specific score matrix Template Protein

来源：评论

学校读者我要写书评

暂无评论

regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution

引用

HUMAN GENETICS 2017年第9期136卷 1279-1289页

作者： Zhang, Xinjun Li, Meng Lin, Hai Rao, Xi Feng, Weixing Yang, Yuedong Mort, Matthew Cooper, David N. Wang, Yue Wang, Yadong Wells, Clark Zhou, Yaoqi Liu, Yunlong Indiana Univ Sch Informat & Comp Bloomington IN 47408 USA Indiana Univ Sch Med Ctr Computat Biol & Bioinformat 410 W 10th StHS 5000 Indianapolis IN 46202 USA Harbin Engn Univ Automat Coll Pattern Recognit & Intelligent Syst Inst Harbin 150001 Heilongjiang Peoples R China Indiana Univ Purdue Univ Sch Informat & Comp Indianapolis IN 46202 USA Griffith Univ Sch Informat & Commun Technol Gold Coast Campus Southport Qld 4222 Australia Cardiff Univ Inst Med Genet Heath Pk Cardiff CF14 4XN S Glam Wales Indiana Univ Sch Med Dept Med Genet Indianapolis IN 46202 USA Indiana Univ Sch Med Dept Mol Genet Indianapolis IN 46202 USA Harbin Inst Technol Sch Comp Sci & Technol Harbin 150001 Heilongjiang Peoples R China Indiana Univ Sch Med Dept Biochem & Mol Biol Indianapolis IN 46202 USA Griffith Univ Inst Glyc Parklands Dr Southport Qld 4215 Australia Griffith Univ Sch Informat & Commun Technol Parklands Dr Southport Qld 4215 Australia Indiana Univ Sch Med Ctr Med Genom Indianapolis IN 46202 USA

While synonymous single-nucleotide variants (sSNVs) have largely been unstudied, since they do not alter protein sequence, mounting evidence suggests that they may affect RNA conformation, splicing, and the stability of nascent-mRNAs to promote various diseases. Accurately prioritizing deleterious sSNVs from a pool of neutral ones can significantly improve our ability of selecting functional genetic variants identified from various genome-sequencing projects, and, therefore, advance our understanding of disease etiology. In this study, we develop a computational algorithm to prioritize sSNVs based on their impact on mRNA splicing and protein function. In addition to genomic features that potentially affect splicing regulation, our proposed algorithm also includes dozens structural features that characterize the functions of alternatively spliced exons on protein function. Our systematical evaluation on thousands of sSNVs suggests that several structural features, including intrinsic disorder protein scores, solvent accessible surface areas, protein secondary structures, and known and predicted protein family domains, show significant differences between disease-causing and neutral sSNVs. Our result suggests that the protein structure features offer an added dimension of information while distinguishing disease-causing and neutral synonymous variants. The inclusion of structural features increases the predictive accuracy for functional sSNV prioritization.

关键词： position specific score matrix position Weight matrix Random Forest Solvent Accessible Surface Area Splice Site

来源：评论

学校读者我要写书评

暂无评论

Extracting transcription factor binding sites from unaligned gene sequences with statistical models

引用

BMC BIOINFORMATICS 2008年第Sup12期9卷 S7-S7页

作者： Lu, Chung-Chin Yuan, Wei-Hao Chen, Te-Ming Natl Tsing Hua Univ Dept Elect Engn Hsinchu 30013 Taiwan Alpha Imaging Technol Corp Jubei City 302 Hsinchu Taiwan

Background: Transcription factor binding sites (TFBSs) are crucial in the regulation of gene transcription. Recently, chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-chip array) has been used to identify potential regulatory sequences, but the procedure can only map the probable protein-DNA interaction loci within 1-2 kb resolution. To find out the exact binding motifs, it is necessary to build a computational method to examine the ChIP-chip array binding sequences and search for possible motifs representing the transcription factor binding sites. Results: We developed a program to find out accurate motif sites from a set of unaligned DNA sequences in the yeast genome. Compared with MDscan, the prediction results suggest that, overall, our algorithm outperforms MDscan since the predicted motifs are more consistent with previously known specificities reported in the literature and have better prediction ranks. Our program also outperforms the constraint-less Cosmo program, especially in the elimination of false positives. Conclusion: In this study, an improved sampling algorithm is proposed to incorporate the binomial probability model to build significant initial candidate motif sets. By investigating the statistical dependence between base positions in TFBSs, the method of dependency graphs and their expanded Bayesian networks is combined. The results show that our program satisfactorily extract transcription factor binding sites from unaligned gene sequences.

关键词： Transcription Factor Binding Site position specific score matrix Phylogenetic Footprinting Candidate Motif Motif Finding Algorithm

来源：评论

学校读者我要写书评

暂无评论

Co-receptor usage prediction at quasispecies level using ultra-deep pyrosequencing on both circulating and proviral HIV in patients candidates to CCR5 antagonist treatment

引用

RETROVIROLOGY 2010年第1-Sup期7卷 13-14页

作者： Abbate, Isabella Rozera, Gabriella Tommasi, Chiara Bruselles, Alessandro Bartolini, Barbara Nicastri, Emanuele Narciso, Pasquale Capobianchi, Maria R. INMI L Spallanzani Rome Italy

An abstract of the article 'Co-receptor Usage Prediction at Quasispecies Level Using Ultra-Deep Pyrosequencing on Both Circulating and Proviral HIV in Patients Candidates to CCR5 Antagonist Treatment,' by Isabella Abbate, Gabriella Rozera, Chiara Tommasi, Alessandro Bruselles, Barbara Bartolini, Emanuele Nicastri, Pasquale Narciso and Maria R. Capobianchi is presented.

关键词： score matrix Phenotypic Test position specific score matrix CCR5 Antagonist Patient Candidate

来源：评论

学校读者我要写书评

暂无评论

A modular kernel approach for integrative analysis of protein domain boundaries

引用

BMC Genomics 2009年第SUPPL. 3期10卷 S21-S21页

作者： Yoo, Paul D. Zhou, Bing B. Zomaya, Albert Y. Advanced Networks Research Group School of Information Technologies (J12) The University of Sydney NSW 2006 Australia Sydney Bioinformatics Centre and the Centre for Mathematical Biology The University of Sydney Sydney NSW 2006 Australia

Background: In this paper, we introduce a novel inter-range interaction integrated approach for protein domain boundary prediction. It involves (1) the design of modular kernel algorithm, which is able to effectively exploit the information of non-local interactions in amino acids, and (2) the development of a novel profile that can provide suitable information to the algorithm. One of the key features of this profiling technique is the use of multiple structural alignments of remote homologues to create an extended sequence profile and combines the structural information with suitable chemical information that plays an important role in protein stability. This profile can capture the sequence characteristics of an entire structural superfamily and extend a range of profiles generated from sequence similarity alone. Results: Our novel profile that combines homology information with hydrophobicity from SARAH1 scale was successful in providing more structural and chemical information. In addition, the modular approach adopted in our algorithm proved to be effective in capturing information from non-local interactions. Our approach achieved 82.1%, 50.9% and 31.5% accuracies for one-domain, two-domain, and three- and more domain proteins respectively. Conclusion: The experimental results in this study are encouraging, however, more work is need to extend it to a broader range of applications. We are currently developing a novel interactive (human in the loop) profiling that can provide information from more distantly related homology. This approach will further enhance the current study. © 2009 Yoo et al;licensee BioMed Central Ltd.

关键词： Protein Structure Prediction position specific score matrix Relative Solvent Accessibility Expert Network Hydrophobicity Scale

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：